diff --git a/DESCRIPTION b/DESCRIPTION index a62fe21..9f98f9b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ManyEcoEvo Title: Meta-analyse data from 'Many-Analysts' style studies -Version: 1.1.0 +Version: 1.2.0.9000 Authors@R: c(person(given = "Elliot", family = "Gould", email = "elliot.gould@unimelb.edu.au", @@ -68,7 +68,7 @@ Remotes: Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 URL: https://github.com/egouldo/ManyEcoEvo, https://egouldo.github.io/ManyEcoEvo/ BugReports: https://github.com/egouldo/ManyEcoEvo/issues diff --git a/NAMESPACE b/NAMESPACE index a132ab2..ed05740 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -37,6 +37,7 @@ export(fit_metafor_mv_reduced) export(fit_metafor_uni) export(fit_sorensen_glm) export(fit_uni_mixed_effects) +export(generate_collinearity_subset) export(generate_exclusion_subsets) export(generate_expertise_subsets) export(generate_outlier_subsets) @@ -56,6 +57,8 @@ export(meta_analyse_datasets) export(named_group_split) export(plot_cont_rating_effects) export(plot_effects_diversity) +export(plot_model_means_box_cox_cat) +export(plot_model_means_orchard) export(power_back) export(pred_to_Z) export(prepare_ManyEcoEvo) @@ -89,7 +92,12 @@ export(summarise_variable_counts) export(validate_predictions) export(validate_predictions_df_blue_tit) export(validate_predictions_df_euc) +import(dplyr) +import(ggbeeswarm) +import(ggplot2) import(metafor) +import(see) +importFrom(EnvStats,stat_n_text) importFrom(broom,tidy) importFrom(dplyr,across) importFrom(dplyr,case_when) @@ -108,6 +116,7 @@ importFrom(dplyr,rename) importFrom(dplyr,right_join) importFrom(dplyr,select) importFrom(dplyr,summarise) +importFrom(forcats,fct_relevel) importFrom(magrittr,"%>%") importFrom(pointblank,col_vals_not_null) importFrom(purrr,map) @@ -115,6 +124,7 @@ importFrom(purrr,map_dfr) importFrom(purrr,set_names) importFrom(rlang,is_na) importFrom(rlang,na_chr) +importFrom(sae,bxcx) importFrom(tidyr,pivot_longer) importFrom(tidyr,pivot_wider) importFrom(tidyr,separate) diff --git a/R/generate_collinearity_subset.R b/R/generate_collinearity_subset.R new file mode 100644 index 0000000..50193d6 --- /dev/null +++ b/R/generate_collinearity_subset.R @@ -0,0 +1,70 @@ +#' Generate Collinearity Data Subset +#' +#' This function generates a subset of the data that is used to demonstrate the +#' effects of collinearity on regression models. The data is generated by +#' sampling from a multivariate normal distribution with a specified correlation +#' matrix. +#' +#' #' +#' @param ManyEcoEvo a ManyEcoEvo dataframe containing formatted raw `data`, formatted `diversity_data`, the `estimate_type`, `dataset`, `publishable_subset`, and `exclusion_set`. See details. +#' @param collinearity_subset a dataframe containing the column `response_id` containing response ID's to be included in the expert subset +#' +#' @return A ManyEcoEvo dataframe with added column `expertise_subset` with new subsets of `data` and `diversity_data` +#' @export +#' @details +#' Note that this function needs to be run on `ManyEcoEvo` after the following functions have been run (See examples): +#' - `prepare_response_variables()` +#' - `generate_exclusion_subsets()` +#' - `generate_rating_subsets()` +#' +#' `generate_collinearity_subset()` only creates expertise subsets based on the full dataset where `exclusion_set == "complete"` and `publishable_subset == "All"` and `expertise_subset == "All"`. +#' @examples +#' ManyEcoEvo %>% +#' prepare_response_variables(estimate_type = "Zr") |> +#' generate_exclusion_subsets(estimate_type = "Zr") |> +#' generate_rating_subsets() |> +#' generate_expertise_subsets(expert_subset) |> +#' generate_collinearity_subset(collinearity_subset = collinearity_subset) +generate_collinearity_subset <- function(ManyEcoEvo, collinearity_subset) { + # Check if the inputs are a dataframe + if (!is.data.frame(collinearity_subset)) { + stop("collinearity_subset must be a dataframe.") + } + + if (!is.data.frame(ManyEcoEvo)) { + stop("ManyEcoEvo must be a dataframe.") + } + + # Check if the subset_collumn dataframe has the correct column names + if (!all(c("response_id", "id_col") %in% colnames(collinearity_subset))) { + stop("The input dataframe must contain the column 'response_id' and 'id_col'.") + } + + # Check if the response_id column is unique + if (length(unique(collinearity_subset$id_col)) != nrow(collinearity_subset)) { + stop("The 'id_col' column in collinearity_subset must be unique.") + } + + collinearity_subset_dataset <- collinearity_subset %>% pluck("dataset", unique) + + collinear_removed <- ManyEcoEvo %>% + filter(publishable_subset == "All" & exclusion_set == "complete" & expertise_subset == "All", + dataset %in% collinearity_subset_dataset) %>% + mutate(data = map(.x = data, + .f = dplyr::anti_join, collinearity_subset, + by = join_by(response_id, id_col, dataset) )) %>% + mutate(diversity_data = + map2(.x = diversity_data, + .y = data, + .f = ~ semi_join(.x, .y) %>% distinct), + collinearity_subset = "collinearity_removed") + + out <- bind_rows( + ManyEcoEvo %>% + mutate(collinearity_subset = "All"), + collinear_removed + ) + + return(out) + +} \ No newline at end of file diff --git a/R/generate_expertise_subsets.R b/R/generate_expertise_subsets.R index d98aee0..173be3d 100644 --- a/R/generate_expertise_subsets.R +++ b/R/generate_expertise_subsets.R @@ -24,6 +24,8 @@ #' generate_rating_subsets() |> #' generate_expertise_subsets(expert_subset) generate_expertise_subsets <- function(ManyEcoEvo, expert_subset) { + #TODO idea, allow ellipses arg in function and pass those expressions to filter. + # that way isn't hardcoded in the function. Repeat for all other generate / exclude map funs # NOTE: should be run *after* computing Zr with compute_MA_inputs() out <- ManyEcoEvo %>% filter(publishable_subset == "All" & exclusion_set == "complete") %>% diff --git a/R/generate_outlier_subsets.R b/R/generate_outlier_subsets.R index 24ef61f..d252ffc 100644 --- a/R/generate_outlier_subsets.R +++ b/R/generate_outlier_subsets.R @@ -13,12 +13,12 @@ generate_outlier_subsets <- function(ManyEcoEvo){ # TODO: will nolonger work on Zr dataset, because this doesn't contain an estimate_type col? # TODO: Don't run with the reduced publishability subset.... some of these already only have 10 data points!! # apply conditional behaviour to trigger both - # + # TODO: do not run for collinearity_removed datasets if(str_detect(ManyEcoEvo$estimate_type, "Zr") %>% any(na.rm = TRUE)){ ManyEcoEvo_Zr <- ManyEcoEvo %>% filter(estimate_type == "Zr") %>% bind_rows(., {ManyEcoEvo %>% - filter(estimate_type == "Zr") %>% + filter(estimate_type == "Zr", collinearity_subset != "collinearity_removed") %>% mutate(effects_analysis = map(effects_analysis, ~ slice_max(.x, Zr, n = -2) %>% slice_min(Zr, n = -2))) %>% diff --git a/R/make_viz.R b/R/make_viz.R index 009da5e..356a323 100644 --- a/R/make_viz.R +++ b/R/make_viz.R @@ -18,7 +18,7 @@ make_viz <- function(data) { if(any(str_detect(unique(data$estimate_type),pattern = "Zr"))){ data_Zr <- data %>% filter(estimate_type == "Zr") %>% - group_by(exclusion_set, dataset, estimate_type, publishable_subset, expertise_subset, data) %>% + group_by(exclusion_set, dataset, estimate_type, publishable_subset, expertise_subset, collinearity_subset, data) %>% pivot_longer(names_to = "model_name", values_to = "model", cols = c(-exclusion_set, @@ -29,7 +29,8 @@ make_viz <- function(data) { -diversity_indices, -effects_analysis, -publishable_subset, - -expertise_subset)) %>% + -expertise_subset, + -collinearity_subset)) %>% ungroup %>% select(-data, -diversity_data, diff --git a/R/sysdata.rda b/R/sysdata.rda index bdc9454..e41f60b 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/_targets.R b/_targets.R index cf08993..1cfb2c0 100644 --- a/_targets.R +++ b/_targets.R @@ -29,7 +29,7 @@ tar_option_set( packages = pkgs, imports = "ManyEcoEvo", # debug = c("augmented_data_3efd9941")#, #augmented_data_a4d78efa - cue = tar_cue(mode = "always") #because we have silent errors! + # cue = tar_cue(mode = "always") #because we have silent errors! ) list(tarchetypes::tar_file_read(name = euc_reviews, @@ -80,6 +80,7 @@ list(tarchetypes::tar_file_read(name = euc_reviews, generate_exclusion_subsets(estimate_type = "Zr") |> generate_rating_subsets() |> generate_expertise_subsets(expert_subset) |> + generate_collinearity_subset(ManyEcoEvo:::collinearity_subset) |> compute_MA_inputs(estimate_type = "Zr") |> generate_outlier_subsets() |> # TODO run before MA_inputs? diversity indices need to be recalculated!! filter(expertise_subset != "expert" | exclusion_set != "complete-rm_outliers") |> #TODO mv into generate_outlier_subsets() so aren't created in the first place diff --git a/_targets/meta/meta b/_targets/meta/meta index ef12b98..06d07f8 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -1,4 +1,5 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error +collinearity_subset|object|e6e522e071f5b347 gg_forest|function|8a8d7abdca044d49 read_submission_data|function|2277dcfe2e859751 summarise_analyses_by_reviewer|function|f25be6cfe4796fa6 @@ -29,6 +30,7 @@ get_diversity_data|function|8e045391a001c91e augment_prediction_data|function|2a16e40ebf93c015 fit_uni_mixed_effects|function|66212bb22d80f16e blue_tit_data|object|10ce24c6dd33e700 +plot_model_means_orchard|function|6b6a2434b7e7be45 est_to_zr|function|8fd9931e7a599188 prepare_review_data|function|e357cf3c18befa17 compare_ml_MA|function|d714430291165972 @@ -40,7 +42,7 @@ poss_fit_boxcox_ratings_cat|function|c99630ccc4951b35 exclude_extreme_VZ|function|4ee53e55687aa21a count_binary_coded_features|function|e4724c5ce132d41c summarise_reviews_per_analysis|function|f0303f71d902a2ee -.Random.seed|object|af4a43da3bde10e0 +.Random.seed|object|d1fd399abfcbaae9 preprocess_prediction_files|function|10c65ef09b2b1a72 analysis_data_param_tables|object|76990960304ed12d poss_fit_sorensen_glm|function|c99630ccc4951b35 @@ -62,8 +64,8 @@ calculate_deviation_score|function|d1815d690cb6b586 fit_boxcox_ratings_cont|function|5e3561161c317081 fit_metafor_mv|function|386ecbbad60cfac7 rm_inf_na|function|836f2578e57b6b48 +generate_collinearity_subset|function|73253e7ee5d7dcee generate_expertise_subsets|function|de63fc5815753233 -generate_outlier_subsets|function|7b2a835e0927494f count_teams_analyses|function|7c5f52a3fddfacf7 anonymise_teams|function|7430d98fda6f6b87 clean_response_transformation|function|a7d363eac4397587 @@ -72,6 +74,7 @@ Z_VZ_preds|function|fbbb70e17be09084 poss_fit_boxcox_ratings_cont|function|c99630ccc4951b35 log_transform|function|d012412c64b17e53 fit_boxcox_ratings_cat|function|92f478da1ad693b9 +generate_outlier_subsets|function|ffaa88d1e2699bc2 summarise_conclusions|function|da138700d6bcbfbb conversion_2|function|e93b7e339c0eb160 conversion|function|762dc38beba86a06 @@ -85,7 +88,8 @@ summarise_reviews|function|fba9891b001c8a6d apply_sorensen_calc|function|3457c0401205390c summarise_variable_counts|function|efc20754f19e1751 validate_predictions|function|7ef020257e0a630d -make_viz|function|95d067406feba70f +plot_model_means_box_cox_cat|function|a134d3bd2d2474f5 +make_viz|function|0744ee2114399af8 generate_exclusion_subsets|function|af281ac91624a51f meta_analyse_datasets|function|ec1db9415d6207f5 summarise_analysis_types|function|080f028a7d267d1a @@ -100,649 +104,649 @@ compute_metaanalysis_inputs|function|cec840b57757a8f3 standardise_response|function|4ae7efffde949231 prepare_response_variables_yi|function|6bfaf0117ba662bf 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-master_metadata|stem|6f23bb2804d330fa|7bcb92a89e8a1c8d|1a3b1035a03d5a3f|345383712||t19867.3486200534s|b4042a09054cda7a|4985|rds|local|vector|||0.013|| -euc_reviews|stem|f73cc6e8b65ca2d4|9c622431a02e3308|88c761dc25131ee6|-665853428||t19867.3486202616s|5009e7f03d7c5f76|4181|rds|local|vector|||0.015|| -updated_prediction_files|stem|691b62e6eabe6bce|b33ca9159f38d41e|7d686864d9f52e92|-1778899494||t19867.3486760626s|147702cf8477fcbf|6634|rds|local|vector|||4.817|There were 3 warnings in mutate.The first warning wasℹ In argument updated_checks map.x updated_checks, .f pointblankinterrogate.ℹ In group 5 response_id R_1LRqq2WHrQaENtM, submission_id 1, analysis_id 1, split_id 1, csv_number 3.Caused by warning Failure to validate that column se.fit is of type numeric.The col_is_numeric validation failed beyond the absolute threshold level 1. failure level 1 failure threshold 1ℹ Run dplyrlast_dplyr_warnings to see the 2 remaining warnings.| 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a/data-raw/analysis_data_param_tables.R b/data-raw/analysis_data_param_tables.R deleted file mode 100644 index c82397d..0000000 --- a/data-raw/analysis_data_param_tables.R +++ /dev/null @@ -1,17 +0,0 @@ -# ---- Make Parameter Tables for Standardising out-of-sample Predictions ---- - -#NOTE: relies on package being built after running `data-raw/osf_load_analyst_datasets.R` - -library(tidyverse) -library(ManyEcoEvo) - -analysis_data_param_tables <- - bind_rows( - make_param_table(ManyEcoEvo::blue_tit_data) %>% - mutate(dataset = "blue tit"), - make_param_table(ManyEcoEvo::euc_data) %>% - mutate(dataset = "eucalyptus") - ) - - -usethis::use_data(analysis_data_param_tables, internal = TRUE, overwrite = TRUE) diff --git a/data-raw/anonymised_data/master_data.csv b/data-raw/anonymised_data/master_data.csv index d991e98..dd01bf9 100644 --- a/data-raw/anonymised_data/master_data.csv +++ b/data-raw/anonymised_data/master_data.csv @@ -1,17 +1,17 @@ response_id,id_col,submission_id,analysis_id,split_id,beta_estimate,contrast,adjusted_df,beta_SE,transformation,link_function_reported,dataset,mixed_model,response_transformation_description,response_transformation_status,response_variable_type,response_construction_description,response_variable_name,response_id_S2,test_variable,sample_size,Bayesian,linear_model,model_subclass,num_variables,num_effects,num_fixed_variables,num_fixed_effects,num_random_variables,num_random_effects,num_interactions,num_duplicate_terms,exclusions_all,exclusions_effect_analysis,exclusion_predictions,ConclusionS1,Conclusion,software,data_cleaning_preprocessing_tool,data_cleaning_preprocessing_version,data_analysis_tool,data_analysis_version,SurveyID,Date,Season,Property,Quadrat no,Easting,Northing,Aspect,Landscape position,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NativeShrub_cover,BareGround_cover,Litter_cover,MossLichen_cover,Rock_cover,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,annual_precipitation,precipitation_warmest_quarter,precipitation_coldest_quarter,PET,MrVBF,K_perc,Th_ppm,U_ppm,SRad_Jan,SRad_Jul,all_grass,all_exotic_grass,all_native_grass_graminoid,all_non-grass_veg,shrub_cover,herb_cover,other_veg,bare,month,all_exotic_herb,native_herb_fern_gram,growing_space,soilPC1,coverPC1,coverPC2,coverPC3,precip_max_range,year,size_class,all_perennial_grass,sample,hatch_year,hatch_nest_breed_ID,hatch_Area,hatch_Box,hatch_mom_Ring,hatch_nest_dad_Ring,Extra-pair_paternity,Extra-pair_dad_ring,genetic_dad_ring_(WP_or_EP),hatch_nest_LD,hatch_nest_CS,hatch_nest_OH,d0_hatch_nest_brood_size,d14_hatch_nest_brood_size,rear_nest_breed_ID,rear_area,rear_Box,rear_mom_Ring,rear_dad_Ring,rear_nest_trt,home_or_away,rear_nest_LD,rear_nest_CS,rear_nest_OH,rear_d0_rear_nest_brood_size,rear_Cs_out,rear_Cs_in,net_rearing_manipulation,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,number_chicks_fledged_from_rear_nest,Date_of_day14,day_14_tarsus_length,day_14_weight,day14_measurer,chick_sex_molec,chick_survival_to_first_breed_season,within-area_movement,brood_reduction,blood_sib,hatch_incub_length,rear_incub_length,relatedness,competition_weight,relative_CS,envir_rear,percent_change,parentage,manipulation_non,seasonal_timing,brood_mortality,brood_sex_ratio,TeamIdentifier -R_0MuZ4chnmwTaLiV,Bicheno-1-1-1,1,1,1,NA,NA,21,0.29212,NA,NA,eucalyptus,NA,NA,NA,constructed variable (combining information from two or more original variables),euc_sdlgs0_50cm + euc_sdlgs50cm-2m,euc_sdlgs0_2m,R_0MuZ4chnmwTaLiV,NA,NA,0,generalised,zero_inflated_hurdle,18,NA,18,NA,0,NA,NA,NA,exclude,exclude,NA,"Potential evapotranspiration was positively related to seedling abundances, which is contrary to expectations with regard to the influence of water stress (i.e., high evaporative demand) on seedling recruitment. Yet, potential evapotranspiration was positively and highly correlated to the index of valley bottom flatness (MrVBF; Pearson’s r = 0.61) and to northing (Pearson’s r = 0.98), suggesting it may reflect other processes that are spatially structured. Indeed, properties with lower seedling abundances are located at the margin of the Eucalyptus open forest region, which has a rougher topography (i.e., lower MrVBF) and is a hotspot of production forestry in south-eastern Australia. - -Distance to the nearest Eucalyptus canopy correlated negatively with seedling’s presence. This relationship reveals that seedling’s recruitment is probably controlled by seed dispersion rather than by intra-specific competition, or selection processes due to climatic and edaphic conditions. Furthermore, seedling’s presence was negatively related to grass and herb cover, although not seedling abundances. Low germination rates and early seedlings mortality could explain the negative effect of the understorey plant cover on Eucalyptus’ recruitment. The latter interpretation is supported by the negative relationship observed between litter cover and the probability of observing seedlings. - -Our analyses of Eucalyptus seedlings show that recruitment at a site is affected negatively by grass, herb and litter cover, but positively by its proximity to mother trees (Eucalyptus canopy), which suggest that seed dispersal and germination are bottleneck processes. Once Eucalyptus seedlings have established, their abundances vary along a north-south gradient of potential evapotranspiration that is associated with other landscape attributes (e.g., change in topography and land-use). It is not entirely clear what are the processes that drive seedlings’ abundances along this gradient. -",neg_q,"R version 3.6.2 +R_0MuZ4chnmwTaLiV,Bicheno-1-1-1,1,1,1,NA,NA,21,0.29212,NA,NA,eucalyptus,NA,NA,NA,constructed variable (combining information from two or more original variables),euc_sdlgs0_50cm + euc_sdlgs50cm-2m,euc_sdlgs0_2m,R_0MuZ4chnmwTaLiV,NA,NA,0,generalised,zero_inflated_hurdle,18,NA,18,NA,0,NA,NA,NA,exclude,exclude,NA,"Potential evapotranspiration was positively related to seedling abundances, which is contrary to expectations with regard to the influence of water stress (i.e., high evaporative demand) on seedling recruitment. Yet, potential evapotranspiration was positively and highly correlated to the index of valley bottom flatness (MrVBF; Pearson’s r = 0.61) and to northing (Pearson’s r = 0.98), suggesting it may reflect other processes that are spatially structured. Indeed, properties with lower seedling abundances are located at the margin of the Eucalyptus open forest region, which has a rougher topography (i.e., lower MrVBF) and is a hotspot of production forestry in south-eastern Australia. + +Distance to the nearest Eucalyptus canopy correlated negatively with seedling’s presence. This relationship reveals that seedling’s recruitment is probably controlled by seed dispersion rather than by intra-specific competition, or selection processes due to climatic and edaphic conditions. Furthermore, seedling’s presence was negatively related to grass and herb cover, although not seedling abundances. Low germination rates and early seedlings mortality could explain the negative effect of the understorey plant cover on Eucalyptus’ recruitment. The latter interpretation is supported by the negative relationship observed between litter cover and the probability of observing seedlings. + +Our analyses of Eucalyptus seedlings show that recruitment at a site is affected negatively by grass, herb and litter cover, but positively by its proximity to mother trees (Eucalyptus canopy), which suggest that seed dispersal and germination are bottleneck processes. Once Eucalyptus seedlings have established, their abundances vary along a north-south gradient of potential evapotranspiration that is associated with other landscape attributes (e.g., change in topography and land-use). It is not entirely clear what are the processes that drive seedlings’ abundances along this gradient. +",neg_q,"R version 3.6.2 Hurdle model was adjusted with the hurdle function from the pscl package version 1.5.5",R,3.6.2,R,3.6.2,NA,NA,Season,NA,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NA,BareGround_cover,Litter_cover,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,euc_sdlgs50cm-2m,NA,NA,NA,NA,PET,NA,NA,NA,NA,NA,SRad_Jul,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bicheno -R_0MuZ4chnmwTaLiV,Bicheno-1-1-2,1,1,2,-0.763443,slope,21,0.242942,NA,NA,eucalyptus,NA,NA,NA,constructed variable (combining information from two or more original variables),euc_sdlgs0_50cm + euc_sdlgs50cm-2m,euc_sdlgs0_2m,R_0MuZ4chnmwTaLiV,NA,NA,0,generalised,zero_inflated_hurdle,18,NA,18,NA,0,NA,NA,NA,exclude,retain,NA,"Potential evapotranspiration was positively related to seedling abundances, which is contrary to expectations with regard to the influence of water stress (i.e., high evaporative demand) on seedling recruitment. Yet, potential evapotranspiration was positively and highly correlated to the index of valley bottom flatness (MrVBF; Pearson’s r = 0.61) and to northing (Pearson’s r = 0.98), suggesting it may reflect other processes that are spatially structured. Indeed, properties with lower seedling abundances are located at the margin of the Eucalyptus open forest region, which has a rougher topography (i.e., lower MrVBF) and is a hotspot of production forestry in south-eastern Australia. - -Distance to the nearest Eucalyptus canopy correlated negatively with seedling’s presence. This relationship reveals that seedling’s recruitment is probably controlled by seed dispersion rather than by intra-specific competition, or selection processes due to climatic and edaphic conditions. Furthermore, seedling’s presence was negatively related to grass and herb cover, although not seedling abundances. Low germination rates and early seedlings mortality could explain the negative effect of the understorey plant cover on Eucalyptus’ recruitment. The latter interpretation is supported by the negative relationship observed between litter cover and the probability of observing seedlings. - -Our analyses of Eucalyptus seedlings show that recruitment at a site is affected negatively by grass, herb and litter cover, but positively by its proximity to mother trees (Eucalyptus canopy), which suggest that seed dispersal and germination are bottleneck processes. Once Eucalyptus seedlings have established, their abundances vary along a north-south gradient of potential evapotranspiration that is associated with other landscape attributes (e.g., change in topography and land-use). It is not entirely clear what are the processes that drive seedlings’ abundances along this gradient. -",neg_q,"R version 3.6.2 +R_0MuZ4chnmwTaLiV,Bicheno-1-1-2,1,1,2,-0.763443,slope,21,0.242942,NA,NA,eucalyptus,NA,NA,NA,constructed variable (combining information from two or more original variables),euc_sdlgs0_50cm + euc_sdlgs50cm-2m,euc_sdlgs0_2m,R_0MuZ4chnmwTaLiV,NA,NA,0,generalised,zero_inflated_hurdle,18,NA,18,NA,0,NA,NA,NA,exclude,retain,NA,"Potential evapotranspiration was positively related to seedling abundances, which is contrary to expectations with regard to the influence of water stress (i.e., high evaporative demand) on seedling recruitment. Yet, potential evapotranspiration was positively and highly correlated to the index of valley bottom flatness (MrVBF; Pearson’s r = 0.61) and to northing (Pearson’s r = 0.98), suggesting it may reflect other processes that are spatially structured. Indeed, properties with lower seedling abundances are located at the margin of the Eucalyptus open forest region, which has a rougher topography (i.e., lower MrVBF) and is a hotspot of production forestry in south-eastern Australia. + +Distance to the nearest Eucalyptus canopy correlated negatively with seedling’s presence. This relationship reveals that seedling’s recruitment is probably controlled by seed dispersion rather than by intra-specific competition, or selection processes due to climatic and edaphic conditions. Furthermore, seedling’s presence was negatively related to grass and herb cover, although not seedling abundances. Low germination rates and early seedlings mortality could explain the negative effect of the understorey plant cover on Eucalyptus’ recruitment. The latter interpretation is supported by the negative relationship observed between litter cover and the probability of observing seedlings. + +Our analyses of Eucalyptus seedlings show that recruitment at a site is affected negatively by grass, herb and litter cover, but positively by its proximity to mother trees (Eucalyptus canopy), which suggest that seed dispersal and germination are bottleneck processes. Once Eucalyptus seedlings have established, their abundances vary along a north-south gradient of potential evapotranspiration that is associated with other landscape attributes (e.g., change in topography and land-use). It is not entirely clear what are the processes that drive seedlings’ abundances along this gradient. +",neg_q,"R version 3.6.2 Hurdle model was adjusted with the hurdle function from the pscl package version 1.5.5",R,3.6.2,R,3.6.2,NA,NA,Season,NA,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NA,BareGround_cover,Litter_cover,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,euc_sdlgs50cm-2m,NA,NA,NA,NA,PET,NA,NA,NA,NA,NA,SRad_Jul,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bicheno R_11787O3NmejXKAH,Ayr-1-2-2,1,2,2,NA,NA,484.0193,NA,NA,NA,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_11787O3NmejXKAH,net_rearing_manipulation,3720,0,generalised,standard,12,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"Chicks reared in clutches of 5-6 were the biggest in weight, tarsus length, and overall growth. Although sibling competition affected chick growth, this effect was outweighed by the random effects of each model, illustrating the importance of parental, geographical, and weather-related influences.",CHECK,R studio Version 1.2.5042,R,NA,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,hatch_mom_Ring,NA,NA,NA,NA,NA,NA,NA,d0_hatch_nest_brood_size,NA,NA,rear_area,NA,rear_mom_Ring,NA,NA,home_or_away,NA,NA,NA,NA,NA,NA,net_rearing_manipulation,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,Date_of_day14,day_14_tarsus_length,day_14_weight,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Ayr R_11787O3NmejXKAH,Ayr-1-2-3,1,2,3,NA,NA,666.56874,NA,NA,NA,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_11787O3NmejXKAH,net_rearing_manipulation,3720,0,generalised,standard,12,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"Chicks reared in clutches of 5-6 were the biggest in weight, tarsus length, and overall growth. Although sibling competition affected chick growth, this effect was outweighed by the random effects of each model, illustrating the importance of parental, geographical, and weather-related influences.",CHECK,R studio Version 1.2.5042,R,NA,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,hatch_mom_Ring,NA,NA,NA,NA,NA,NA,NA,d0_hatch_nest_brood_size,NA,NA,rear_area,NA,rear_mom_Ring,NA,NA,home_or_away,NA,NA,NA,NA,NA,NA,net_rearing_manipulation,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,Date_of_day14,day_14_tarsus_length,day_14_weight,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Ayr @@ -30,10 +30,10 @@ R_12cozGev3IOOBG2,Bell-5-5-1,5,5,1,NA,NA,NA,NA,identity,identity,blue tit,1,NA,N R_12cozGev3IOOBG2,Bell-5-5-2,5,5,2,NA,NA,NA,NA,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_12cozGev3IOOBG2,NA,3720,0,linear,standard,7,NA,3,NA,4,NA,0,NA,exclude,exclude_all,NA,"Body mass showed similar relationships. Body mass was lower in broods with increased size, and was negatively related to the net change in brood size. Additionally, body mass was negatively related to the brood size at day 14 when mass was measured.",neg_c,R 3.2.3,R,3.2.3,R,3.2.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,hatch_nest_LD,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Date_of_day14,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bell R_12R6XuSRUcRemui,Biloela-1-1-1,1,1,1,-0.054898,slope,292.80011,0.018974,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),"We combined the first two seedling measures of 0-50cm and 50cm-2m into one response variable. These two measures were highly correlated across all three seasons, with no pattern for the >2m seedling measure. Quadrats with high counts for 0-50cm are more likely to also have high counts for 50cm-2m, regardless of season, and thus, treating them as two different response variables with the same set of predictor variables is unnecessary, if not invalid. A further look at the third seedling measure of >2m shows that a total of 40 observations were made, all within 9 quadrats, and all within the Autumn 2007 season only. Otherwise, >340 quadrats had no seedlings observed. This class provided no meaningful info.",euc_sdlgs_all,R_12R6XuSRUcRemui,NA,NA,0,generalised,zero_inflated,17,NA,NA,NA,NA,NA,NA,NA,exclude,retain,NA,"A simple model shows that exotic annual grass cover can significantly explain seedling recruitment, measured as counts at 0-2m in height, with a specific positive relationship. However, additional biotic and abiotic variables, which are highly correlated with grass cover in general, also contribute in a significant way to seedling recruitment. Increased seedling recruitment was significantly predicted by higher exotic herb cover, lower litter cover, higher element deposit, greater Eucalyptus canopy cover, and N/S-facing landscape. Thus, while grass does influence Eucalyptus seedling recruitment, other landscape, environmental, and biological variables are necessary to consider if we are to model seedling recruitment. In fact, this model, while including several parameters with significant prediction, could benefit from other factors. For example, of note, variables that reflect spatial patterning (“northing”) were also highly correlated with grass cover, and their incorporation into an additional complex set of spatial models may shed light on these interactions. Finally, while season was not a significant predictor here, collecting data on seedling counts over multiple years may better tease out seasonal effects. Related, the lack of data beyond 2m means all prediction here is telling us about a small period of ""recruitment"". If we are to make predictions about ""successful"" recruitment, then we need better data to understand what happens beyond 2m of growth. Following seedlings over multiple years and/or in a ""time series"" would help track what factors may cull not only recruitment but development.",pos_q,"All data cleaning, statistical analyses, data plotting, and model fitting were performed in R 3.6.3.",R,3.6.3,R,3.6.3,NA,NA,Season,Property,Quadrat no,NA,NA,Aspect,NA,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NA,NativePerennialGrass_cover,NA,NA,NA,BareGround_cover,Litter_cover,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,euc_sdlgs50cm-2m,NA,NA,NA,NA,NA,NA,NA,Th_ppm,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Biloela R_1BWpZlSbkmSofe1,Bingara-1-1-1,1,1,1,NA,NA,NA,0.007831,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),I summed all seedlings eucalyptus variables,euc_sdlgs_all,R_1BWpZlSbkmSofe1,ExoticAnnualGrass_cover,346,0,generalised,standard,13,13,10,10,3,3,0,0,retain,exclude_all,exclude,"The results showed that in order to conserve the eucalyptus, the owners of private properties have to consider the removal of exotic grasses, mainly those of annual cycle, and the native grasses. In addition, the results indicate that planting seedlings at distances close to eucalyptus trees should be considered. However, it is necessary to evaluate what is the best distance so that the canopy of eucalyptus trees does not interfere with the seedlings. The canopy cover can decrease the entry of solar radiation and the very close distance of the seedlings from trees can leads to competition nutrients and water from the soil.",neg_c,All analysis were runned in R version 3.6.0.,R,3.6.0,R,3.6.0,NA,Date,NA,Property,Quadrat no,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NativePerennialGraminoid_cover,NA,BareGround_cover,NA,MossLichen_cover,Rock_cover,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),NA,NA,NA,NA,NA,NA,NA,NA,K_perc,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bingara -R_1CC5PPCXcQPgu42,Berr-1-1-1,1,1,1,-0.1811,slope,325,0.01475,identity,identity,blue tit,1,z.score,z.score,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1CC5PPCXcQPgu42,net_rearing_manipulation,3635,0,linear,standard,7,7,5,5,2,2,0,0,retain,retain,NA,"Nestling weight at 14 days of age, on average, is negatively affected when additional competitors are added to the nest (by 0.37g per added nestling), but there is no beneficial effect of reducing a brood size.",neg_q,"organizing the data: Excel +R_1CC5PPCXcQPgu42,Berr-1-1-1,1,1,1,-0.1811,slope,325,0.01475,identity,identity,blue tit,1,z.score,z.score,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1CC5PPCXcQPgu42,net_rearing_manipulation,3635,0,linear,standard,7,7,5,5,2,2,0,0,retain,retain,NA,"Nestling weight at 14 days of age, on average, is negatively affected when additional competitors are added to the nest (by 0.37g per added nestling), but there is no beneficial effect of reducing a brood size.",neg_q,"organizing the data: Excel model estimation: ‘lme4’ package V1.1-23 in R V3.4.3",Excel,NA,R,3.4.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,NA,home_or_away,NA,NA,NA,NA,NA,NA,net_rearing_manipulation,NA,NA,NA,Date_of_day14,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Berr R_1d0uRf5iNWOLD8M,Brim-1-1-1,1,1,1,NA,NA,481,NA,identity,identity,blue tit,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1d0uRf5iNWOLD8M,NA,497,0,linear,standard,7,NA,7,NA,0,NA,NA,NA,exclude,exclude_all,exclude,"The more offspring there are within a nest, the more competition for food exists, and therefore the greater the difference in sizes between birds within the nest box. Standard deviation and range both increase significantly as number of nestlings increases.",neg_c,R version 3.6.3,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,hatch_Box,NA,NA,NA,NA,NA,NA,NA,NA,NA,d14_hatch_nest_brood_size,NA,rear_area,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,day_14_tarsus_length,day_14_weight,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Brim -R_1dzfML4yheLxG0D,Bruc-1-1-1,1,1,1,-0.02717,slope,458.2,0.01015,log,log,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),I calculated scaled body mass based on body mass (day_14_weight) and tarsus length (day_14_tarsus_length) to have an estimate of chicks’ body mass independently of body size following the method of Peig and Green (2009).,SMI,R_1dzfML4yheLxG0D,rear_Cs_at_start_of_rearing,3315,0,generalised,standard,11,21,9,19,2,2,10,0,retain,retain,exclude,"From my analysis, it appears that sibling competition affect growth of nestling blue tits a scaled body mass decreased with increasing brood size. However, it not the only factor that influence growth as the date at which the individuals were measured influenced body mass with lower body mass later in the breeding season compare to the beginning. This relationship differed between years. It suggests that environmental conditions likely through their impact on food resources also influenced growth.",neg_q,"standardized major axis regression - R 3.6.2 +R_1dzfML4yheLxG0D,Bruc-1-1-1,1,1,1,-0.02717,slope,458.2,0.01015,log,log,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),I calculated scaled body mass based on body mass (day_14_weight) and tarsus length (day_14_tarsus_length) to have an estimate of chicks’ body mass independently of body size following the method of Peig and Green (2009).,SMI,R_1dzfML4yheLxG0D,rear_Cs_at_start_of_rearing,3315,0,generalised,standard,11,21,9,19,2,2,10,0,retain,retain,exclude,"From my analysis, it appears that sibling competition affect growth of nestling blue tits a scaled body mass decreased with increasing brood size. However, it not the only factor that influence growth as the date at which the individuals were measured influenced body mass with lower body mass later in the breeding season compare to the beginning. This relationship differed between years. It suggests that environmental conditions likely through their impact on food resources also influenced growth.",neg_q,"standardized major axis regression - R 3.6.2 Generalized Linear Mixed Model - SAS University Edition","R,SAS","3.6.2,University Edition","R,SAS","3.6.2,University Edition",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,hatch_Area,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,NA,NA,NA,NA,net_rearing_manipulation,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,Date_of_day14,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bruc R_1E099fIoICERZIZ,Burr-1-1-2,1,1,2,-0.23341,control-enlarged,488.07,0.07759,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1E099fIoICERZIZ,rear_nest_trt_C.E,NA,0,linear,standard,8,8,5,5,3,3,0,0,retain,exclude_partial,NA,Tarsus length also decreased somewhat with increasing clutch size,neg_c,R version 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,d0_hatch_nest_brood_size,NA,NA,rear_area,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Burr R_1E099fIoICERZIZ,Burr-1-1-1,1,1,1,-0.35656,reduced-enlarged,488.07,0.02514,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1E099fIoICERZIZ,rear_nest_trt_R.E,NA,0,linear,standard,8,8,5,5,3,3,0,0,retain,exclude_partial,NA,Tarsus length also decreased somewhat with increasing clutch size,neg_c,R version 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,d0_hatch_nest_brood_size,NA,NA,rear_area,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Burr @@ -45,40 +45,40 @@ R_1eXlFKlQdiD2F59,Cape-1-1-1,1,1,1,-0.49,slope,225.996,0.052,identity,identity,b R_1eXlFKlQdiD2F59,Cape-2-2-1,2,2,1,-0.022548,slope,26.45,0.178,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1eXlFKlQdiD2F59,rear_Cs_at_start_of_rearing,NA,0,linear,standard,0,0,NA,NA,NA,NA,NA,NA,exclude,retain,NA,NA,CHECK,NA,CHECK,CHECK,CHECK,CHECK,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Cape R_1f9Lv1lWGLjMFk8,Clar-2-2-1,2,2,1,-0.04298,slope,18,0.01459,identity,identity,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),"This variable was constructed by pairing groups of individuals with different treatments (rear_nest_trt) based on several variables, finding the mean day_14_tarsus_length for each group, and taking the difference between those means. The groups were made by pairing individuals with the same mother (hatch_nest_breed_ID), father (genetic_dad_ring_(WP_or_EP)), sex (chick_sex_molec), rear nest area (rear_area), and person who measured them (day14_measurer). Note: Because I modelled differences between groups of individuals that I paired (change in weight/size for every additional sibling), I cannot make predictions for the new data provided (single individuals that cannot be paired in the same manner)",day_14_tarsus_length_group_deviation,R_1f9Lv1lWGLjMFk8,net_rearing_manipulation,76,0,linear,standard,2,2,1,1,1,1,0,0,retain,retain,NA,"For both measures of chick size, the magnitude of difference between the two treatments significantly improved models of the difference in chick size (tarsus length: Χ2 = 7.5, df = 1, p-value = 0.006; weight: Χ2 = 13.2, df = 1, p-value < 0.001). Also, in line with the expectation that manipulations that do not change the number of siblings will not affect chick size, the addition of a non-zero y-intercept did not improve model fits (tarsus length: Χ2 = 0.81, df = 1, p-value = 0.37; weight: Χ2 = 0.05, df = 1, p-value =0.82). According to the final models, for every additional sibling in a nest, chicks had 0.04 mm (SE = 0.015 mm) shorter tarsi and were 0.14 g (SE = 0.034 g) lighter (Table 1, Figure 1).",neg_c,R version 4.0.0,R,4.0.0,R,4.0.0,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,net_rearing_manipulation,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Clar R_1f9Lv1lWGLjMFk8,Clar-1-1-1,1,1,1,-0.1444,slope,18,0.03388,identity,identity,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),"This variable was constructed by pairing groups of individuals with different treatments (rear_nest_trt) based on several variables, finding the mean day_14_weight for each group, and taking the difference between those means. The groups were made by pairing individuals with the same mother (hatch_nest_breed_ID), father (genetic_dad_ring_(WP_or_EP)), sex (chick_sex_molec), rear nest area (rear_area), and person who measured them (day14_measurer). Note: Because I modelled differences between groups of individuals that I paired (change in weight/size for every additional sibling), I cannot make predictions for the new data provided (single individuals that cannot be paired in the same manner)",day_14_weight_group_deviation,R_1f9Lv1lWGLjMFk8,net_rearing_manipulation,76,0,linear,standard,2,2,1,1,1,1,0,0,retain,retain,NA,"For both measures of chick size, the magnitude of difference between the two treatments significantly improved models of the difference in chick size (tarsus length: Χ2 = 7.5, df = 1, p-value = 0.006; weight: Χ2 = 13.2, df = 1, p-value < 0.001). Also, in line with the expectation that manipulations that do not change the number of siblings will not affect chick size, the addition of a non-zero y-intercept did not improve model fits (tarsus length: Χ2 = 0.81, df = 1, p-value = 0.37; weight: Χ2 = 0.05, df = 1, p-value =0.82). According to the final models, for every additional sibling in a nest, chicks had 0.04 mm (SE = 0.015 mm) shorter tarsi and were 0.14 g (SE = 0.034 g) lighter (Table 1, Figure 1).",neg_c,R version 4.0.0,R,4.0.0,R,4.0.0,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,net_rearing_manipulation,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Clar -R_1ff6slHNcrTJ2JS,Clev-1-1-1,1,1,1,-0.167,slope,180.5,0.01431,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1ff6slHNcrTJ2JS,rear_Cs_at_start_of_rearing,1764,0,linear,standard,12,12,4,4,8,8,0,0,retain,retain,NA,"Enlarging broods led to worse outcomes both for individual nestlings and for reproductive success of parents. -Nestlings in enlarged broods tended to be smaller in mass and skeletal size (tarsus length). Mass and tarsus length were both significantly negatively associated with brood size. Parents of enlarged broods also fledged a smaller proportion of their broods compared to controls. On the other hand, nestlings in reduced broods were not larger compared to controls, although they did seem more likely to survive to the next year, suggesting that they did receive more or better care from their parents. Parents of enlarged broods seemed unable or unwilling to increase care, which likely resulted in poorer quality nestlings and lower fledging success. - -The variance in quality among nestlings in the enlarged brood was likewise larger compared to controls, consistent with the hypothesis that parents of enlarged broods struggled to care for all nestlings equally. It is difficult to determine, however, whether these results demonstrate that nestlings are competing within the brood. Although having more siblings tended to reduce a nestling's condition and likelihood of fledging, that does not necessarily -mean that nestlings were directly competing with one another. Parents may have limited their investment in enlarged broods according to their own condition and/or opportunuties for future reproduction, leading to poorer quality broods, independent of interactions between individual nestmates. However, the fact that variance in quality was higher in reduced broods is consistent with the hypothesis that some nestlings in enlarged broods were still managing to grow and develop at the expense of their nestmates. - -Provisioning and begging data could help identify whether parents are feeding nestlings according to need or according to which nestling signals most vigorously. If parents feed the biggest and most active nestlings disproportionately, -that would be a strong indication that dominant nestlings can outcompete siblings for food. +R_1ff6slHNcrTJ2JS,Clev-1-1-1,1,1,1,-0.167,slope,180.5,0.01431,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1ff6slHNcrTJ2JS,rear_Cs_at_start_of_rearing,1764,0,linear,standard,12,12,4,4,8,8,0,0,retain,retain,NA,"Enlarging broods led to worse outcomes both for individual nestlings and for reproductive success of parents. +Nestlings in enlarged broods tended to be smaller in mass and skeletal size (tarsus length). Mass and tarsus length were both significantly negatively associated with brood size. Parents of enlarged broods also fledged a smaller proportion of their broods compared to controls. On the other hand, nestlings in reduced broods were not larger compared to controls, although they did seem more likely to survive to the next year, suggesting that they did receive more or better care from their parents. Parents of enlarged broods seemed unable or unwilling to increase care, which likely resulted in poorer quality nestlings and lower fledging success. + +The variance in quality among nestlings in the enlarged brood was likewise larger compared to controls, consistent with the hypothesis that parents of enlarged broods struggled to care for all nestlings equally. It is difficult to determine, however, whether these results demonstrate that nestlings are competing within the brood. Although having more siblings tended to reduce a nestling's condition and likelihood of fledging, that does not necessarily +mean that nestlings were directly competing with one another. Parents may have limited their investment in enlarged broods according to their own condition and/or opportunuties for future reproduction, leading to poorer quality broods, independent of interactions between individual nestmates. However, the fact that variance in quality was higher in reduced broods is consistent with the hypothesis that some nestlings in enlarged broods were still managing to grow and develop at the expense of their nestmates. + +Provisioning and begging data could help identify whether parents are feeding nestlings according to need or according to which nestling signals most vigorously. If parents feed the biggest and most active nestlings disproportionately, +that would be a strong indication that dominant nestlings can outcompete siblings for food. ",neg_q,R version 3.6.2,R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),hatch_nest_LD,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,rear_Box,rear_mom_Ring,rear_dad_Ring,NA,home_or_away,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Clev -R_1FJQlMO4buRu6S2,Birdwoo-1-1-1,1,1,1,-0.449,slope,331.27,0.191,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),"I summed the total values contained in 'euc_sdlgs0_50cm', 'euc_sdlgs50cm-2m' and ''euc_sdlgs>2m'",euc_sdlgs_all,R_1FJQlMO4buRu6S2,NA,NA,0,generalised,standard,9,9,7,7,2,2,0,0,exclude,exclude_all,NA,"My question: How does grass cover influence Eucalyptus spp. seedling recruitment? - -I would not use these data in a hypothesis-testing situation, rather I would use these data for hypothesis-generation. In this context, all three grass variables that I analysed (native_perennial_grass_cover, exotic_annual_grass_cover and exotic_perennial_grass_cover) were retained in at least one plausible model explaining Eucalyptus spp. seedling recruitment. To me, this indicates that grass cover may be a potentially important predictor of Eucalyptus spp. seedling recruitment. - -However, none of the parameter estimate 95% confidence intervals did not overlap with 0, which indicates that there was no evidence for a statistically significant effect of grass cover variables on Eucalyptus spp. seedling recruitment - -",none_q,"All analyses were performed using R version 3.6.2 (2019-12-12). - +R_1FJQlMO4buRu6S2,Birdwoo-1-1-1,1,1,1,-0.449,slope,331.27,0.191,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),"I summed the total values contained in 'euc_sdlgs0_50cm', 'euc_sdlgs50cm-2m' and ''euc_sdlgs>2m'",euc_sdlgs_all,R_1FJQlMO4buRu6S2,NA,NA,0,generalised,standard,9,9,7,7,2,2,0,0,exclude,exclude_all,NA,"My question: How does grass cover influence Eucalyptus spp. seedling recruitment? + +I would not use these data in a hypothesis-testing situation, rather I would use these data for hypothesis-generation. In this context, all three grass variables that I analysed (native_perennial_grass_cover, exotic_annual_grass_cover and exotic_perennial_grass_cover) were retained in at least one plausible model explaining Eucalyptus spp. seedling recruitment. To me, this indicates that grass cover may be a potentially important predictor of Eucalyptus spp. seedling recruitment. + +However, none of the parameter estimate 95% confidence intervals did not overlap with 0, which indicates that there was no evidence for a statistically significant effect of grass cover variables on Eucalyptus spp. seedling recruitment + +",none_q,"All analyses were performed using R version 3.6.2 (2019-12-12). + Packages and version numbers are provided in a sessionInfo() file in the .zip documentation attached.",R,3.6.2,R,3.6.2,NA,NA,NA,Property,Quadrat no,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,SRad_Jan,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Birdwoo R_1GEw0p99dpeSW3E,Alban-4-4-1,4,4,1,NA,NA,366.3,0.029,logit,logit,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,NA,R_1GEw0p99dpeSW3E,rear_Cs_at_start_of_rearing,NA,0,generalised,standard,6,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"Higher level of sibling competition, as in enlarged broods, reduced nestling body mass and tarsus length before fledging and also reduced fledging success.Nestling pre-fledging body mass in turn predicted the probability of recruitment in the next breeding season.",neg_c,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Date_of_day14,NA,day_14_weight,NA,NA,chick_survival_to_first_breed_season,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Alban R_1GEw0p99dpeSW3E,Alban-1-1-1,1,1,1,-0.052,slope,333.265,0.005,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1GEw0p99dpeSW3E,rear_Cs_at_start_of_rearing,3333,0,linear,standard,9,9,3,3,6,6,0,0,retain,retain,NA,"Higher level of sibling competition, as in enlarged broods, reduced nestling body mass and tarsus length before fledging and also reduced fledging success.",neg_c,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,hatch_Box,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,rear_Box,NA,NA,NA,home_or_away,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,Date_of_day14,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Alban R_1GEw0p99dpeSW3E,Alban-2-2-1,2,2,1,-0.148,slope,273.604,0.012,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1GEw0p99dpeSW3E,rear_Cs_at_start_of_rearing,3333,0,linear,standard,9,9,3,3,6,6,0,0,retain,retain,NA,"Higher level of sibling competition, as in enlarged broods, reduced nestling body mass and tarsus length before fledging and also reduced fledging success.",neg_c,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,hatch_Area,hatch_Box,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,rear_Box,NA,NA,NA,home_or_away,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,Date_of_day14,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Alban R_1GEw0p99dpeSW3E,Alban-3-3-1,3,3,1,NA,NA,NA,0.042,logit,logit,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),I used a two-column variable that combines the number of chicks that successfully fledged and the number of chicks that failed for each nest.,NA,R_1GEw0p99dpeSW3E,rear_Cs_at_start_of_rearing,NA,0,generalised,standard,5,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"Higher level of sibling competition, as in enlarged broods, reduced nestling body mass and tarsus length before fledging and also reduced fledging success.",neg_c,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,rear_Box,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,number_chicks_fledged_from_rear_nest,Date_of_day14,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Alban -R_1GJlffAgZv6SY4y,Alpha-1-1-1,1,1,1,NA,NA,NA,NA,NA,NA,blue tit,NA,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,NA,R_1GJlffAgZv6SY4y,NA,NA,CHECK,CHECK,standard,2,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"a) The experiment was poorly planned to answer the question - -or - +R_1GJlffAgZv6SY4y,Alpha-1-1-1,1,1,1,NA,NA,NA,NA,NA,NA,blue tit,NA,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,NA,R_1GJlffAgZv6SY4y,NA,NA,CHECK,CHECK,standard,2,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"a) The experiment was poorly planned to answer the question + +or + b) The question can not be answered by the given data.",none_c,R 4.0.0,R,4.0.0,R,4.0.0,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_Box,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_Box,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Alpha -R_1HeLJJFDOVIZbac,Appin-2-2-1,2,2,1,0.04738,slope,89.21005,0.04189,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1HeLJJFDOVIZbac,d14_rear_nest_brood_size,599,0,linear,standard,2,2,1,1,1,1,0,0,retain,retain,NA,No significant effect of sibling number of growth of nestlings,none_c,"Paring data = LibreOffice Calc version 6.4.4.2 +R_1HeLJJFDOVIZbac,Appin-2-2-1,2,2,1,0.04738,slope,89.21005,0.04189,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1HeLJJFDOVIZbac,d14_rear_nest_brood_size,599,0,linear,standard,2,2,1,1,1,1,0,0,retain,retain,NA,No significant effect of sibling number of growth of nestlings,none_c,"Paring data = LibreOffice Calc version 6.4.4.2 Analysis = RStudio version 1.3.959",LibreOffice Calc,6.4.4.2,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Appin -R_1HeLJJFDOVIZbac,Appin-1-1-1,1,1,1,-1.78E-04,slope,89.5955749,0.0421586,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1HeLJJFDOVIZbac,rear_d0_rear_nest_brood_size,599,0,linear,standard,2,2,1,1,1,1,0,0,retain,retain,NA,No significant effect of sibling number of growth of nestlings,none_c,"Paring data = LibreOffice Calc version 6.4.4.2 +R_1HeLJJFDOVIZbac,Appin-1-1-1,1,1,1,-1.78E-04,slope,89.5955749,0.0421586,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1HeLJJFDOVIZbac,rear_d0_rear_nest_brood_size,599,0,linear,standard,2,2,1,1,1,1,0,0,retain,retain,NA,No significant effect of sibling number of growth of nestlings,none_c,"Paring data = LibreOffice Calc version 6.4.4.2 Analysis = RStudio version 1.3.959",LibreOffice Calc,6.4.4.2,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Appin -R_1HeLJJFDOVIZbac,Appin-4-4-1,4,4,1,6.83E-04,slope,78.6,0.0232,identity,identity,blue tit,1,log(max(weight+1)-weight),log(max(weight+1)-weight),original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_1HeLJJFDOVIZbac,d14_rear_nest_brood_size,599,0,linear,standard,2,2,1,1,1,1,0,0,retain,retain,NA,No significant effect of sibling number of growth of nestlings,none_c,"Paring data = LibreOffice Calc version 6.4.4.2 +R_1HeLJJFDOVIZbac,Appin-4-4-1,4,4,1,6.83E-04,slope,78.6,0.0232,identity,identity,blue tit,1,log(max(weight+1)-weight),log(max(weight+1)-weight),original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_1HeLJJFDOVIZbac,d14_rear_nest_brood_size,599,0,linear,standard,2,2,1,1,1,1,0,0,retain,retain,NA,No significant effect of sibling number of growth of nestlings,none_c,"Paring data = LibreOffice Calc version 6.4.4.2 Analysis = RStudio version 1.3.959",LibreOffice Calc,6.4.4.2,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Appin -R_1HeLJJFDOVIZbac,Appin-3-3-1,3,3,1,0.03884,slope,80.18534,0.02283,identity,identity,blue tit,1,log(max(weight+1)-weight),log(max(weight+1)-weight),original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_1HeLJJFDOVIZbac,rear_d0_rear_nest_brood_size,599,0,linear,standard,2,2,1,1,1,1,0,0,retain,retain,NA,No significant effect of sibling number of growth of nestlings,none_c,"Paring data = LibreOffice Calc version 6.4.4.2 +R_1HeLJJFDOVIZbac,Appin-3-3-1,3,3,1,0.03884,slope,80.18534,0.02283,identity,identity,blue tit,1,log(max(weight+1)-weight),log(max(weight+1)-weight),original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_1HeLJJFDOVIZbac,rear_d0_rear_nest_brood_size,599,0,linear,standard,2,2,1,1,1,1,0,0,retain,retain,NA,No significant effect of sibling number of growth of nestlings,none_c,"Paring data = LibreOffice Calc version 6.4.4.2 Analysis = RStudio version 1.3.959",LibreOffice Calc,6.4.4.2,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Appin R_1ib6zw7qoq0lHlf,Blayney-1-1-1,1,1,1,-0.014094,slope,303.490672,0.010622,NA,NA,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),"sum of ""euc_sdlgs0_50cm"" and ""euc_sdlgs.2m""",euc_sdlgs_all,R_1ib6zw7qoq0lHlf,all_exotic_grass,NA,0,generalised,standard,21,NA,NA,NA,NA,NA,NA,NA,exclude,retain,NA,exotic grass cover and Eucalyptus spp. seedling recruitment had a negative correlation,neg_c,R version 3.6.2 (2019-12-12),R,3.6.2,R,3.6.2,NA,NA,Season,Property,NA,NA,NA,Aspect,NA,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NativeShrub_cover,NA,NA,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,annual_precipitation,NA,NA,NA,MrVBF,NA,NA,NA,SRad_Jan,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Blayney R_1ItMbxJAVt7RRtX,Bodalla-1-1-1,1,1,1,-0.0223707,slope,81.87859,0.003826,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs_all,R_1ItMbxJAVt7RRtX,ExoticAnnualGrass_cover,90,0,generalised,standard,4,4,3,3,1,1,0,0,retain,retain,NA,"There is no clear relationship between grass cover and Eucalyptus spp. seedling recruitment. On a significantly reduced dataset there is a significant negative relationship between exotic annual grasses, though further surveys would be needed to confirm this relationship given the relatively low sample size (n = 91) of this dataset.",none_q,"Initial data exploration, summarising grass and seedling columns - Microsoft Excel; Data analysis (model diagnostics and testing) - R 4.0.0, RStudio 1.2.5033.",Excel,NA,R,4.0.0,NA,NA,NA,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bodalla @@ -94,23 +94,23 @@ R_1LRqq2WHrQaENtM,Boorowa-1-2-1,1,2,1,-0.026084,slope,335.40604,0.028092,log,log R_1LTZWsikoIaKdMu,Brookto-1-1-1,1,1,1,-0.101004592,slope,324,0.0749372,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),euc_sdlgs50cm_2m + euc_sdlgs0-50cm + euc_sdlgs>2m,euc_sdlgs_all,R_1LTZWsikoIaKdMu,all_grass,276,0,generalised,mixture_model,9,9,7,7,2,2,0,0,retain,retain,NA,Grass cover does not significantly affect Eucalyptus spp. seedling recruitment across the sampled properties.,none_c,R 4.0.0,R,4.0.0,R,4.0.0,NA,NA,Season,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NativeShrub_cover,BareGround_cover,Litter_cover,MossLichen_cover,Rock_cover,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,NA,NA,NA,PET,NA,K_perc,Th_ppm,U_ppm,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,soilPC1,coverPC1,coverPC2,coverPC3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Brookto R_1LXqc8NAdABndjl,Broulee-1-1-1,1,1,1,NA,NA,NA,0.57,log,log,eucalyptus,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_1LXqc8NAdABndjl,ExoticPerennialGrass_cover,NA,1,generalised,standard,12,13,9,10,3,3,1,0,retain,exclude_all,NA,"There are to different principal results: 1) When we look for variation between seasons recruitment significantly decreases in winter as a function of exotic annual grass cover and exotic perennial grass. On another hand, recruitment increasing in spring in response to native perennial grass. Finally, recruitment declines in the autumn in response to perennial grass cover (both native and exotic; 2) The structural model shows that eucalyptus recruitment had a negative indirect effect by native perennial grass and exotic annual grass via eucalyptus establishment.",mixed,All analysis as performed using R 4.0.1 (2020-06-06),R,4.0.1,R,4.0.1,NA,NA,Season,Property,NA,NA,NA,NA,Landscape position,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,Litter_cover,NA,NA,NA,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,NA,NA,annual_precipitation,NA,NA,NA,NA,K_perc,NA,NA,NA,SRad_Jul,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Broulee R_1M0cMZL2IPYWHoi,Bruthen-1-1-1,1,1,1,NA,NA,NA,NA,NA,NA,eucalyptus,NA,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs_all,R_1M0cMZL2IPYWHoi,NA,NA,CHECK,CHECK,CHECK,0,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,NA,CHECK,NA,CHECK,CHECK,CHECK,CHECK,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bruthen -R_1M0cMZL2IPYWHoi,Buderim-1-1-1,1,1,1,NA,NA,NA,NA,NA,NA,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs_all,R_1M0cMZL2IPYWHoi,NA,NA,1,generalised,CHECK,18,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"""How does grass cover influence Eucalyptus spp. seedling recruitment?"" was not the research question!! - -The questions were the following: - -""The first question that is addressed is whether tree regeneration is happening"" - -Result: ""Regarding the first question, whether tree regeneration is happening, we found very strong support (Fig. 1, Table 1: P[effect>0]=100%) for large seedlings to become more abundant (posterior mean = 6% increase) over time, but found no support for a change in occurrence of small and medium seedlings ([P[effect>0]=70.6% and 78.3], respectively)."" - -""The second question that is address is what factors drives eucalyptus tree regeneration."" - -Result: ""With respect to the second question, concerning what is driving the difference in tree regeneration, we found that all our selected explanatory variables were very likely (P[effect>0] at least 93.1%) to decrease seedling mean occurrences in magnitudes ranging between 6 and 21 %.""",NA,"R version 3.6.3 (2020-02-29) -other attached packages: - [1] Hmsc_3.0-6 coda_0.19-3 - [3] readxl_1.3.1 forcats_0.5.0 - [5] stringr_1.4.0 dplyr_1.0.0 - [7] purrr_0.3.4 readr_1.3.1 - [9] tidyr_1.1.0 tibble_3.0.1 +R_1M0cMZL2IPYWHoi,Buderim-1-1-1,1,1,1,NA,NA,NA,NA,NA,NA,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs_all,R_1M0cMZL2IPYWHoi,NA,NA,1,generalised,CHECK,18,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"""How does grass cover influence Eucalyptus spp. seedling recruitment?"" was not the research question!! + +The questions were the following: + +""The first question that is addressed is whether tree regeneration is happening"" + +Result: ""Regarding the first question, whether tree regeneration is happening, we found very strong support (Fig. 1, Table 1: P[effect>0]=100%) for large seedlings to become more abundant (posterior mean = 6% increase) over time, but found no support for a change in occurrence of small and medium seedlings ([P[effect>0]=70.6% and 78.3], respectively)."" + +""The second question that is address is what factors drives eucalyptus tree regeneration."" + +Result: ""With respect to the second question, concerning what is driving the difference in tree regeneration, we found that all our selected explanatory variables were very likely (P[effect>0] at least 93.1%) to decrease seedling mean occurrences in magnitudes ranging between 6 and 21 %.""",NA,"R version 3.6.3 (2020-02-29) +other attached packages: + [1] Hmsc_3.0-6 coda_0.19-3 + [3] readxl_1.3.1 forcats_0.5.0 + [5] stringr_1.4.0 dplyr_1.0.0 + [7] purrr_0.3.4 readr_1.3.1 + [9] tidyr_1.1.0 tibble_3.0.1 [11] ggplot2_3.3.1 tidyverse_1.3.0",R,3.6.3,R,3.6.3,NA,Date,NA,NA,NA,Easting,Northing,NA,NA,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NativeShrub_cover,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,NA,NA,NA,PET,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Buderim R_1MRquC7DrqOiQ5p,Avoca-1-1-1,1,1,1,-0.1753,reduced-enlarged,2375.96487,0.15,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1MRquC7DrqOiQ5p,rear_nest_trt_R.E,NA,0,linear,standard,5,6,3,4,2,2,1,0,retain,retain,NA,"These results suggest that the growth of nestling blue tits is strongly influenced by the number of nestlings. These results also suggest, however, that competition with siblings is tempered by some additional factor, as increases in nest size beyond the unmanipulated state did not significantly reduce sibling growth.",neg_q,R 4.0.2,R,4.0.2,R,4.0.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Avoca R_1NqVW3amqwy69rK,Candelo-4-4-1,4,4,1,NA,NA,NA,NA,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),Euc_data$euc_sdlgs0_50cm + Euc_data$euc_sdlgs50cm.2m + Euc_data$euc_sdlgs.2m,euc_sdlgs_all,R_1NqVW3amqwy69rK,NA,NA,0,generalised,zero_inflated,5,0,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"Grass cover in general might have a mild negative effect on eucalypt seedling establishment, yet support for this hypothesis is weak.",neg_q,All analyses were performed in R version 4.0.2 (R Core Team 2020),R,4.0.2,R,4.0.2,NA,NA,NA,Property,Quadrat no,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Candelo @@ -121,73 +121,73 @@ R_1o4ElmLsRiBa4FJ,Bargo-1-1-1,1,1,1,-0.026830707,slope,383.391807,0.009092046,id R_1o4ElmLsRiBa4FJ,Bargo-3-3-1,3,3,1,-0.0295659,slope,299.30603,0.010420679,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1o4ElmLsRiBa4FJ,rear_Cs_at_start_of_rearing,3189,0,linear,standard,14,16,6,8,8,8,0,2,retain,retain,NA,"Overall, our results showed that the more competition, the less nestlings grow. These results were particularly evident when focusing on nestlings’ body mass rather than tarsus length, which is likely due to the larger lability (and lower heritability) of body mass compared to tarsus length.",neg_c,R programming language v.3.5.1 (R Core Team 2018),R,3.5.1,R,3.5.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,rear_mom_Ring,rear_dad_Ring,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,brood_mortality,NA,Bargo R_1o4ElmLsRiBa4FJ,Bargo-2-2-1,2,2,1,-0.09949535,slope,394.77937,0.018919666,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1o4ElmLsRiBa4FJ,rear_Cs_at_start_of_rearing,3189,0,linear,standard,10,12,6,8,4,4,0,2,retain,retain,NA,"Overall, our results showed that the more competition, the less nestlings grow. These results were particularly evident when focusing on nestlings’ body mass rather than tarsus length, which is likely due to the larger lability (and lower heritability) of body mass compared to tarsus length.",neg_c,R programming language v.3.5.1 (R Core Team 2018),R,3.5.1,R,3.5.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,rear_mom_Ring,NA,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,brood_mortality,NA,Bargo R_1o4ElmLsRiBa4FJ,Bargo-4-4-1,4,4,1,-0.112223317,slope,320.77503,0.020133793,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1o4ElmLsRiBa4FJ,rear_Cs_at_start_of_rearing,3189,0,linear,standard,13,15,6,8,7,7,0,2,retain,retain,NA,"Overall, our results showed that the more competition, the less nestlings grow. These results were particularly evident when focusing on nestlings’ body mass rather than tarsus length, which is likely due to the larger lability (and lower heritability) of body mass compared to tarsus length.",neg_c,R programming language v.3.5.1 (R Core Team 2018),R,3.5.1,R,3.5.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,rear_mom_Ring,rear_dad_Ring,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,brood_mortality,NA,Bargo -R_1QlnXdW5tKuUQIr,Capella-1-1-1,1,1,1,NA,NA,343.24787,0.2328,log,log,eucalyptus,NA,check.mixed.team,check.mixed.team,constructed variable (combining information from two or more original variables),"We added ""euc_sdlgs0_50cm"" and ""euc_sdlgs50cm-2m"" together",euc_sdlgs>2m,R_1QlnXdW5tKuUQIr,CHECK,NA,CHECK,CHECK,CHECK,22,NA,20,NA,2,NA,NA,NA,check.mixed.team,CHECK,NA,"Both net_rearing_manipulation and rear_Cs_at_start_of_rearing were associated with the outcome variables, though net_rearing_manipulation was not significantly associated with tarsus length in my final model. Net_rearing_manipulation was still associated with weight, so an increase in the number of chicks in the nest was linked to lower weights. Similarly, more rear_Cs_at_start_of_rearing was linked shorter tarsus lengths and lower weights. More siblings, and presumably additional competition, was on balance worse for nestling growth. - +R_1QlnXdW5tKuUQIr,Capella-1-1-1,1,1,1,NA,NA,343.24787,0.2328,log,log,eucalyptus,NA,check.mixed.team,check.mixed.team,constructed variable (combining information from two or more original variables),"We added ""euc_sdlgs0_50cm"" and ""euc_sdlgs50cm-2m"" together",euc_sdlgs>2m,R_1QlnXdW5tKuUQIr,CHECK,NA,CHECK,CHECK,CHECK,22,NA,20,NA,2,NA,NA,NA,check.mixed.team,CHECK,NA,"Both net_rearing_manipulation and rear_Cs_at_start_of_rearing were associated with the outcome variables, though net_rearing_manipulation was not significantly associated with tarsus length in my final model. Net_rearing_manipulation was still associated with weight, so an increase in the number of chicks in the nest was linked to lower weights. Similarly, more rear_Cs_at_start_of_rearing was linked shorter tarsus lengths and lower weights. More siblings, and presumably additional competition, was on balance worse for nestling growth. + I was especially interested in the interactions I might find between net_rearing_manipulation or rear_Cs_at_start_of_rearing and other variables, but for the most part, I could not confirm any such relationships. The exception was the interaction between net_rearing_manipulation and the square of hatch_nest_LD. This suggests that chicks in nests manipulated to have more chicks had greater growth when the lay date of the nest that chick was born in was later in the month.",neg_q,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,hatch_Area,NA,NA,NA,Extra-pair_paternity,NA,NA,hatch_nest_LD,hatch_nest_CS,hatch_nest_OH,d0_hatch_nest_brood_size,d14_hatch_nest_brood_size,NA,rear_area,NA,NA,NA,NA,home_or_away,rear_nest_LD,rear_nest_CS,rear_nest_OH,rear_d0_rear_nest_brood_size,NA,NA,net_rearing_manipulation,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,Date_of_day14,day_14_tarsus_length,day_14_weight,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Capella R_1QoRu2birFKL9Hx,Berry-1-1-1,1,1,1,-0.05996286,slope,150.69387,0.005510245,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1QoRu2birFKL9Hx,rear_Cs_at_start_of_rearing,1854,0,linear,standard,8,8,2,2,6,6,0,0,retain,retain,NA,Sibling competition significantly affects the growth of nestling blue tits.,neg_c,R 3.6.3,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,rear_Box,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,parentage,NA,NA,NA,NA,Berry R_1r2FSn2AXuCimpi,Carcoar-1-1-1,1,1,1,-0.00221,slope,338.57425,0.009873,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),agg_regen <- data.complete$euc_sdlgs0_50cm*0.25 + data.complete$euc_sdlgs50cm.2m*1.25 + data.complete$euc_sdlgs.2m*2.5,small*0.25+medium*1.25+large*2.5,R_1r2FSn2AXuCimpi,ExoticAnnualGrass_cover,345,0,generalised,standard,5,5,3,3,2,2,0,0,retain,retain,NA,"After fitting a final model including this nuisance variable along with our parameters of interest, annual and perennial grass cover, we did not find evidence for strong effects of annual or perennial grass cover on eucalyptus seedling aggregate height",none_c,Program R Version 3.6.1,R,3.6.1,R,3.6.1,NA,NA,Season,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_perennial_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Carcoar R_1reUKfTYXhTqVMo,Carnama-1-1-1,1,1,1,NA,NA,NA,0.3188723,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_1reUKfTYXhTqVMo,NativePerennialGrass_cover,NA,1,generalised,standard,6,6,4,4,2,2,0,0,retain,exclude_all,NA,"Cover of exotic perennial grass only influences seedling persistence, with no effects of grass cover on seedling recruitment.",mixed,R v.3.6.3 with calls to Stan v.2.19,R,3.6.3,"R,Stan","3.6.3,2.19",SurveyID,NA,Season,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Carnama -R_1rq3aFo8fdXcGP3,Binda-2-2-2,2,2,2,-0.211,control-enlarged,392.63,0.061,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1rq3aFo8fdXcGP3,rear_nest_trt_C.E,NA,0,linear,standard,7,7,4,4,3,3,0,0,retain,retain,NA,"I found that nestling growth decreases when competition with siblings is experimentally increased. However, I did not find an increase in nestling growth when competition with siblings is experimentally decreased.",mixed,"Data cleaning - Microsoft Excel +R_1rq3aFo8fdXcGP3,Binda-2-2-2,2,2,2,-0.211,control-enlarged,392.63,0.061,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1rq3aFo8fdXcGP3,rear_nest_trt_C.E,NA,0,linear,standard,7,7,4,4,3,3,0,0,retain,retain,NA,"I found that nestling growth decreases when competition with siblings is experimentally increased. However, I did not find an increase in nestling growth when competition with siblings is experimentally decreased.",mixed,"Data cleaning - Microsoft Excel Analysis - R 3.6.1",Excel,NA,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Binda -R_1rq3aFo8fdXcGP3,Binda-2-2-1,2,2,1,-0.013,reduced-control,450.29,0.058,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1rq3aFo8fdXcGP3,rear_nest_trt_R.C,NA,0,linear,standard,7,7,4,4,3,3,0,0,retain,retain,NA,"I found that nestling growth decreases when competition with siblings is experimentally increased. However, I did not find an increase in nestling growth when competition with siblings is experimentally decreased.",mixed,"Data cleaning - Microsoft Excel +R_1rq3aFo8fdXcGP3,Binda-2-2-1,2,2,1,-0.013,reduced-control,450.29,0.058,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_1rq3aFo8fdXcGP3,rear_nest_trt_R.C,NA,0,linear,standard,7,7,4,4,3,3,0,0,retain,retain,NA,"I found that nestling growth decreases when competition with siblings is experimentally increased. However, I did not find an increase in nestling growth when competition with siblings is experimentally decreased.",mixed,"Data cleaning - Microsoft Excel Analysis - R 3.6.1",Excel,NA,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Binda -R_1rq3aFo8fdXcGP3,Binda-1-1-1,1,1,1,-0.616,control-enlarged,424.2,0.12,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1rq3aFo8fdXcGP3,rear_nest_trt_C.E,NA,0,linear,standard,8,8,4,4,4,4,0,0,retain,retain,NA,"I found that nestling growth decreases when competition with siblings is experimentally increased. However, I did not find an increase in nestling growth when competition with siblings is experimentally decreased.",mixed,"Data cleaning - Microsoft Excel +R_1rq3aFo8fdXcGP3,Binda-1-1-1,1,1,1,-0.616,control-enlarged,424.2,0.12,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1rq3aFo8fdXcGP3,rear_nest_trt_C.E,NA,0,linear,standard,8,8,4,4,4,4,0,0,retain,retain,NA,"I found that nestling growth decreases when competition with siblings is experimentally increased. However, I did not find an increase in nestling growth when competition with siblings is experimentally decreased.",mixed,"Data cleaning - Microsoft Excel Analysis - R 3.6.1",Excel,NA,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Binda -R_1rq3aFo8fdXcGP3,Binda-1-1-2,1,1,2,0.139,reduced-control,393.7,0.129,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1rq3aFo8fdXcGP3,rear_nest_trt_R.C,NA,0,linear,standard,8,8,4,4,4,4,0,0,retain,retain,NA,"I found that nestling growth decreases when competition with siblings is experimentally increased. However, I did not find an increase in nestling growth when competition with siblings is experimentally decreased.",mixed,"Data cleaning - Microsoft Excel +R_1rq3aFo8fdXcGP3,Binda-1-1-2,1,1,2,0.139,reduced-control,393.7,0.129,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_1rq3aFo8fdXcGP3,rear_nest_trt_R.C,NA,0,linear,standard,8,8,4,4,4,4,0,0,retain,retain,NA,"I found that nestling growth decreases when competition with siblings is experimentally increased. However, I did not find an increase in nestling growth when competition with siblings is experimentally decreased.",mixed,"Data cleaning - Microsoft Excel Analysis - R 3.6.1",Excel,NA,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Binda -R_210APF6gYFATf7Y,Borde-1-1-1,1,1,1,-0.24384524,slope,332.37685,0.02546829,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_210APF6gYFATf7Y,rear_Cs_at_start_of_rearing,2581,0,linear,standard,16,16,6,6,10,10,0,0,retain,retain,NA,"Competition with siblings has an overall negative effect on the growth of nestling blue tits. However, the large variance within and between chicks shows that there are many parental and rearing effects that influence the body mass and length of tarsus in the species.",neg_q,"All processes were done using: +R_210APF6gYFATf7Y,Borde-1-1-1,1,1,1,-0.24384524,slope,332.37685,0.02546829,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_210APF6gYFATf7Y,rear_Cs_at_start_of_rearing,2581,0,linear,standard,16,16,6,6,10,10,0,0,retain,retain,NA,"Competition with siblings has an overall negative effect on the growth of nestling blue tits. However, the large variance within and between chicks shows that there are many parental and rearing effects that influence the body mass and length of tarsus in the species.",neg_q,"All processes were done using: R version 4.0.0 (2020-04-24) -- ""Arbor Day"" on R Studio Version 1.2.5042",R,4.0.0,R,4.0.0,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,hatch_Area,hatch_Box,hatch_mom_Ring,hatch_nest_dad_Ring,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,rear_Box,rear_mom_Ring,rear_dad_Ring,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Borde -R_21AEcUhC7tWDsN6,Chewton-1-1-1,1,1,1,NA,NA,NA,NA,log,log,eucalyptus,1,z.score,z.score,constructed variable (combining information from two or more original variables),"""euc_sdlgs_overall = euc_sdlgs0_50cm + euc_sdlgs50cm_2m + euc_sdlgs_over2m"" as well as a binomial identifier on whether a seedling was present or not",euc_sdlgs_all,R_21AEcUhC7tWDsN6,all_grass:Euc_canopy_cover,NA,1,generalised,hurdle,5,7,4,6,1,1,2,0,retain,exclude_all,exclude,Across the investigated properties overall grass cover increased Eucalyptus spp. seedling recruitment.,pos_c,"R version 4.0.0 (2020-04-24) -Platform: x86_64-w64-mingw32/x64 (64-bit) -Running under: Windows 10 x64 (build 18363) - -Matrix products: default - -locale: -[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 -[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C -[5] LC_TIME=English_United Kingdom.1252 - -attached base packages: -[1] stats graphics grDevices utils datasets methods base - -other attached packages: - [1] flextable_0.5.10 kableExtra_1.1.0 assertthat_0.2.1 furrr_0.1.0 future_1.17.0 mice_3.9.0 - [7] see_0.5.0 logspline_2.1.16 lubridate_1.7.8 mapview_2.7.8 sf_0.9-3 tmap_3.0 -[13] gt_0.2.0.5 performance_0.4.6 effectsize_0.3.1 parameters_0.7.0 tidybayes_2.0.3 cowplot_1.0.0 -[19] forcats_0.5.0 stringr_1.4.0 dplyr_0.8.5 purrr_0.3.4 readr_1.3.1 tidyr_1.0.3 -[25] tibble_3.0.1 ggplot2_3.3.1 tidyverse_1.3.0 brms_2.13.0 Rcpp_1.0.4.6 knitr_1.28 - -loaded via a namespace (and not attached): - [1] tidyselect_1.1.0 lme4_1.1-23 htmlwidgets_1.5.1 grid_4.0.0 munsell_0.5.0 - [6] codetools_0.2-16 units_0.6-6 statmod_1.4.34 DT_0.13 miniUI_0.1.1.1 - [11] withr_2.2.0 Brobdingnag_1.2-6 colorspace_1.4-1 uuid_0.1-4 highr_0.8 - [16] rstudioapi_0.11 stats4_4.0.0 officer_0.3.11 bayesplot_1.7.2 listenv_0.8.0 - [21] labeling_0.3 emmeans_1.4.6 rstan_2.19.3 farver_2.0.3 bridgesampling_1.0-0 - [26] coda_0.19-3 vctrs_0.3.0 generics_0.0.2 TH.data_1.0-10 xfun_0.13 - [31] randomForest_4.6-14 R6_2.4.1 markdown_1.1 HDInterval_0.2.0 promises_1.1.0 - [36] scales_1.1.1 multcomp_1.4-13 gtable_0.3.0 globals_0.12.5 lwgeom_0.2-3 - [41] processx_3.4.2 sandwich_2.5-1 rlang_0.4.6 systemfonts_0.2.2 splines_4.0.0 - [46] dichromat_2.0-0 checkmate_2.0.0 broom_0.5.6 inline_0.3.15 yaml_2.2.1 - [51] reshape2_1.4.4 abind_1.4-5 modelr_0.1.7 threejs_0.3.3 crosstalk_1.1.0.1 - [56] backports_1.1.7 httpuv_1.5.2 rsconnect_0.8.16 tools_4.0.0 ellipsis_0.3.1 - [61] raster_3.1-5 RColorBrewer_1.1-2 ggridges_0.5.2 plyr_1.8.6 base64enc_0.1-3 - [66] classInt_0.4-3 ps_1.3.3 prettyunits_1.1.1 viridis_0.5.1 tmaptools_3.0 - [71] zoo_1.8-8 haven_2.2.0 fs_1.4.1 leafem_0.1.1 magrittr_1.5 - [76] data.table_1.12.8 colourpicker_1.0 reprex_0.3.0 mvtnorm_1.1-0 packrat_0.5.0 - [81] matrixStats_0.56.0 hms_0.5.3 shinyjs_1.1 mime_0.9 evaluate_0.14 - [86] arrayhelpers_1.1-0 xtable_1.8-4 shinystan_2.5.0 XML_3.99-0.3 leaflet_2.0.3 - [91] readxl_1.3.1 gridExtra_2.3 rstantools_2.0.0 compiler_4.0.0 KernSmooth_2.23-16 - [96] crayon_1.3.4 minqa_1.2.4 StanHeaders_2.19.2 htmltools_0.4.0 later_1.0.0 -[101] DBI_1.1.0 dbplyr_1.4.3 MASS_7.3-51.5 boot_1.3-24 Matrix_1.2-18 -[106] cli_2.0.2 parallel_4.0.0 insight_0.8.4 igraph_1.2.5 pkgconfig_2.0.3 -[111] sp_1.4-1 xml2_1.3.2 svUnit_1.0.3 dygraphs_1.1.1.6 webshot_0.5.2 -[116] estimability_1.3 rvest_0.3.5 callr_3.4.3 digest_0.6.25 rmarkdown_2.1 -[121] cellranger_1.1.0 leafsync_0.1.0 gdtools_0.2.2 shiny_1.4.0.2 gtools_3.8.2 -[126] satellite_1.0.2 nloptr_1.2.2.1 lifecycle_0.2.0 nlme_3.1-147 jsonlite_1.6.1 -[131] viridisLite_0.3.0 fansi_0.4.1 pillar_1.4.4 lattice_0.20-41 loo_2.2.0 -[136] fastmap_1.0.1 httr_1.4.1 pkgbuild_1.0.8 survival_3.1-12 glue_1.4.1 -[141] xts_0.12-0 zip_2.0.4 bayestestR_0.6.0 png_0.1-7 shinythemes_1.1.2 +R_21AEcUhC7tWDsN6,Chewton-1-1-1,1,1,1,NA,NA,NA,NA,log,log,eucalyptus,1,z.score,z.score,constructed variable (combining information from two or more original variables),"""euc_sdlgs_overall = euc_sdlgs0_50cm + euc_sdlgs50cm_2m + euc_sdlgs_over2m"" as well as a binomial identifier on whether a seedling was present or not",euc_sdlgs_all,R_21AEcUhC7tWDsN6,all_grass:Euc_canopy_cover,NA,1,generalised,hurdle,5,7,4,6,1,1,2,0,retain,exclude_all,exclude,Across the investigated properties overall grass cover increased Eucalyptus spp. seedling recruitment.,pos_c,"R version 4.0.0 (2020-04-24) +Platform: x86_64-w64-mingw32/x64 (64-bit) +Running under: Windows 10 x64 (build 18363) + +Matrix products: default + +locale: +[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 +[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C +[5] LC_TIME=English_United Kingdom.1252 + +attached base packages: +[1] stats graphics grDevices utils datasets methods base + +other attached packages: + [1] flextable_0.5.10 kableExtra_1.1.0 assertthat_0.2.1 furrr_0.1.0 future_1.17.0 mice_3.9.0 + [7] see_0.5.0 logspline_2.1.16 lubridate_1.7.8 mapview_2.7.8 sf_0.9-3 tmap_3.0 +[13] gt_0.2.0.5 performance_0.4.6 effectsize_0.3.1 parameters_0.7.0 tidybayes_2.0.3 cowplot_1.0.0 +[19] forcats_0.5.0 stringr_1.4.0 dplyr_0.8.5 purrr_0.3.4 readr_1.3.1 tidyr_1.0.3 +[25] tibble_3.0.1 ggplot2_3.3.1 tidyverse_1.3.0 brms_2.13.0 Rcpp_1.0.4.6 knitr_1.28 + +loaded via a namespace (and not attached): + [1] tidyselect_1.1.0 lme4_1.1-23 htmlwidgets_1.5.1 grid_4.0.0 munsell_0.5.0 + [6] codetools_0.2-16 units_0.6-6 statmod_1.4.34 DT_0.13 miniUI_0.1.1.1 + [11] withr_2.2.0 Brobdingnag_1.2-6 colorspace_1.4-1 uuid_0.1-4 highr_0.8 + [16] rstudioapi_0.11 stats4_4.0.0 officer_0.3.11 bayesplot_1.7.2 listenv_0.8.0 + [21] labeling_0.3 emmeans_1.4.6 rstan_2.19.3 farver_2.0.3 bridgesampling_1.0-0 + [26] coda_0.19-3 vctrs_0.3.0 generics_0.0.2 TH.data_1.0-10 xfun_0.13 + [31] randomForest_4.6-14 R6_2.4.1 markdown_1.1 HDInterval_0.2.0 promises_1.1.0 + [36] scales_1.1.1 multcomp_1.4-13 gtable_0.3.0 globals_0.12.5 lwgeom_0.2-3 + [41] processx_3.4.2 sandwich_2.5-1 rlang_0.4.6 systemfonts_0.2.2 splines_4.0.0 + [46] dichromat_2.0-0 checkmate_2.0.0 broom_0.5.6 inline_0.3.15 yaml_2.2.1 + [51] reshape2_1.4.4 abind_1.4-5 modelr_0.1.7 threejs_0.3.3 crosstalk_1.1.0.1 + [56] backports_1.1.7 httpuv_1.5.2 rsconnect_0.8.16 tools_4.0.0 ellipsis_0.3.1 + [61] raster_3.1-5 RColorBrewer_1.1-2 ggridges_0.5.2 plyr_1.8.6 base64enc_0.1-3 + [66] classInt_0.4-3 ps_1.3.3 prettyunits_1.1.1 viridis_0.5.1 tmaptools_3.0 + [71] zoo_1.8-8 haven_2.2.0 fs_1.4.1 leafem_0.1.1 magrittr_1.5 + [76] data.table_1.12.8 colourpicker_1.0 reprex_0.3.0 mvtnorm_1.1-0 packrat_0.5.0 + [81] matrixStats_0.56.0 hms_0.5.3 shinyjs_1.1 mime_0.9 evaluate_0.14 + [86] arrayhelpers_1.1-0 xtable_1.8-4 shinystan_2.5.0 XML_3.99-0.3 leaflet_2.0.3 + [91] readxl_1.3.1 gridExtra_2.3 rstantools_2.0.0 compiler_4.0.0 KernSmooth_2.23-16 + [96] crayon_1.3.4 minqa_1.2.4 StanHeaders_2.19.2 htmltools_0.4.0 later_1.0.0 +[101] DBI_1.1.0 dbplyr_1.4.3 MASS_7.3-51.5 boot_1.3-24 Matrix_1.2-18 +[106] cli_2.0.2 parallel_4.0.0 insight_0.8.4 igraph_1.2.5 pkgconfig_2.0.3 +[111] sp_1.4-1 xml2_1.3.2 svUnit_1.0.3 dygraphs_1.1.1.6 webshot_0.5.2 +[116] estimability_1.3 rvest_0.3.5 callr_3.4.3 digest_0.6.25 rmarkdown_2.1 +[121] cellranger_1.1.0 leafsync_0.1.0 gdtools_0.2.2 shiny_1.4.0.2 gtools_3.8.2 +[126] satellite_1.0.2 nloptr_1.2.2.1 lifecycle_0.2.0 nlme_3.1-147 jsonlite_1.6.1 +[131] viridisLite_0.3.0 fansi_0.4.1 pillar_1.4.4 lattice_0.20-41 loo_2.2.0 +[136] fastmap_1.0.1 httr_1.4.1 pkgbuild_1.0.8 survival_3.1-12 glue_1.4.1 +[141] xts_0.12-0 zip_2.0.4 bayestestR_0.6.0 png_0.1-7 shinythemes_1.1.2 [146] class_7.3-16 stringi_1.4.6 stars_0.4-1 e1071_1.7-3",R,4.0.0,R,4.0.0,NA,NA,NA,Property,NA,NA,NA,Aspect,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,MossLichen_cover,NA,Euc_canopy_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Chewton R_21an1zgH6j5Vfds,Bowen-4-3-1,4,3,1,-0.01933209,control-enlarged,284.3718554,0.01123897,identity,identity,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),(day_14_weight) divided by (day_14_tarsus_length),day_14_weight/day_14_tarsus_length,R_21an1zgH6j5Vfds,rear_nest_trt_C.E,NA,0,linear,standard,15,15,10,10,5,5,0,0,retain,retain,NA,"Overall, there was a trend for decreased body condition due to nest treatment (Table 5), however both increasing and decreasing the nest trended in the same direction.",neg_q,R,R,NA,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,hatch_Area,NA,hatch_mom_Ring,NA,Extra-pair_paternity,NA,NA,NA,NA,NA,NA,NA,NA,rear_area,NA,rear_mom_Ring,rear_dad_Ring,rear_nest_trt,home_or_away,rear_nest_LD,rear_nest_CS,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,rear_incub_length,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bowen R_21an1zgH6j5Vfds,Bowen-4-3-2,4,3,2,0.02349155,reduced-control,255.7547186,0.01198362,identity,identity,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),(day_14_weight) divided by (day_14_tarsus_length),day_14_weight/day_14_tarsus_length,R_21an1zgH6j5Vfds,rear_nest_trt_R.C,NA,0,linear,standard,15,15,10,10,5,5,0,0,retain,retain,NA,"Overall, there was a trend for decreased body condition due to nest treatment (Table 5), however both increasing and decreasing the nest trended in the same direction.",neg_q,R,R,NA,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,hatch_Area,NA,hatch_mom_Ring,NA,Extra-pair_paternity,NA,NA,NA,NA,NA,NA,NA,NA,rear_area,NA,rear_mom_Ring,rear_dad_Ring,rear_nest_trt,home_or_away,rear_nest_LD,rear_nest_CS,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,rear_incub_length,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bowen @@ -205,8 +205,8 @@ R_21jtSu9hB9Shf6Y,Andamook-3-3-1,3,3,1,-0.0121,slope,272.3422,0.01222,log,log,eu R_21jtSu9hB9Shf6Y,Andamook-1-1-1,1,1,1,-1.28E-04,slope,310.00345,0.0194497,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_21jtSu9hB9Shf6Y,ExoticAnnualGrass_cover,350,0,generalised,standard,4,4,3,3,1,1,0,0,retain,retain,NA,"We found no effect of individual grass cover types or total grass cover on the number of eucalypt seedlings in either the 0-50 or 50-200 cm height categories. Estimated effects were weak for all variables and accompanied by large standard errors, with 95% confidence intervals overlapping zero in all cases",none_c,R,R,NA,R,NA,NA,NA,NA,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Andamook R_21jtSu9hB9Shf6Y,Andamook-4-4-1,4,4,1,3.00E-04,slope,344.28924,0.0075425,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_21jtSu9hB9Shf6Y,all_grass,350,0,generalised,standard,2,2,1,1,1,1,0,0,retain,retain,NA,"We found no effect of individual grass cover types or total grass cover on the number of eucalypt seedlings in either the 0-50 or 50-200 cm height categories. Estimated effects were weak for all variables and accompanied by large standard errors, with 95% confidence intervals overlapping zero in all cases",none_c,R,R,NA,R,NA,NA,NA,NA,Property,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Andamook R_21jtSu9hB9Shf6Y,Andamook-2-2-1,2,2,1,0.010453,slope,343.19973,0.012184,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_21jtSu9hB9Shf6Y,ExoticAnnualGrass_cover,350,0,generalised,standard,4,4,3,3,1,1,0,0,retain,retain,NA,"We found no effect of individual grass cover types or total grass cover on the number of eucalypt seedlings in either the 0-50 or 50-200 cm height categories. Estimated effects were weak for all variables and accompanied by large standard errors, with 95% confidence intervals overlapping zero in all cases",none_c,R,R,NA,R,NA,NA,NA,NA,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Andamook -R_22mEYpP8f0QXcTl,Cedun-1-1-1,1,1,1,NA,NA,2372.82,0.030382264,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_22mEYpP8f0QXcTl,NA,NA,0,linear,standard,7,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"We conclude that growth of Blue tits is strongly impacted by competition with siblings. - +R_22mEYpP8f0QXcTl,Cedun-1-1-1,1,1,1,NA,NA,2372.82,0.030382264,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_22mEYpP8f0QXcTl,NA,NA,0,linear,standard,7,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"We conclude that growth of Blue tits is strongly impacted by competition with siblings. + Growth is strongly influenced by the number of siblings in the nest that a particular chick is reared with- growth parameters decrease with an increase in the number of siblings in a nest. In addition, sex strongly effects growth parameters- male chicks are heavier and have a longer tarsus than females. The experiment itself appears to have an impact- weight of chicks who were reared in the home nest were s heavier than experimental chicks, whereas the tarsus length was significantly higher for chicks that were reared in a nest away from their hatching nest.",neg_c,We conducted all analysis in R (version 3.6.2),R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_CS,NA,NA,NA,NA,NA,rear_Box,NA,NA,NA,home_or_away,NA,NA,NA,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,NA,day_14_tarsus_length,day_14_weight,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Cedun R_234CYWFp3pm7mxh,Albury-2-2-1,2,2,1,-0.07829,slope,203.8221,0.0119,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_234CYWFp3pm7mxh,net_rearing_manipulation,2533,0,linear,standard,16,16,8,8,8,8,0,0,retain,retain,NA,"We found a clear and consistent negative effect of brood size manipulation for all of our three indicators of hatchling growth, tarsus length (β = -0.09, 95% CI = -0.11  -0.07), body mass (β = -0.22, 95% CI = -0.27  -0.18), and scaled mass index (β = -0.21, 95% CI = -0.25  -0.17; Table 1, Figure 1). An increase in brood size resulted in lower growth of hatchlings and conversely, a decrease in brood size resulted in higher growth rate.",neg_c,R version 3.6.2,R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,hatch_Area,NA,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),hatch_nest_LD,hatch_nest_CS,NA,NA,NA,NA,rear_area,rear_Box,rear_mom_Ring,rear_dad_Ring,NA,home_or_away,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,net_rearing_manipulation,NA,d14_rear_nest_brood_size,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Albury R_234CYWFp3pm7mxh,Albury-1-1-1,1,1,1,-0.25916,slope,233.1086,0.0286,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_234CYWFp3pm7mxh,net_rearing_manipulation,2533,0,linear,standard,16,16,8,8,8,8,0,0,retain,retain,NA,"We found a clear and consistent negative effect of brood size manipulation for all of our three indicators of hatchling growth, tarsus length (β = -0.09, 95% CI = -0.11  -0.07), body mass (β = -0.22, 95% CI = -0.27  -0.18), and scaled mass index (β = -0.21, 95% CI = -0.25  -0.17; Table 1, Figure 1). An increase in brood size resulted in lower growth of hatchlings and conversely, a decrease in brood size resulted in higher growth rate.",neg_c,R version 3.6.2,R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,hatch_Area,NA,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),hatch_nest_LD,hatch_nest_CS,NA,NA,NA,NA,rear_area,rear_Box,rear_mom_Ring,rear_dad_Ring,NA,home_or_away,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,net_rearing_manipulation,NA,d14_rear_nest_brood_size,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Albury @@ -222,7 +222,7 @@ R_27QNfbdXCi5JjQT,Anglesea-2-2-1,2,2,1,-0.065537,slope,339,0.026071,log,log,euca R_2AHKlq0vRRQTSVz,Ardrossa-1-1-1,1,1,1,-0.002203604,slope,327.5273531,0.008427101,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),Sum of euc_sdlgs0_50cm + euc_sdlgs50cm.2m,euc_sdlgs0_2m,R_2AHKlq0vRRQTSVz,all_grass,350,1,generalised,standard,3,3,2,2,1,1,0,0,retain,retain,NA,Grass cover does not appear to influence Eucalyptus seedling recruitment.,none_c,All analyses completed with R 4.0.0. Model fitting done with package brms 2.12.0.,R,4.0.0,R,4.0.0,NA,NA,NA,Property,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Ardrossa R_2anLJGpWhjUjzes,Arkarool-1-1-1,1,1,1,NA,NA,1,0.0059286,logit,logit,eucalyptus,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_2anLJGpWhjUjzes,all_grass,NA,0,generalised,hurdle,3,3,3,3,0,0,0,0,retain,exclude_all,exclude,Grass cover does not influence recruitments of seedlings between 0 to 50cm nor between 50cm and 2 m.,none_c,R 3.3.3,R,3.3.3,R,3.3.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,K_perc,Th_ppm,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Arkarool R_2aPKje1xa8BzFa8,Alding-1-1-1,1,1,1,-0.17,(control+reduced)-enlarged,3663,0.01,identity,identity,blue tit,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_2aPKje1xa8BzFa8,rear_nest_trt_CR.E,2062,0,linear,standard,3,3,3,3,0,0,0,0,retain,retain,NA,The data supports that growth of nestling blue tits is influenced by competition with siblings.,neg_c,JMP Pro 15,JMP Pro,15,JMP Pro,15,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,seasonal_timing,NA,NA,Alding -R_2CEpr5R0zCk1v1Q,Allora-1-1-1,1,1,1,-0.05921,slope,277.756839,0.00652,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_2CEpr5R0zCk1v1Q,rear_Cs_at_start_of_rearing,NA,0,linear,standard,7,7,2,2,5,5,0,0,retain,retain,NA,"Increased clutch size inhibits growth in blue tits, and the most relevant estimate of clutch size is that directly after experimental manipulation",neg_c,"Rstudio Version 1.2.5001 +R_2CEpr5R0zCk1v1Q,Allora-1-1-1,1,1,1,-0.05921,slope,277.756839,0.00652,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_2CEpr5R0zCk1v1Q,rear_Cs_at_start_of_rearing,NA,0,linear,standard,7,7,2,2,5,5,0,0,retain,retain,NA,"Increased clutch size inhibits growth in blue tits, and the most relevant estimate of clutch size is that directly after experimental manipulation",neg_c,"Rstudio Version 1.2.5001 ",R,NA,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_LD,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Allora R_2D5BccM9OleEDwh,Armidale-1-1-1,1,1,1,0.020905,slope,278.98693,0.009828,NA,NA,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_2D5BccM9OleEDwh,NA,NA,0,generalised,zero_inflated,0,NA,NA,NA,NA,NA,NA,NA,exclude,retain,NA,"Results suggest that eucalypt seedling recruitment was greater in plots with higher cover of annual herbaceous species (including true grasses of the family Poaceae). However, this effect was relatively weak compared to that of annual precipitation, landscape position, mature eucalypt canopy cover and other intrinsic differences among study sites (e.g., past management history or soils).",pos_q,R version 3.6.3,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Armidale R_2EgAnNXZmEg7LoJ,Atherton-3-3-1,3,3,1,-2.893,slope,226.089686,1.367,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs>2m,R_2EgAnNXZmEg7LoJ,ExoticAnnualGrass_cover,NA,0,generalised,standard,3,3,1,1,2,2,0,0,retain,retain,NA,"Grass cover influences Eucalyptus seedling recruitment, but this effect depends both on whether grass is native or exotic and on the seedling stage. Specifically, exotic grass cover positively influences the number of seedlings in the first two seedling stages, but this effect is reversed in the latest seedling stage due to a negative influence of exotic annual grass cover. In contrast, native grass seems not to have an influence on seedling recruitment.",mixed,R 3.5.2.,R,3.5.2,R,3.5.2,NA,NA,Season,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Atherton @@ -232,14 +232,14 @@ R_2eQ3csRDLG0n4YO,Bell-3-8-1,3,8,1,NA,NA,NA,0.01409,identity,identity,blue tit,1 R_2eQ3csRDLG0n4YO,Bell-2-7-1,2,7,1,NA,NA,NA,0.008781,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2eQ3csRDLG0n4YO,NA,NA,0,linear,standard,8,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,exclude,"Body mass showed similar relationships. Body mass was lower in broods with increased size, and was negatively related to the net change in brood size. Additionally, body mass was negatively related to the brood size at day 14 when mass was measured.",neg_c,R 3.2.3,R,3.2.3,R,3.2.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,hatch_nest_LD,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,NA,NA,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,Date_of_day14,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bell R_2eQ3csRDLG0n4YO,Bell-1-6-1,1,6,1,NA,NA,NA,0.014853,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2eQ3csRDLG0n4YO,net_rearing_manipulation,3720,0,linear,standard,9,NA,5,NA,4,NA,0,NA,exclude,exclude_all,exclude,"Body mass showed similar relationships. Body mass was lower in broods with increased size, and was negatively related to the net change in brood size. Additionally, body mass was negatively related to the brood size at day 14 when mass was measured.",neg_c,R 3.2.3,R,3.2.3,R,3.2.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,hatch_nest_LD,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,net_rearing_manipulation,NA,NA,NA,Date_of_day14,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bell R_2Pjoz1X4q5XRClO,Anakie-2-1-1,2,1,1,NA,NA,NA,NA,identity,identity,blue tit,NA,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2Pjoz1X4q5XRClO,NA,NA,CHECK,CHECK,standard,0,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,NA,CHECK,NA,CHECK,CHECK,CHECK,CHECK,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Anakie -R_2Pjoz1X4q5XRClO,Aramac-1-1-1,1,1,1,-1.117943,control-enlarged,496.444018,0.1106223,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2Pjoz1X4q5XRClO,rear_nest_trt_C.E,3720,1,linear,standard,8,8,4,4,4,4,0,0,retain,retain,NA,"From my results, I would mainly conclude that increased competition with siblings by brood size increase reduces nestling growth. However, reducing sibling competition by reducing brood size does not impact the growth of nestlings: they do not have enhanced growth because of reduced competition. -Another conclusion from my results would be that nestlings reared away from their natal nest tend to have an increased growth compared to chicks reared in their natal nest. This would mean that nestlings get a competitive advantage when reared by foster parents, surrounded mostly by non-kin “siblings”. +R_2Pjoz1X4q5XRClO,Aramac-1-1-1,1,1,1,-1.117943,control-enlarged,496.444018,0.1106223,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2Pjoz1X4q5XRClO,rear_nest_trt_C.E,3720,1,linear,standard,8,8,4,4,4,4,0,0,retain,retain,NA,"From my results, I would mainly conclude that increased competition with siblings by brood size increase reduces nestling growth. However, reducing sibling competition by reducing brood size does not impact the growth of nestlings: they do not have enhanced growth because of reduced competition. +Another conclusion from my results would be that nestlings reared away from their natal nest tend to have an increased growth compared to chicks reared in their natal nest. This would mean that nestlings get a competitive advantage when reared by foster parents, surrounded mostly by non-kin “siblings”. ",neg_q,"For data preparation and analyses, the software R version 3.5.1 (2018-07-02) was used. More specifically, the software JAGS 4.3.0. was used for analyses, but the R package ‘R2jags’ version 0.5-7 was used to run JAGS through R.",R,3.5.1,"R,JAGS","3.5.1,4.3.0",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Aramac -R_2Pjoz1X4q5XRClO,Aramac-1-1-2,1,1,2,-0.02219836,reduced-control,513.041457,0.1080778,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2Pjoz1X4q5XRClO,rear_nest_trt_R.C,3720,1,linear,standard,8,8,4,4,4,4,0,0,retain,retain,NA,"From my results, I would mainly conclude that increased competition with siblings by brood size increase reduces nestling growth. However, reducing sibling competition by reducing brood size does not impact the growth of nestlings: they do not have enhanced growth because of reduced competition. -Another conclusion from my results would be that nestlings reared away from their natal nest tend to have an increased growth compared to chicks reared in their natal nest. This would mean that nestlings get a competitive advantage when reared by foster parents, surrounded mostly by non-kin “siblings”. +R_2Pjoz1X4q5XRClO,Aramac-1-1-2,1,1,2,-0.02219836,reduced-control,513.041457,0.1080778,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2Pjoz1X4q5XRClO,rear_nest_trt_R.C,3720,1,linear,standard,8,8,4,4,4,4,0,0,retain,retain,NA,"From my results, I would mainly conclude that increased competition with siblings by brood size increase reduces nestling growth. However, reducing sibling competition by reducing brood size does not impact the growth of nestlings: they do not have enhanced growth because of reduced competition. +Another conclusion from my results would be that nestlings reared away from their natal nest tend to have an increased growth compared to chicks reared in their natal nest. This would mean that nestlings get a competitive advantage when reared by foster parents, surrounded mostly by non-kin “siblings”. ",neg_q,"For data preparation and analyses, the software R version 3.5.1 (2018-07-02) was used. More specifically, the software JAGS 4.3.0. was used for analyses, but the R package ‘R2jags’ version 0.5-7 was used to run JAGS through R.",R,3.5.1,"R,JAGS","3.5.1,4.3.0",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Aramac -R_2q46Az9oG9EuskN,Balaklav-1-1-1,1,1,1,NA,NA,NA,NA,log,log,eucalyptus,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_2q46Az9oG9EuskN,NativePerennialGrass_cover,346,0,generalised,hurdle,7,7,7,7,0,0,0,0,retain,exclude_all,exclude,"Native grass cover reduces eucalyptus seedling recruitment - potentially by limiting growth and survival of seedlings rather than by preventing germination in the first place. Exotic annual grasses had a non-significant but also potentially negative effect along the same lines. Sampling did not provide a basis to make similar conclusions about exotic perennial grasses. - +R_2q46Az9oG9EuskN,Balaklav-1-1-1,1,1,1,NA,NA,NA,NA,log,log,eucalyptus,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_2q46Az9oG9EuskN,NativePerennialGrass_cover,346,0,generalised,hurdle,7,7,7,7,0,0,0,0,retain,exclude_all,exclude,"Native grass cover reduces eucalyptus seedling recruitment - potentially by limiting growth and survival of seedlings rather than by preventing germination in the first place. Exotic annual grasses had a non-significant but also potentially negative effect along the same lines. Sampling did not provide a basis to make similar conclusions about exotic perennial grasses. + This relationship is mediated by a negative feedback look: distance from existing eucalyptus canopy cover reduces litter cover, which promotes grass growth, suppressing eucalyptus recruitment.",neg_q,R 3.6.3,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,NA,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,Litter_cover,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),NA,NA,NA,annual_precipitation,NA,NA,NA,NA,K_perc,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Balaklav R_2qt4UsEXYCfKubj,Ballarat-1-1-1,1,1,1,-0.004,slope,219,0.011,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_2qt4UsEXYCfKubj,NativePerennialGrass_cover,NA,0,generalised,standard,15,15,13,13,2,2,0,0,retain,retain,NA,Exotic grass cover (both of perennial and annual grasses) had a small positive association with the number of Eucalyptus spp. plants below 50cm - using this as a proxy for Eucalyptus spp. seedling recruitment seems valid and therefore exotic grass cover has a weak positive effect on recruitment. There was no evidence that native perennial grass cover influenced Eucalyptus spp. seedling recruitment.,pos_q,Data cleaning in excel and R 3.4.4. Modelling in R 3.4.4.,"Excel,R","NA,3.4.4",R,3.4.4,NA,NA,NA,Property,Quadrat no,NA,NA,NA,Landscape position,ExoticAnnualGrass_cover,NA,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NativePerennialHerb_cover,NA,NA,NA,NA,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),NA,NA,NA,NA,NA,NA,NA,NA,K_perc,Th_ppm,U_ppm,NA,NA,NA,NA,NA,NA,NA,NA,NA,bare,NA,NA,NA,NA,NA,NA,NA,NA,precip_max_range,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Ballarat R_2RWagSaG4jPYGlh,Balmoral-1-1-1,1,1,1,-0.03336,slope,303.4907,0.03211,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),"Sum of ""euc_sdlgs0_50cm"", ""euc_sdlgs50cm.2m"", and ""euc_sdlgs.2m""",euc_sdlgs_all,R_2RWagSaG4jPYGlh,ExoticPerennialGrass_cover,350,0,generalised,standard,5,5,3,3,2,2,0,0,retain,retain,NA,Grass cover does not appear to influence Eucalyptus seedling recruitment.,none_c,R 3.6.0 - all analyses.,R,3.6.0,R,3.6.0,NA,NA,Season,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Balmoral @@ -253,27 +253,27 @@ R_2TFNREdJSxTXZBQ,Avenel-1-2-1,1,2,1,-0.033987,slope,401.35281,0.008781,identity R_2TFNREdJSxTXZBQ,Avenel-2-1-1,2,1,1,-1000.98,control-enlarged,376.1959,224.28,identity,identity,blue tit,1,power3.675,back.transformed,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_2TFNREdJSxTXZBQ,rear_nest_trt_C.E,NA,0,linear,standard,5,5,2,2,3,3,0,0,retain,retain,NA,"From our analyses, we found that the competition between siblings does affect the growth of the nestlings. It is evident in our linear mixed-effects model where both the weight and tarsus length is affected by the total number of chicks present in the nest. It is especially true when extra chicks were added to a nest as a part of experimental manipulation, however, removal of chicks did not show a significant effect. The results from random variable effects also suggest that area where the nest is located can also affect the growth of the chicks, probably due to proximity to resources (as compared to some other area) which makes foraging easier for the parents. These findings can help us understand sibling competition for resources in nestling blue tits (Cyanistes caeruleus) which can further be replicated in other species as well.",neg_q,R version 3.6.3,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_Area,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Avenel R_2TFNREdJSxTXZBQ,Avenel-2-1-2,2,1,2,-122.75,reduced-control,401.3696,200.42,identity,identity,blue tit,1,power3.675,back.transformed,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_2TFNREdJSxTXZBQ,rear_nest_trt_R.C,NA,0,linear,standard,5,5,2,2,3,3,0,0,retain,retain,NA,"From our analyses, we found that the competition between siblings does affect the growth of the nestlings. It is evident in our linear mixed-effects model where both the weight and tarsus length is affected by the total number of chicks present in the nest. It is especially true when extra chicks were added to a nest as a part of experimental manipulation, however, removal of chicks did not show a significant effect. The results from random variable effects also suggest that area where the nest is located can also affect the growth of the chicks, probably due to proximity to resources (as compared to some other area) which makes foraging easier for the parents. These findings can help us understand sibling competition for resources in nestling blue tits (Cyanistes caeruleus) which can further be replicated in other species as well.",neg_q,R version 3.6.3,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_Area,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Avenel R_2THmmIkaHjHzDVz,Bamaga-1-1-1,1,1,1,-0.3188,control-enlarged,500.6,0.0569,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_2THmmIkaHjHzDVz,rear_nest_trt_C.E,3538,1,generalised,standard,14,14,5,5,9,9,0,0,retain,retain,NA," -Here, I assume that brood size reflects the amount of within-nest competition. -When the brood size, and thus competition, increase ~25% (see methods), tarsus length is reduced by 0.319 units (-0.319 (-0.431; -0.208)) in the average sized brood. Moreover, when brood size is decreased by ~25%, the tarsus size increased, but only marginally so, by 0.090 units (estimate (95% CI): 0.090 (-0.017; 0.197)) in the average size brood. Thus, the general conclusion is that increasing competition has negative effects on the growth of a blue tit nestlings. +Here, I assume that brood size reflects the amount of within-nest competition. +When the brood size, and thus competition, increase ~25% (see methods), tarsus length is reduced by 0.319 units (-0.319 (-0.431; -0.208)) in the average sized brood. Moreover, when brood size is decreased by ~25%, the tarsus size increased, but only marginally so, by 0.090 units (estimate (95% CI): 0.090 (-0.017; 0.197)) in the average size brood. Thus, the general conclusion is that increasing competition has negative effects on the growth of a blue tit nestlings. ",neg_q,Data cleaning and model estimation – R3.6.0. (R-packet “brms” for statistical model).,R,3.6.0,R,3.6.0,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,hatch_Area,hatch_Box,hatch_mom_Ring,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,rear_Box,rear_mom_Ring,NA,rear_nest_trt,home_or_away,NA,NA,NA,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,Date_of_day14,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bamaga R_2tLsM42vnTf9wX6,Bangalow-1-1-1,1,1,1,0.001644,slope,53.56599,0.008132,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_2tLsM42vnTf9wX6,all_grass,NA,0,generalised,standard,7,7,4,4,3,3,NA,0,retain,retain,NA,"Generally, grass cover did not significantly influence the Eucalyptus spp. seedling recruitment",none_q,R version 3.5.2,R,3.5.2,R,3.5.2,NA,NA,Season,Property,Quadrat no,NA,NA,NA,Landscape position,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,annual_precipitation,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bangalow R_2tLsM42vnTf9wX6,Bangalow-2-2-1,2,2,1,0.0075,slope,64.00647,0.010482,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_2tLsM42vnTf9wX6,NativePerennialGrass_cover,NA,0,generalised,standard,9,9,6,6,3,3,NA,0,retain,retain,NA,"Generally, grass cover did not significantly influence the Eucalyptus spp. seedling recruitment",none_q,R version 3.5.2,R,3.5.2,R,3.5.2,NA,NA,Season,Property,Quadrat no,NA,NA,NA,Landscape position,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,annual_precipitation,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bangalow R_2tLsM42vnTf9wX6,Bangalow-3-3-1,3,3,1,0.003866,slope,338.94777,0.005815,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_2tLsM42vnTf9wX6,all_grass,NA,0,generalised,standard,7,7,4,4,3,3,NA,0,retain,retain,NA,"Generally, grass cover did not significantly influence the Eucalyptus spp. seedling recruitment",none_q,R version 3.5.2,R,3.5.2,R,3.5.2,NA,NA,Season,Property,Quadrat no,NA,NA,NA,Landscape position,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,annual_precipitation,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bangalow R_2tLsM42vnTf9wX6,Bangalow-4-4-1,4,4,1,-0.003407,slope,42.13188,0.292787,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_2tLsM42vnTf9wX6,NA,NA,0,generalised,standard,10,NA,NA,NA,NA,NA,NA,NA,exclude,retain,NA,"Generally, grass cover did not significantly influence the Eucalyptus spp. seedling recruitment, with the exception that native perennial grass cover did significantly effect the number of seedlings between 50cm and 2 metres.",none_q,R version 3.5.2,R,3.5.2,R,3.5.2,NA,NA,Season,Property,Quadrat no,NA,NA,NA,Landscape position,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,euc_sdlgs50cm-2m,NA,annual_precipitation,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bangalow R_2Tzp6JznvkvCY4h,Barham-1-1-1,1,1,1,-0.086031415,slope,1169.823066,0.05578043,identity,identity,blue tit,1,z.score,z.score,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_tarsus_length,R_2Tzp6JznvkvCY4h,net_rearing_manipulation,1181,0,linear,standard,10,14,7,11,3,3,2,2,retain,retain,exclude,"Similarly, more rear_Cs_at_start_of_rearing was linked shorter tarsus lengths and lower weights. More siblings, and presumably additional competition, was on balance worse for nestling growth",neg_q,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,hatch_nest_LD,NA,NA,NA,NA,NA,rear_area,NA,NA,NA,NA,NA,rear_nest_LD,NA,NA,NA,NA,NA,net_rearing_manipulation,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,Date_of_day14,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Barham -R_2Tzp6JznvkvCY4h,Barham-2-2-1,2,2,1,-0.24251547,slope,1167.67507,0.04785429,identity,identity,blue tit,1,z.score,z.score,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_2Tzp6JznvkvCY4h,net_rearing_manipulation,1178,0,linear,standard,9,12,6,9,3,3,2,1,retain,retain,exclude,"Both net_rearing_manipulation and rear_Cs_at_start_of_rearing were associated with the outcome variables, though net_rearing_manipulation was not significantly associated with tarsus length in my final model. Net_rearing_manipulation was still associated with weight, so an increase in the number of chicks in the nest was linked to lower weights. Similarly, more rear_Cs_at_start_of_rearing was linked shorter tarsus lengths and lower weights. More siblings, and presumably additional competition, was on balance worse for nestling growth. - +R_2Tzp6JznvkvCY4h,Barham-2-2-1,2,2,1,-0.24251547,slope,1167.67507,0.04785429,identity,identity,blue tit,1,z.score,z.score,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_2Tzp6JznvkvCY4h,net_rearing_manipulation,1178,0,linear,standard,9,12,6,9,3,3,2,1,retain,retain,exclude,"Both net_rearing_manipulation and rear_Cs_at_start_of_rearing were associated with the outcome variables, though net_rearing_manipulation was not significantly associated with tarsus length in my final model. Net_rearing_manipulation was still associated with weight, so an increase in the number of chicks in the nest was linked to lower weights. Similarly, more rear_Cs_at_start_of_rearing was linked shorter tarsus lengths and lower weights. More siblings, and presumably additional competition, was on balance worse for nestling growth. + I was especially interested in the interactions I might find between net_rearing_manipulation or rear_Cs_at_start_of_rearing and other variables, but for the most part, I could not confirm any such relationships. The exception was the interaction between net_rearing_manipulation and the square of hatch_nest_LD. This suggests that chicks in nests manipulated to have more chicks had greater growth when the lay date of the nest that chick was born in was later in the month.",neg_q,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,hatch_nest_LD,NA,NA,NA,NA,NA,rear_area,NA,NA,NA,NA,NA,rear_nest_LD,NA,NA,NA,NA,NA,net_rearing_manipulation,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Barham R_2Uf2SxOynEElDZN,Barellan-1-1-1,1,1,1,-0.0136,slope,323.5,0.0171,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_2Uf2SxOynEElDZN,NA,346,0,NA,standard,33,NA,NA,NA,NA,NA,0,NA,exclude,retain,NA,"I did not detect an effect of grass cover or any type of plant cover on seedling recruitment, and this conclusion was robust to different groupings of the non-woody plant cover.",none_c,R 4.0,R,4.0.0,R,4.0.0,SurveyID,NA,Season,Property,NA,NA,NA,Aspect,NA,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NativeShrub_cover,BareGround_cover,Litter_cover,MossLichen_cover,Rock_cover,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,annual_precipitation,precipitation_warmest_quarter,precipitation_coldest_quarter,PET,MrVBF,K_perc,Th_ppm,U_ppm,SRad_Jan,SRad_Jul,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Barellan R_2Uh2qaU1UayMOvG,Barmah-1-1-1,1,1,1,-0.157605394,slope,1300.984954,0.011345939,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2Uh2qaU1UayMOvG,net_rearing_manipulation,3263,0,linear,standard,6,6,5,5,1,1,0,0,retain,retain,exclude,"Results indicate that competition with siblings has a significant effect on the growth (average and variation) and survivorship of nestling blue tits. These effects were still significant after accounting for potential confounding variables related to environmental conditions and experimental manipulation. However, it should be highlighted that the relationship among the variables is usually weak, especially for growth variance and survivorship.",neg_q,R and Jupyter Notebook,R,NA,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_CS,NA,NA,NA,NA,rear_area,rear_Box,NA,NA,NA,home_or_away,rear_nest_LD,NA,NA,NA,NA,NA,net_rearing_manipulation,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Barmah R_2uIDO25lv0nHjfH,Barmer-1-1-1,1,1,1,-0.186,slope,114.9,0.019,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_2uIDO25lv0nHjfH,net_rearing_manipulation,1854,0,linear,standard,10,16,6,6,4,10,0,6,retain,retain,NA,"All in all, our results suggest that natural blue tit brood sizes are adjusted to resource availability, as fledging rate does not strongly depend on brood size and is not increased by the net removal of chicks. However, we found evidence that brood sizes are too large to guarantee an optimal growth rate for all chicks and that chicks from smaller broods tend to grow faster. These observations clearly demonstrate a trade-off between the numerosity of offspring and its average quality.",neg_q,R v. 3.4.4,R,3.4.4,R,3.4.4,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,NA,home_or_away,NA,NA,rear_nest_OH,rear_d0_rear_nest_brood_size,NA,NA,net_rearing_manipulation,NA,NA,NA,NA,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Barmer -R_2V7qaLEfdbgUGg3,Batchelo-1-1-1,1,1,1,NA,NA,3.50E-25,0.007385,log,log,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"euc_sdlgs.2m, euc_sdlgs0_50cm, euc_sdlgs50cm.2m",euc_sdlgs_all,R_2V7qaLEfdbgUGg3,all_grass,NA,0,linear,standard,1,1,1,1,0,0,0,0,retain,exclude_all,NA,Though visually there appears to be an overall decrease in number of seedlings with percent grass cover I did not find it to statistically significant. I did find that there seem to be few mid sized seedlings in areas with more grass cover.,none_q,"R 3.6.1 GUI 1.70 El Capitan build +R_2V7qaLEfdbgUGg3,Batchelo-1-1-1,1,1,1,NA,NA,3.50E-25,0.007385,log,log,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"euc_sdlgs.2m, euc_sdlgs0_50cm, euc_sdlgs50cm.2m",euc_sdlgs_all,R_2V7qaLEfdbgUGg3,all_grass,NA,0,linear,standard,1,1,1,1,0,0,0,0,retain,exclude_all,NA,Though visually there appears to be an overall decrease in number of seedlings with percent grass cover I did not find it to statistically significant. I did find that there seem to be few mid sized seedlings in areas with more grass cover.,none_q,"R 3.6.1 GUI 1.70 El Capitan build (7684)",R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Batchelo -R_2V7qaLEfdbgUGg3,Batchelo-2-2-1,2,2,1,NA,NA,3.50E-25,0.052462,NA,NA,eucalyptus,0,NA,NA,original variable (transformed prior to analysis [not with a link function in analysis]),NA,NA,R_2V7qaLEfdbgUGg3,NA,NA,0,linear,standard,6,NA,6,NA,0,NA,NA,NA,exclude,exclude_all,NA,Though visually there appears to be an overall decrease in number of seedlings with percent grass cover I did not find it to statistically significant. I did find that there seem to be few mid sized seedlings in areas with more grass cover.,none_q,"R 3.6.1 GUI 1.70 El Capitan build +R_2V7qaLEfdbgUGg3,Batchelo-2-2-1,2,2,1,NA,NA,3.50E-25,0.052462,NA,NA,eucalyptus,0,NA,NA,original variable (transformed prior to analysis [not with a link function in analysis]),NA,NA,R_2V7qaLEfdbgUGg3,NA,NA,0,linear,standard,6,NA,6,NA,0,NA,NA,NA,exclude,exclude_all,NA,Though visually there appears to be an overall decrease in number of seedlings with percent grass cover I did not find it to statistically significant. I did find that there seem to be few mid sized seedlings in areas with more grass cover.,none_q,"R 3.6.1 GUI 1.70 El Capitan build (7684)",R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Batchelo R_2vYtB65EABDGMNB,Batlow-1-1-1,1,1,1,-0.83,control-enlarged,278.27,0.57,identity,identity,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),body mass (“day_14_weight”) and tarsus length (“day_14_tarsus_length”),PC1.day_14_weight.day_14_tarsus_length,R_2vYtB65EABDGMNB,rear_nest_trt_C.E,2385,0,linear,standard,8,10,6,8,2,2,2,0,retain,retain,exclude,"Nestlings from larger broods were smaller when measured at 14 d, relative to nestlings from smaller broods. However, the effect of brood size on nestling size was very weak among unmanipulated control broods",neg_q,R. 3.6.3,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Batlow R_2vYtB65EABDGMNB,Batlow-1-1-2,1,1,2,-0.47,reduced-enlarged,272.69,0.52,identity,identity,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),body mass (“day_14_weight”) and tarsus length (“day_14_tarsus_length”),PC1.day_14_weight.day_14_tarsus_length,R_2vYtB65EABDGMNB,rear_nest_trt_R.E,2385,0,linear,standard,8,10,6,8,2,2,2,0,retain,retain,exclude,"Nestlings from larger broods were smaller when measured at 14 d, relative to nestlings from smaller broods. However, the effect of brood size on nestling size was very weak among unmanipulated control broods",neg_q,R. 3.6.3,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Batlow -R_2vYtB65EABDGMNB,Batlow-1-1-3,1,1,3,-1.2,slope,233,1,identity,identity,blue tit,1,NA,NA,original variable (transformed prior to analysis [not with a link function in analysis]),NA,PC1.day_14_weight.day_14_tarsus_length,R_2vYtB65EABDGMNB,rear_Cs_at_start_of_rearing,2385,0,linear,standard,8,10,6,8,2,2,2,0,retain,retain,exclude,"We conclude that sibling competition influences nestling growth because nestlings from experimentally increased broods were smaller relative to experimentally decreased broods. Further, there was a negative relationship between nestling size and brood size among nestlings from manipulated broods. However, there was little evidence of this pattern within the unmanipulated control broods, likely because parents optimize clutch size based on individual state and annual environmental conditions. Finally, the strength of the effect of sibling competition on nestling growth varied across the study years. +R_2vYtB65EABDGMNB,Batlow-1-1-3,1,1,3,-1.2,slope,233,1,identity,identity,blue tit,1,NA,NA,original variable (transformed prior to analysis [not with a link function in analysis]),NA,PC1.day_14_weight.day_14_tarsus_length,R_2vYtB65EABDGMNB,rear_Cs_at_start_of_rearing,2385,0,linear,standard,8,10,6,8,2,2,2,0,retain,retain,exclude,"We conclude that sibling competition influences nestling growth because nestlings from experimentally increased broods were smaller relative to experimentally decreased broods. Further, there was a negative relationship between nestling size and brood size among nestlings from manipulated broods. However, there was little evidence of this pattern within the unmanipulated control broods, likely because parents optimize clutch size based on individual state and annual environmental conditions. Finally, the strength of the effect of sibling competition on nestling growth varied across the study years. ",neg_c,We did all the data cleaning and analysis in R Studio 1.2.5033 and R. 3.6.3 (R Core Team 2020).,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Batlow R_2wFd1Uodrx19dK3,Baxter-2-2-1,2,2,1,NA,NA,NA,NA,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_2wFd1Uodrx19dK3,NA,NA,1,linear,standard,16,17,4,5,12,12,1,0,retain,exclude_all,NA,The competition with sibling is an important determinant of growth.,neg_c,R 3.5.3,R,3.5.3,R,3.5.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,hatch_Area,hatch_Box,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,rear_Box,rear_mom_Ring,rear_dad_Ring,rear_nest_trt,NA,rear_nest_LD,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Baxter R_2wFd1Uodrx19dK3,Baxter-1-1-1,1,1,1,NA,NA,NA,NA,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2wFd1Uodrx19dK3,NA,NA,1,linear,standard,16,17,4,5,12,12,1,0,retain,exclude_all,NA,The competition with sibling is an important determinant of growth.,neg_c,R 3.5.3,R,3.5.3,R,3.5.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,hatch_Area,hatch_Box,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,rear_Box,rear_mom_Ring,rear_dad_Ring,rear_nest_trt,NA,rear_nest_LD,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Baxter @@ -282,13 +282,13 @@ R_2Wwn0cMK5hFC4vB,Beltan-1-1-1,1,1,1,-153.621,slope,344.62,14.96,identity,identi R_2xPmP71Af1t1YR5,Bethan-1-1-1,1,1,1,NA,NA,NA,NA,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2xPmP71Af1t1YR5,net_rearing_manipulation,3267,1,generalised,standard,17,18,7,8,10,10,1,0,retain,exclude_all,NA,"The growth of nestling blue tits is directly impaired by competition with siblings, by about 0.22 grams per additional sibling. The lack of a negative association with the number of fledged birds from the rearing nest suggests that this may be less related to the absolute number of siblings, but rather the extent to which the number of siblings exceeds the number which the provisioning adults are capable of rearing.",neg_q,"Data cleaning - R 3.6.0, model estimation - rstan 2.19.3",R,3.6.0,"R,Stan","3.6.0,NA",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,hatch_Area,hatch_Box,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,d0_hatch_nest_brood_size,NA,rear_nest_breed_ID,rear_area,rear_Box,rear_mom_Ring,rear_dad_Ring,NA,home_or_away,NA,NA,NA,NA,NA,NA,net_rearing_manipulation,NA,NA,number_chicks_fledged_from_rear_nest,Date_of_day14,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bethan R_2y3muAnh5ZdPNsd,Beulah-1-1-1,1,1,1,-0.24464,control-enlarged,391.56154,0.06377,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_2y3muAnh5ZdPNsd,rear_nest_trt_C.E,2789,0,linear,standard,5,5,2,2,3,3,0,0,retain,retain,NA,THP paraphrase: competition reduced chick growth regardless of how competition is defined,neg_c,NA,R,4.0.0,R,4.0.0,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,rear_Box,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Beulah R_2YDnnczYjl21ufr,Bilpin-1-1-1,1,1,1,-0.18247,slope,198.335,0.01605,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_2YDnnczYjl21ufr,net_rearing_manipulation,NA,0,linear,standard,6,6,4,4,2,2,0,0,retain,retain,NA,Competition has a negative effect on growth.,neg_c,R 3.63,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,net_rearing_manipulation,NA,NA,NA,NA,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bilpin -R_2YQeDDkUPqS56ew,Bathurst-1-1-1,1,1,1,-0.01025,slope,329.86647,0.01226211,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),"The constructed variable 'euc_stem' was created by summing the different counts for eucalyptus stems: 'euc_sdlgs0_50cm', 'euc_sdlgs50cm-2m', 'euc_sdlgs>2m'. This should be the same as 'total_seedlings (temp)' in the new data set provided.",euc_sdlgs_all,R_2YQeDDkUPqS56ew,all_grass,345,0,generalised,standard,10,10,8,8,2,2,0,0,retain,retain,NA,From this analysis I would have to say that grass cover has no influence on Eucalyptus seedling recruitment.,none_c,"viewing data -Microsoft Excel, R 3.6.2 -data cleaning - R 3.6.2 -data exploration - R 3.6.2 -data storage -Microsoft Excel, R 3.6.2 -model fitting -R 3.6.2 -model selection -R 3.6.2 -analyses -R 3.6.2 +R_2YQeDDkUPqS56ew,Bathurst-1-1-1,1,1,1,-0.01025,slope,329.86647,0.01226211,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),"The constructed variable 'euc_stem' was created by summing the different counts for eucalyptus stems: 'euc_sdlgs0_50cm', 'euc_sdlgs50cm-2m', 'euc_sdlgs>2m'. This should be the same as 'total_seedlings (temp)' in the new data set provided.",euc_sdlgs_all,R_2YQeDDkUPqS56ew,all_grass,345,0,generalised,standard,10,10,8,8,2,2,0,0,retain,retain,NA,From this analysis I would have to say that grass cover has no influence on Eucalyptus seedling recruitment.,none_c,"viewing data -Microsoft Excel, R 3.6.2 +data cleaning - R 3.6.2 +data exploration - R 3.6.2 +data storage -Microsoft Excel, R 3.6.2 +model fitting -R 3.6.2 +model selection -R 3.6.2 +analyses -R 3.6.2 data summary -R 3.6.2","Excel,R","NA,3.6.2",R,3.6.2,NA,NA,Season,Property,Quadrat no,NA,NA,NA,Landscape position,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Litter_cover,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,NA,NA,NA,PET,NA,K_perc,NA,NA,NA,NA,all_grass,NA,NA,all_non-grass_veg,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bathurst R_2yr82cdDjPysYtS,Bindoo-1-1-1,1,1,1,NA,NA,NA,7.69E-04,identity,identity,blue tit,0,NA,NA,constructed variable (combining information from two or more original variables),"GL, was calculated as the difference between its day 14 tarsus length and the average day 14 tarsus length for all members of its hatch nest. GL = xday_14_tarsus_length - x Ì…day_14_tarsus_length | hatch_nest_breed_ID",day_14_tarsus_length_deviation,R_2yr82cdDjPysYtS,competition_weight,3720,0,linear,standard,1,1,1,1,0,0,0,0,retain,exclude_all,NA,"All definitions of sibling competition had a statistically significant, negative impact on all definitions of growth, while controlling for expected growth on the basis of the average of the hatch nest. However, the effect sizes were small, and only two measures of growth (weight and BMI) had enough variance explained by the tarsus length measure of sibling competition to be considered of practical interest. Thus, overall sibling competition has a modest negative impact on growth.",neg_q,SPSS version 25,SPSS,25,SPSS,25,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,competition_weight,NA,NA,NA,NA,NA,NA,NA,NA,Bindoo R_2zj7U8UJE7GgEYS,Beachpor-1-1-1,1,1,1,0.00892267,slope,112,0.0072222,identity,identity,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_2zj7U8UJE7GgEYS,ExoticAnnualGrass_cover,348,0,linear,standard,7,7,4,4,3,3,0,0,retain,exclude_partial,NA,Grass cover did not have an influence on Eucalyptus spp. seedling recruitment.,none_c,R 4.0.0,R,4.0.0,R,4.0.0,NA,NA,Season,NA,NA,Easting,Northing,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,Euc_canopy_cover,NA,NA,euc_sdlgs50cm-2m,NA,NA,NA,NA,NA,MrVBF,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Beachpor @@ -315,80 +315,80 @@ R_31tNDcbaXNaQp1y,Bermagui-1-2-1,1,2,1,NA,NA,NA,0.529,log,log,eucalyptus,0,NA,NA R_31tNDcbaXNaQp1y,Bermagui-1-2-2,1,2,2,NA,NA,NA,2.89,log,log,eucalyptus,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_31tNDcbaXNaQp1y,ExoticPerennialGrass_cover,NA,0,generalised,standard,7,33,5,31,2,2,26,0,retain,exclude_all,NA,"Therefore, we find that while the coverage of exotic annual grass and perennial grass coverage negatively impacts the initial development of the eucalyptus seedlings, it does not affect larger size classes. We found no evidence for exotic perennial grass coverage significantly impacting recruitment of eucalypt seedling.",mixed,All analyses conducted in R version 3.63,R,3.6.3,R,3.6.3,NA,NA,Season,NA,NA,NA,NA,NA,NA,NA,NA,NA,ExoticPerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,annual_precipitation,NA,NA,NA,MrVBF,K_perc,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,sample,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bermagui R_31tNDcbaXNaQp1y,Bermagui-1-2-3,1,2,3,NA,NA,NA,0.605,log,log,eucalyptus,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_31tNDcbaXNaQp1y,NativePerennialGrass_cover,NA,0,generalised,standard,7,33,5,31,2,2,26,0,retain,exclude_all,NA,"Therefore, we find that while the coverage of exotic annual grass and perennial grass coverage negatively impacts the initial development of the eucalyptus seedlings, it does not affect larger size classes. We found no evidence for exotic perennial grass coverage significantly impacting recruitment of eucalypt seedling.",mixed,All analyses conducted in R version 3.63,R,3.6.3,R,3.6.3,NA,NA,Season,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,annual_precipitation,NA,NA,NA,MrVBF,K_perc,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,sample,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bermagui R_3D10yCylth7wFPg,Berrigan-1-1-1,1,1,1,-0.053928,slope,346,0.009584,log,log,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"additive combinations of euc_sdlgs0_50cm, euc_sdlgs50cm.2m, euc_sdlgs.2m",euc_sdlgs_all,R_3D10yCylth7wFPg,ExoticPerennialGrass_cover,350,0,generalised,standard,1,NA,1,NA,0,NA,0,NA,exclude,retain,NA,There are fewer Eucalyptus seedlings with higher grass cover.,neg_c,R 3.6.3,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Berrigan -R_3dWjjdkDbTRCUqs,Bourke-1-1-1,1,1,1,-0.52386,slope,244.43311,0.04904,log,log,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),day_14_tarsus_length and day_14_weight,SMI,R_3dWjjdkDbTRCUqs,rear_Cs_at_start_of_rearing,NA,0,linear,standard,6,6,1,1,5,5,0,0,retain,retain,NA,"To what extent is the growth of nestling blue tits (Cyanistes caeruleus) influenced by competition with siblings? - -The cross-foster experiment showed that brood size and treatment level significantly affected nestling growth at 14 days (Table 1). Our analysis suggests that nestlings’ growth decreased with increasing number of siblings (Table 2, beta= -0.057). - - +R_3dWjjdkDbTRCUqs,Bourke-1-1-1,1,1,1,-0.52386,slope,244.43311,0.04904,log,log,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),day_14_tarsus_length and day_14_weight,SMI,R_3dWjjdkDbTRCUqs,rear_Cs_at_start_of_rearing,NA,0,linear,standard,6,6,1,1,5,5,0,0,retain,retain,NA,"To what extent is the growth of nestling blue tits (Cyanistes caeruleus) influenced by competition with siblings? + +The cross-foster experiment showed that brood size and treatment level significantly affected nestling growth at 14 days (Table 1). Our analysis suggests that nestlings’ growth decreased with increasing number of siblings (Table 2, beta= -0.057). + + ",neg_c,R 3.5,R,3.5,R,3.5,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_CS,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,NA,home_or_away,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bourke R_3dYDpQUfDUXjtDy,Binalong-2-2-1,2,2,1,NA,NA,NA,NA,NA,NA,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),see above (sum),NA,R_3dYDpQUfDUXjtDy,NA,NA,0,generalised,PCA,24,NA,24,NA,0,NA,NA,NA,exclude,exclude_all,exclude,"Grass cover limits eucalyptus recruitment. however, environmental conditions, origin and life cycle of the grass affect this relationship.",neg_q,R 4.0.0,R,4.0.0,R,4.0.0,NA,NA,Season,NA,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NativeShrub_cover,NA,NA,MossLichen_cover,NA,NA,NA,euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,annual_precipitation,precipitation_warmest_quarter,precipitation_coldest_quarter,PET,NA,K_perc,Th_ppm,U_ppm,SRad_Jan,SRad_Jul,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Binalong R_3dYDpQUfDUXjtDy,Binalong-1-1-1,1,1,1,NA,NA,NA,NA,NA,NA,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"tab$euca_PA<-ifelse(rowSums(tab[,26:28])==0,0,1)# Row sums of the 3 seedling level:Presence/abscence",NA,R_3dYDpQUfDUXjtDy,NA,NA,0,generalised,PCA,24,NA,24,NA,0,NA,NA,NA,exclude,exclude_all,exclude,"Grass cover limits eucalyptus recruitment. however, environmental conditions, origin and life cycle of the grass affect this relationship.",neg_q,R 4.0.0,R,4.0.0,R,4.0.0,NA,NA,Season,NA,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NativeShrub_cover,NA,NA,MossLichen_cover,NA,NA,NA,euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,annual_precipitation,precipitation_warmest_quarter,precipitation_coldest_quarter,PET,NA,K_perc,Th_ppm,U_ppm,SRad_Jan,SRad_Jul,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Binalong -R_3E20pSupmdXAXDz,Bowral-2-2-1,2,2,1,-0.171161,slope,212.1669,0.016699,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_3E20pSupmdXAXDz,net_rearing_manipulation,3315,0,linear,standard,9,10,6,7,3,3,1,0,retain,retain,NA,"We conclude that the evidence is mixed regarding whether competition with siblings affects growth. On one hand, when analyzing control nests (which have naturally occurring variation in brood size), we find no evidence that chicks that tend to be smaller in larger broods. - -In all nests analyses, we find in one set of analyses that the effect of adding chicks depends on the original brood size--there is a larger effect in nests that were bigger to begin with, and close to no effect when original brood size is small. Chick substraction appears to have little effect in these analyses. - -On the other hand, in our other set of all nests analyses we see some positive evidence for an effect of siblings, as there were significant negative main effects for both brood size and net manipulation, suggesting that extra chicks lead to smaller average sizes in the nest. - +R_3E20pSupmdXAXDz,Bowral-2-2-1,2,2,1,-0.171161,slope,212.1669,0.016699,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_3E20pSupmdXAXDz,net_rearing_manipulation,3315,0,linear,standard,9,10,6,7,3,3,1,0,retain,retain,NA,"We conclude that the evidence is mixed regarding whether competition with siblings affects growth. On one hand, when analyzing control nests (which have naturally occurring variation in brood size), we find no evidence that chicks that tend to be smaller in larger broods. + +In all nests analyses, we find in one set of analyses that the effect of adding chicks depends on the original brood size--there is a larger effect in nests that were bigger to begin with, and close to no effect when original brood size is small. Chick substraction appears to have little effect in these analyses. + +On the other hand, in our other set of all nests analyses we see some positive evidence for an effect of siblings, as there were significant negative main effects for both brood size and net manipulation, suggesting that extra chicks lead to smaller average sizes in the nest. + One possible interpretation of these results is that chicks suffer when they grow up in broods that are larger than what the mothers intended to have, perhaps particularly so when those broods were large to begin with. However, within the normal range of brood sizes (i.e. in control nests), parents are able to adjust care levels such that outcomes for chicks are similar across different levels of sibling competition.",mixed,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,NA,home_or_away,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,net_rearing_manipulation,NA,NA,NA,Date_of_day14,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bowral -R_3E20pSupmdXAXDz,Bowral-1-1-1,1,1,1,-0.49643,slope,307.617196,0.038094,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_3E20pSupmdXAXDz,net_rearing_manipulation,3315,0,linear,standard,9,10,6,7,3,3,1,0,retain,retain,NA,"We conclude that the evidence is mixed regarding whether competition with siblings affects growth. On one hand, when analyzing control nests (which have naturally occurring variation in brood size), we find no evidence that chicks that tend to be smaller in larger broods. - -In all nests analyses, we find in one set of analyses that the effect of adding chicks depends on the original brood size--there is a larger effect in nests that were bigger to begin with, and close to no effect when original brood size is small. Chick substraction appears to have little effect in these analyses. - -On the other hand, in our other set of all nests analyses we see some positive evidence for an effect of siblings, as there were significant negative main effects for both brood size and net manipulation, suggesting that extra chicks lead to smaller average sizes in the nest. - +R_3E20pSupmdXAXDz,Bowral-1-1-1,1,1,1,-0.49643,slope,307.617196,0.038094,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_3E20pSupmdXAXDz,net_rearing_manipulation,3315,0,linear,standard,9,10,6,7,3,3,1,0,retain,retain,NA,"We conclude that the evidence is mixed regarding whether competition with siblings affects growth. On one hand, when analyzing control nests (which have naturally occurring variation in brood size), we find no evidence that chicks that tend to be smaller in larger broods. + +In all nests analyses, we find in one set of analyses that the effect of adding chicks depends on the original brood size--there is a larger effect in nests that were bigger to begin with, and close to no effect when original brood size is small. Chick substraction appears to have little effect in these analyses. + +On the other hand, in our other set of all nests analyses we see some positive evidence for an effect of siblings, as there were significant negative main effects for both brood size and net manipulation, suggesting that extra chicks lead to smaller average sizes in the nest. + One possible interpretation of these results is that chicks suffer when they grow up in broods that are larger than what the mothers intended to have, perhaps particularly so when those broods were large to begin with. However, within the normal range of brood sizes (i.e. in control nests), parents are able to adjust care levels such that outcomes for chicks are similar across different levels of sibling competition.",mixed,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,NA,home_or_away,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,net_rearing_manipulation,NA,NA,NA,Date_of_day14,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bowral R_3EbbZxcQ3gctVZu,Binnaway-1-1-1,1,1,1,NA,NA,-2.6269353,0.01312667,logit,logit,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),"wd$zero<-as.logical(wd$total_seeds, wd$total_seeds!=0) - analysis was a hurdle model since there were no seedlings in the new_ecu_data only predictions for the first model were generated",NA,R_3EbbZxcQ3gctVZu,NA,NA,0,CHECK,hurdle,0,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,The odds of seedlings being present in a plot decreases as exotic perennial grass cover increases but is unaffected by annual grass or native grass cover. Herb cover and soil chemistry both have a much greater effect on seedling presence and count than grass cover.,neg_q,R version 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Binnaway R_3EchM6GxZboGwz4,Bright-1-1-1,1,1,1,-0.01699,slope,2384.80707,6.60E-04,identity,identity,blue tit,1,log,log,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_3EchM6GxZboGwz4,rear_Cs_at_start_of_rearing,2564,0,linear,standard,5,5,1,1,4,4,0,0,retain,retain,NA,"Mean nestling mass (as an index of ""growth"") appears to be negatively influenced by number of siblings after accounting for genetics, and spatial and temporal autocorrelation. However, parental genetic effects may be far more important in influencing growth than brood size alone.",neg_q,R version 3.5.1,R,3.5.1,R,3.5.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,NA,NA,NA,rear_area,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,Date_of_day14,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bright R_3eemYAT4onCCt0N,Buchan-1-1-1,1,1,1,-0.002337,slope,391,0.00103,identity,identity,blue tit,1,divided.by.14,divided.by.14,constructed variable (combining information from two or more original variables),"I took day_14_weight and adjusted for body size using a LMM including day_14_tarsus_length as a fixed effect and day14_measurer as a random intercept. I then took the residuals of this model and divided by 14 to give a daily chick growth rate. This was then used as my response. {newline} lmer(day_14_weight ~ day_14_tarsus_length + (1|day14_measurer), data = titdata) {newline} titdata$day_14_weight_SA <- as.vector(resid(model.mass)) #SA = size adjusted {newline} titdata$chick_growth_rate <- titdata$day_14_weight_SA / 14",residual_day14_weight,R_3eemYAT4onCCt0N,rear_Cs_at_start_of_rearing,3328,0,linear,standard,7,7,5,5,2,2,0,0,retain,retain,NA,"The growth of nestlings blue tits generally decreases with increased competition with siblings as shown by the overall relationship between chick growth rate and rear nest brood size (Fig. 1B). Experimental manipulations of nests showed that relative increased in nestling competition results in decreased chick growth rates compared to all other nests (i.e. control and decreased treatments; Fig. 1A). The lack of difference between control and decreased nests (Fig. 1A) could be because breeding adults can only invest in offspring provisioning as much as their condition or fitness allows, and the original clutch may have been close to their maximal investment capacity. Only those in increased treatment nests were pushed beyond their limits to provide and offspring growth suffered as a consequence. Decreased treatment nest chicks may not have been provided with excessive food (which could result in increased in chick growth) as adults save energy for future reproductive efforts, or there may be some other physiological constraint to the rate of growth, regardless of possibly higher provisioning rates at decreased treatment nests.",neg_q,R v3.6.3,R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,NA,NA,NA,brood_reduction,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Buchan R_3EoS37IOWKLRxDV,Blackall-1-1-1,1,1,1,0.12948879,slope,364.8621107,0.05611687,back.transformed,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_3EoS37IOWKLRxDV,ExoticAnnualGrass_cover,NA,1,generalised,standard,10,15,6,11,4,4,5,0,retain,retain,exclude,"There is a positive association between small seedlings (0-50cm) and the cover of exotic annual grasses, a positive association between medium seedlings (50cm-2m) and the cover of native perennial grasses, and a negative association between large seedlings (>2m) and the cover of native perennial and exotic annual grasses.",mixed,R 3.6.3,R,3.6.3,R,3.6.3,NA,NA,Season,Property,Quadrat no,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NativePerennialGraminoid_cover,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,year,size_class,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Blackall R_3ERyi6ZMihKx06s,Bunbur-1-1-1,1,1,1,-0.18158,slope,220.9662,0.01664,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_3ERyi6ZMihKx06s,rear_Cs_at_start_of_rearing,2367,0,linear,standard,5,5,3,3,2,2,0,0,retain,retain,NA,"From this analysis, I conclude that chick growth, as measured by mass and tarsus length at day 14, is less affected by the original brood size than by the study’s manipulation of chicks within a nest. Possibly birds maximize their breeding success by increasing or decreasing clutch size according to environmental conditions, parental experience, or other factors not measured in this study.",none_q,"R version 3.6.3, and the lme4 package.",R,3.6.3,R,3.6.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bunbur -R_3eta2uFp1DLnGVJ,Boggabri-1-1-1,1,1,1,-0.01537,slope,277.0075,0.02793,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_3eta2uFp1DLnGVJ,ExoticPerennialGrass_cover,350,0,generalised,standard,4,4,3,3,1,1,0,0,retain,retain,NA,"How does grass cover influence Eucalyptus spp. seedling recruitment? - +R_3eta2uFp1DLnGVJ,Boggabri-1-1-1,1,1,1,-0.01537,slope,277.0075,0.02793,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_3eta2uFp1DLnGVJ,ExoticPerennialGrass_cover,350,0,generalised,standard,4,4,3,3,1,1,0,0,retain,retain,NA,"How does grass cover influence Eucalyptus spp. seedling recruitment? + There was no evidence that grass cover influenced Eucalyptus spp. seedling recruitment.",none_c,R version 4.0.2,R,4.0.2,R,4.0.2,NA,NA,NA,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Boggabri -R_3EYx3CfuTZ7YNmF,Booligal-3-3-1,3,3,1,-0.0849921,slope,15,0.0938912,logit,logit,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"I used the original variables: ""euc_sdlgs0_50cm"", ""euc_sdlgs_50cm_2m"", ""euc_sdlgs_2m"". For each property-season combination, I calculated the proportion of plots containing at least one seedling. I then averaged across seasons within each property.",average.proportion.of.plots.containing.at.least.one.euc.seedling.of.any.size,R_3EYx3CfuTZ7YNmF,all_exotic_grass,18,0,generalised,standard,1,1,1,1,0,0,0,0,retain,retain,NA,"How does grass cover influence Eucalypt spp. seedlings recruitment? - -If we look across different properties, there is limited evidence that properties grass cover affects seedling recruitment after controlling for difference in total annual precipitation among properties. Specifically, properties with high grass cover (total grass, native grass or exotic grass) do not have higher (or lower) average Eucalypt seedlings recruitment. - -There is some evidence that properties with total grass cover and exotic grass cover reduce the upper boundary of Eucalypt seedling recruitment. Therefore, properties with high total grass cover and exotic grass cover have low Eucalypt seedling recruitment whilst properties with lower total grass cover and exotic grass cover show a range of high and low Eucalypt seedling recruitment I could not separate the effects of other confounding variables. - -However, I did find evidence that, within properties with high total annual precipitation, plots with Eucalypt seedlings had lower grass cover than plots with Eucalypt seedlings. This is consistent with a negative effect of grass cover on seedlings recruitment. This was not the case at drier sites where the effect might be opposite. I could not separate this effect from other confounding variables though. - +R_3EYx3CfuTZ7YNmF,Booligal-3-3-1,3,3,1,-0.0849921,slope,15,0.0938912,logit,logit,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"I used the original variables: ""euc_sdlgs0_50cm"", ""euc_sdlgs_50cm_2m"", ""euc_sdlgs_2m"". For each property-season combination, I calculated the proportion of plots containing at least one seedling. I then averaged across seasons within each property.",average.proportion.of.plots.containing.at.least.one.euc.seedling.of.any.size,R_3EYx3CfuTZ7YNmF,all_exotic_grass,18,0,generalised,standard,1,1,1,1,0,0,0,0,retain,retain,NA,"How does grass cover influence Eucalypt spp. seedlings recruitment? + +If we look across different properties, there is limited evidence that properties grass cover affects seedling recruitment after controlling for difference in total annual precipitation among properties. Specifically, properties with high grass cover (total grass, native grass or exotic grass) do not have higher (or lower) average Eucalypt seedlings recruitment. + +There is some evidence that properties with total grass cover and exotic grass cover reduce the upper boundary of Eucalypt seedling recruitment. Therefore, properties with high total grass cover and exotic grass cover have low Eucalypt seedling recruitment whilst properties with lower total grass cover and exotic grass cover show a range of high and low Eucalypt seedling recruitment I could not separate the effects of other confounding variables. + +However, I did find evidence that, within properties with high total annual precipitation, plots with Eucalypt seedlings had lower grass cover than plots with Eucalypt seedlings. This is consistent with a negative effect of grass cover on seedlings recruitment. This was not the case at drier sites where the effect might be opposite. I could not separate this effect from other confounding variables though. + In conclusion, across properties, grass cover might limit the potential for high Eucalypt seedling recruitment. Moreover, at high rainfall, grass cover may reduce Eucalypt seedling recruitment within properties but the opposite might the case at low rainfall. Therefore, whilst I did find some evidence that grass cover affects Eucalypt seedling recruitment, on the basis of these data, I would not make a firm conclusion about it.",neg_q,"All data exploration, cleaning, manipulation and statistical analysis were conducted in R version 4.0.2 (R Core Team 2020).",R,4.0.2,R,4.0.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_exotic_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Booligal -R_3EYx3CfuTZ7YNmF,Booligal-2-2-1,2,2,1,-0.0281428,slope,15,0.0568708,logit,logit,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"I used the original variables: ""euc_sdlgs0_50cm"", ""euc_sdlgs_50cm_2m"", ""euc_sdlgs_2m"". For each property-season combination, I calculated the proportion of plots containing at least one seedling. I then averaged across seasons within each property.",average.proportion.of.plots.containing.at.least.one.euc.seedling.of.any.size,R_3EYx3CfuTZ7YNmF,all_grass,18,0,generalised,standard,1,1,1,1,0,0,0,0,retain,retain,NA,"How does grass cover influence Eucalypt spp. seedlings recruitment? - -If we look across different properties, there is limited evidence that properties grass cover affects seedling recruitment after controlling for difference in total annual precipitation among properties. Specifically, properties with high grass cover (total grass, native grass or exotic grass) do not have higher (or lower) average Eucalypt seedlings recruitment. - -There is some evidence that properties with total grass cover and exotic grass cover reduce the upper boundary of Eucalypt seedling recruitment. Therefore, properties with high total grass cover and exotic grass cover have low Eucalypt seedling recruitment whilst properties with lower total grass cover and exotic grass cover show a range of high and low Eucalypt seedling recruitment I could not separate the effects of other confounding variables. - -However, I did find evidence that, within properties with high total annual precipitation, plots with Eucalypt seedlings had lower grass cover than plots with Eucalypt seedlings. This is consistent with a negative effect of grass cover on seedlings recruitment. This was not the case at drier sites where the effect might be opposite. I could not separate this effect from other confounding variables though. - +R_3EYx3CfuTZ7YNmF,Booligal-2-2-1,2,2,1,-0.0281428,slope,15,0.0568708,logit,logit,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"I used the original variables: ""euc_sdlgs0_50cm"", ""euc_sdlgs_50cm_2m"", ""euc_sdlgs_2m"". For each property-season combination, I calculated the proportion of plots containing at least one seedling. I then averaged across seasons within each property.",average.proportion.of.plots.containing.at.least.one.euc.seedling.of.any.size,R_3EYx3CfuTZ7YNmF,all_grass,18,0,generalised,standard,1,1,1,1,0,0,0,0,retain,retain,NA,"How does grass cover influence Eucalypt spp. seedlings recruitment? + +If we look across different properties, there is limited evidence that properties grass cover affects seedling recruitment after controlling for difference in total annual precipitation among properties. Specifically, properties with high grass cover (total grass, native grass or exotic grass) do not have higher (or lower) average Eucalypt seedlings recruitment. + +There is some evidence that properties with total grass cover and exotic grass cover reduce the upper boundary of Eucalypt seedling recruitment. Therefore, properties with high total grass cover and exotic grass cover have low Eucalypt seedling recruitment whilst properties with lower total grass cover and exotic grass cover show a range of high and low Eucalypt seedling recruitment I could not separate the effects of other confounding variables. + +However, I did find evidence that, within properties with high total annual precipitation, plots with Eucalypt seedlings had lower grass cover than plots with Eucalypt seedlings. This is consistent with a negative effect of grass cover on seedlings recruitment. This was not the case at drier sites where the effect might be opposite. I could not separate this effect from other confounding variables though. + In conclusion, across properties, grass cover might limit the potential for high Eucalypt seedling recruitment. Moreover, at high rainfall, grass cover may reduce Eucalypt seedling recruitment within properties but the opposite might the case at low rainfall. Therefore, whilst I did find some evidence that grass cover affects Eucalypt seedling recruitment, on the basis of these data, I would not make a firm conclusion about it.",neg_q,"All data exploration, cleaning, manipulation and statistical analysis were conducted in R version 4.0.2 (R Core Team 2020).",R,4.0.2,R,4.0.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Booligal -R_3EYx3CfuTZ7YNmF,Booligal-4-4-1,4,4,1,0.032037,slope,15,0.073426,logit,logit,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"I used the original variables: ""euc_sdlgs0_50cm"", ""euc_sdlgs_50cm_2m"", ""euc_sdlgs_2m"". For each property-season combination, I calculated the proportion of plots containing at least one seedling. I then averaged across seasons within each property.",average.proportion.of.plots.containing.at.least.one.euc.seedling.of.any.size,R_3EYx3CfuTZ7YNmF,all_native_grass_graminoid,18,0,generalised,standard,1,1,1,1,0,0,0,0,retain,retain,NA,"How does grass cover influence Eucalypt spp. seedlings recruitment? - -If we look across different properties, there is limited evidence that properties grass cover affects seedling recruitment after controlling for difference in total annual precipitation among properties. Specifically, properties with high grass cover (total grass, native grass or exotic grass) do not have higher (or lower) average Eucalypt seedlings recruitment. - -There is some evidence that properties with total grass cover and exotic grass cover reduce the upper boundary of Eucalypt seedling recruitment. Therefore, properties with high total grass cover and exotic grass cover have low Eucalypt seedling recruitment whilst properties with lower total grass cover and exotic grass cover show a range of high and low Eucalypt seedling recruitment I could not separate the effects of other confounding variables. - -However, I did find evidence that, within properties with high total annual precipitation, plots with Eucalypt seedlings had lower grass cover than plots with Eucalypt seedlings. This is consistent with a negative effect of grass cover on seedlings recruitment. This was not the case at drier sites where the effect might be opposite. I could not separate this effect from other confounding variables though. - +R_3EYx3CfuTZ7YNmF,Booligal-4-4-1,4,4,1,0.032037,slope,15,0.073426,logit,logit,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"I used the original variables: ""euc_sdlgs0_50cm"", ""euc_sdlgs_50cm_2m"", ""euc_sdlgs_2m"". For each property-season combination, I calculated the proportion of plots containing at least one seedling. I then averaged across seasons within each property.",average.proportion.of.plots.containing.at.least.one.euc.seedling.of.any.size,R_3EYx3CfuTZ7YNmF,all_native_grass_graminoid,18,0,generalised,standard,1,1,1,1,0,0,0,0,retain,retain,NA,"How does grass cover influence Eucalypt spp. seedlings recruitment? + +If we look across different properties, there is limited evidence that properties grass cover affects seedling recruitment after controlling for difference in total annual precipitation among properties. Specifically, properties with high grass cover (total grass, native grass or exotic grass) do not have higher (or lower) average Eucalypt seedlings recruitment. + +There is some evidence that properties with total grass cover and exotic grass cover reduce the upper boundary of Eucalypt seedling recruitment. Therefore, properties with high total grass cover and exotic grass cover have low Eucalypt seedling recruitment whilst properties with lower total grass cover and exotic grass cover show a range of high and low Eucalypt seedling recruitment I could not separate the effects of other confounding variables. + +However, I did find evidence that, within properties with high total annual precipitation, plots with Eucalypt seedlings had lower grass cover than plots with Eucalypt seedlings. This is consistent with a negative effect of grass cover on seedlings recruitment. This was not the case at drier sites where the effect might be opposite. I could not separate this effect from other confounding variables though. + In conclusion, across properties, grass cover might limit the potential for high Eucalypt seedling recruitment. Moreover, at high rainfall, grass cover may reduce Eucalypt seedling recruitment within properties but the opposite might the case at low rainfall. Therefore, whilst I did find some evidence that grass cover affects Eucalypt seedling recruitment, on the basis of these data, I would not make a firm conclusion about it.",neg_q,"All data exploration, cleaning, manipulation and statistical analysis were conducted in R version 4.0.2 (R Core Team 2020).",R,4.0.2,R,4.0.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_native_grass_graminoid,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Booligal -R_3EYx3CfuTZ7YNmF,Booligal-1-1-1,1,1,1,NA,NA,NA,NA,logit,logit,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"I used the variables: ""euc_sdlgs0_50cm"", ""euc_sdlgs_50cm_2m"", ""euc_sdlgs_2m"" from the original dataset. For each property-season combination, I calculated the proportion of plots containing at least one seedling. I then averaged this value over seasons within each property.",NA,R_3EYx3CfuTZ7YNmF,NA,NA,0,generalised,standard,5,NA,5,NA,0,NA,NA,NA,exclude,exclude_all,NA,"How does grass cover influence Eucalypt spp. seedlings recruitment? - -If we look across different properties, there is limited evidence that properties grass cover affects seedling recruitment after controlling for difference in total annual precipitation among properties. Specifically, properties with high grass cover (total grass, native grass or exotic grass) do not have higher (or lower) average Eucalypt seedlings recruitment. - -There is some evidence that properties with total grass cover and exotic grass cover reduce the upper boundary of Eucalypt seedling recruitment. Therefore, properties with high total grass cover and exotic grass cover have low Eucalypt seedling recruitment whilst properties with lower total grass cover and exotic grass cover show a range of high and low Eucalypt seedling recruitment I could not separate the effects of other confounding variables. - -However, I did find evidence that, within properties with high total annual precipitation, plots with Eucalypt seedlings had lower grass cover than plots with Eucalypt seedlings. This is consistent with a negative effect of grass cover on seedlings recruitment. This was not the case at drier sites where the effect might be opposite. I could not separate this effect from other confounding variables though. - +R_3EYx3CfuTZ7YNmF,Booligal-1-1-1,1,1,1,NA,NA,NA,NA,logit,logit,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"I used the variables: ""euc_sdlgs0_50cm"", ""euc_sdlgs_50cm_2m"", ""euc_sdlgs_2m"" from the original dataset. For each property-season combination, I calculated the proportion of plots containing at least one seedling. I then averaged this value over seasons within each property.",NA,R_3EYx3CfuTZ7YNmF,NA,NA,0,generalised,standard,5,NA,5,NA,0,NA,NA,NA,exclude,exclude_all,NA,"How does grass cover influence Eucalypt spp. seedlings recruitment? + +If we look across different properties, there is limited evidence that properties grass cover affects seedling recruitment after controlling for difference in total annual precipitation among properties. Specifically, properties with high grass cover (total grass, native grass or exotic grass) do not have higher (or lower) average Eucalypt seedlings recruitment. + +There is some evidence that properties with total grass cover and exotic grass cover reduce the upper boundary of Eucalypt seedling recruitment. Therefore, properties with high total grass cover and exotic grass cover have low Eucalypt seedling recruitment whilst properties with lower total grass cover and exotic grass cover show a range of high and low Eucalypt seedling recruitment I could not separate the effects of other confounding variables. + +However, I did find evidence that, within properties with high total annual precipitation, plots with Eucalypt seedlings had lower grass cover than plots with Eucalypt seedlings. This is consistent with a negative effect of grass cover on seedlings recruitment. This was not the case at drier sites where the effect might be opposite. I could not separate this effect from other confounding variables though. + In conclusion, across properties, grass cover might limit the potential for high Eucalypt seedling recruitment. Moreover, at high rainfall, grass cover may reduce Eucalypt seedling recruitment within properties but the opposite might the case at low rainfall. Therefore, whilst I did find some evidence that grass cover affects Eucalypt seedling recruitment, on the basis of these data, I would not make a firm conclusion about it.",neg_q,"All data exploration, cleaning, manipulation and statistical analysis were conducted in R version 4.0.2 (R Core Team 2020).",R,4.0.2,R,4.0.2,NA,NA,Season,Property,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Booligal -R_3EYx3CfuTZ7YNmF,Booligal-5-5-1,5,5,1,-0.01899,slope,16,0.00361,NA,NA,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"I used the original variables: ""euc_sdlgs0_50cm"", ""euc_sdlgs_50cm_2m"", ""euc_sdlgs_2m"". For each property-season combination, I calculated the proportion of plots containing at least one seedling. I then averaged across seasons within each property.",average.proportion.of.plots.containing.at.least.one.euc.seedling.of.any.size,R_3EYx3CfuTZ7YNmF,all_grass,18,1,linear,quantile_regression,1,1,1,1,0,0,0,0,retain,retain,NA,"How does grass cover influence Eucalypt spp. seedlings recruitment? - -If we look across different properties, there is limited evidence that properties grass cover affects seedling recruitment after controlling for difference in total annual precipitation among properties. Specifically, properties with high grass cover (total grass, native grass or exotic grass) do not have higher (or lower) average Eucalypt seedlings recruitment. - -There is some evidence that properties with total grass cover and exotic grass cover reduce the upper boundary of Eucalypt seedling recruitment. Therefore, properties with high total grass cover and exotic grass cover have low Eucalypt seedling recruitment whilst properties with lower total grass cover and exotic grass cover show a range of high and low Eucalypt seedling recruitment I could not separate the effects of other confounding variables. - -However, I did find evidence that, within properties with high total annual precipitation, plots with Eucalypt seedlings had lower grass cover than plots with Eucalypt seedlings. This is consistent with a negative effect of grass cover on seedlings recruitment. This was not the case at drier sites where the effect might be opposite. I could not separate this effect from other confounding variables though. - +R_3EYx3CfuTZ7YNmF,Booligal-5-5-1,5,5,1,-0.01899,slope,16,0.00361,NA,NA,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"I used the original variables: ""euc_sdlgs0_50cm"", ""euc_sdlgs_50cm_2m"", ""euc_sdlgs_2m"". For each property-season combination, I calculated the proportion of plots containing at least one seedling. I then averaged across seasons within each property.",average.proportion.of.plots.containing.at.least.one.euc.seedling.of.any.size,R_3EYx3CfuTZ7YNmF,all_grass,18,1,linear,quantile_regression,1,1,1,1,0,0,0,0,retain,retain,NA,"How does grass cover influence Eucalypt spp. seedlings recruitment? + +If we look across different properties, there is limited evidence that properties grass cover affects seedling recruitment after controlling for difference in total annual precipitation among properties. Specifically, properties with high grass cover (total grass, native grass or exotic grass) do not have higher (or lower) average Eucalypt seedlings recruitment. + +There is some evidence that properties with total grass cover and exotic grass cover reduce the upper boundary of Eucalypt seedling recruitment. Therefore, properties with high total grass cover and exotic grass cover have low Eucalypt seedling recruitment whilst properties with lower total grass cover and exotic grass cover show a range of high and low Eucalypt seedling recruitment I could not separate the effects of other confounding variables. + +However, I did find evidence that, within properties with high total annual precipitation, plots with Eucalypt seedlings had lower grass cover than plots with Eucalypt seedlings. This is consistent with a negative effect of grass cover on seedlings recruitment. This was not the case at drier sites where the effect might be opposite. I could not separate this effect from other confounding variables though. + In conclusion, across properties, grass cover might limit the potential for high Eucalypt seedling recruitment. Moreover, at high rainfall, grass cover may reduce Eucalypt seedling recruitment within properties but the opposite might the case at low rainfall. Therefore, whilst I did find some evidence that grass cover affects Eucalypt seedling recruitment, on the basis of these data, I would not make a firm conclusion about it.",neg_q,"All data exploration, cleaning, manipulation and statistical analysis were conducted in R version 4.0.2 (R Core Team 2020).",R,4.0.2,R,4.0.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Booligal R_3EZsdPTvOnZBe9S,Burnie-1-1-1,1,1,1,-0.3185622,slope,351.8376,0.10224,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_3EZsdPTvOnZBe9S,net_rearing_manipulation,2608,0,linear,standard,14,14,5,5,9,9,0,0,retain,retain,NA,"Competition with siblings reduces growth of nestling blue tits when clutch size is artificially increased beyond the size produced by the mother, and presumably, the amount of food brought by the rearing parents is insufficient for all chicks in the nest. The effect of one extra chick beyond the initial size (and presumably, sufficient food supply) corresponds to a decrease of 0.32g at 14 days on average. This effect is biologically significant, as it represents a decline of 3.1% in mean body weight, and 0.25 standard deviations in the body weight of chicks at that age.",neg_q,R 3.6.1; MCMCglmm 2.29 ; glmmTMB 1.0.0,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,hatch_Area,hatch_Box,hatch_mom_Ring,hatch_nest_dad_Ring,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,NA,NA,NA,rear_area,rear_Box,rear_mom_Ring,rear_dad_Ring,NA,home_or_away,NA,NA,NA,NA,NA,NA,net_rearing_manipulation,NA,NA,NA,Date_of_day14,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,manipulation_non,NA,NA,NA,Burnie R_3fqsqu3iZPZDV4J,Bothwell-1-1-1,1,1,1,NA,NA,NA,0.197,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),"sum of euc_sdlgs0_50cm, euc_sdlgs50cm-2m, euc_sdlgs>2m",euc_sdlgs_all,R_3fqsqu3iZPZDV4J,all_grass,NA,0,generalised,zero_inflated,11,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"Grass cover does not appear to significantly influence seedling recruitment, once accounting for the other important variables that influence recruitment. The model coefficient is small not significantly different to zero, and the parameter does not significantly improve overall model fit.",none_q,"R 3.6.3, plus additional libraries (see writeup document)",R,3.6.3,R,3.6.3,NA,NA,Season,NA,NA,Easting,NA,NA,Landscape position,NA,NA,ExoticPerennialHerb_cover,NA,NA,NA,NativePerennialGrass_cover,NA,NativePerennialGraminoid_cover,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,NA,NA,NA,PET,MrVBF,NA,Th_ppm,U_ppm,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bothwell @@ -421,21 +421,21 @@ R_3nBCE4hMLh5s3qt,Cattai-1-1-1,1,1,1,-0.1575,reduced-enlarged,304.078,0.2004,ide R_3NHVKFiOiQBfX9b,Brooklyn-2-2-1,2,2,1,-8.087,slope,115,0.0173,log,log,eucalyptus,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_3NHVKFiOiQBfX9b,all_grass,117,0,generalised,standard,1,1,1,1,0,0,0,0,retain,retain,NA,"A significant negative effect of grass cover on seedlings recruitment densities was detected only in winter 2006 season suggesting land manager to allocate all efforts to restoring these ecosystems in the winter season. For example, incorporate appropriate weed management in winter season to increase recruitment of Eucalyptus spp. seedlings.",neg_q,All done in one software = R 3.6.2,R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Brooklyn R_3NHVKFiOiQBfX9b,Brooklyn-1-1-1,1,1,1,-0.08668,slope,114,0.02385,log,log,eucalyptus,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_3NHVKFiOiQBfX9b,all_grass,116,0,generalised,standard,1,1,1,1,0,0,0,0,retain,retain,NA,"A significant negative effect of grass cover on seedlings recruitment densities was detected only in winter 2006 season suggesting land manager to allocate all efforts to restoring these ecosystems in the winter season. For example, incorporate appropriate weed management in winter season to increase recruitment of Eucalyptus spp. seedlings.",neg_q,All done in one software = R 3.6.2,R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Brooklyn R_3NHVKFiOiQBfX9b,Brooklyn-3-3-1,3,3,1,9.48E-04,slope,115,0.0265946,log,log,eucalyptus,0,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_3NHVKFiOiQBfX9b,all_grass,117,0,generalised,standard,1,1,1,1,0,0,0,0,retain,retain,NA,"A significant negative effect of grass cover on seedlings recruitment densities was detected only in winter 2006 season suggesting land manager to allocate all efforts to restoring these ecosystems in the winter season. For example, incorporate appropriate weed management in winter season to increase recruitment of Eucalyptus spp. seedlings.",neg_q,All done in one software = R 3.6.2,R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Brooklyn -R_3NKz8oHb8nvNIQR,Buckland-1-1-1,1,1,1,-0.08065,slope,339.11099,0.07608,identity,identity,eucalyptus,1,square.root,square.root,constructed variable (combining information from two or more original variables),"I combined all three original size cohorts of eucalyptus seedlings (<0.5m, 0.5-2m, >2m) into one new total eucalyptus seedling variable",euc_sdlgs_all,R_3NKz8oHb8nvNIQR,all_grass,351,0,linear,zero_inflated,7,7,6,6,1,1,0,0,retain,retain,NA,"The number of Eucalyptus seedlings per quadrat, regardless of size, was not influenced by the percent cover of exotic and native grasses and graminoids. Instead, Eucalyptus seedling count was driven by distance from existing Eucalyptus canopy and negatively affected by ground litter cover. the greatest number of seedlings were found within 10m of the canopy edge. As grasses contribute to vegetative litter, we cannot rule out that there is an indirect affect of grass cover on seedling recruitment. However, in this case the data suggests that it is unlikely a negative direct effect of competitive exclusion for space or soil nutrients, or shading out of Eucalyptus seedlings by dense grasses/graminoids. In fact, the presence of grasses may indirectly benefit Eucalyptus recruitment by creating vegetative litter that buffers germinating seedlings from the harsh climate and makes growing conditions more suitable by helping retain soil moisture. On the other hand, if litter is too dense it could reduce the success of seedling germination and growth.",none_q,"All analyses were conducted using R version 3.5.3 (R Development Core team 2019). - +R_3NKz8oHb8nvNIQR,Buckland-1-1-1,1,1,1,-0.08065,slope,339.11099,0.07608,identity,identity,eucalyptus,1,square.root,square.root,constructed variable (combining information from two or more original variables),"I combined all three original size cohorts of eucalyptus seedlings (<0.5m, 0.5-2m, >2m) into one new total eucalyptus seedling variable",euc_sdlgs_all,R_3NKz8oHb8nvNIQR,all_grass,351,0,linear,zero_inflated,7,7,6,6,1,1,0,0,retain,retain,NA,"The number of Eucalyptus seedlings per quadrat, regardless of size, was not influenced by the percent cover of exotic and native grasses and graminoids. Instead, Eucalyptus seedling count was driven by distance from existing Eucalyptus canopy and negatively affected by ground litter cover. the greatest number of seedlings were found within 10m of the canopy edge. As grasses contribute to vegetative litter, we cannot rule out that there is an indirect affect of grass cover on seedling recruitment. However, in this case the data suggests that it is unlikely a negative direct effect of competitive exclusion for space or soil nutrients, or shading out of Eucalyptus seedlings by dense grasses/graminoids. In fact, the presence of grasses may indirectly benefit Eucalyptus recruitment by creating vegetative litter that buffers germinating seedlings from the harsh climate and makes growing conditions more suitable by helping retain soil moisture. On the other hand, if litter is too dense it could reduce the success of seedling germination and growth.",none_q,"All analyses were conducted using R version 3.5.3 (R Development Core team 2019). + R Development Core Team. 2019. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. V3.5.3. https://www.r-project.org. Accessed 1 Mar 2019",R,3.5.3,R,3.5.3,NA,NA,NA,Property,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Litter_cover,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),NA,NA,NA,NA,NA,NA,PET,MrVBF,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Buckland R_3OftgnLM9MoIwf8,Bundarra-1-1-1,1,1,1,NA,NA,NA,0.1,NA,NA,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),This variable was calculated as the total sum of seedlings for each statistical unit,euc_sdlgs_all,R_3OftgnLM9MoIwf8,NA,NA,0,generalised,zero_inflated,18,NA,18,NA,0,NA,NA,NA,exclude,exclude_all,NA,"Grass cover has no effect on Eucalyptus recruitment. Exotic perennial herb cover, landscape position (toe of slope) and thorium concentrations seem to be the variables driving seedling recruitment in the studied landscapes.",none_c,R for data cleaning and model estimation (Version 4.0.0),R,4.0.0,R,4.0.0,NA,NA,Season,NA,NA,NA,NA,NA,Landscape position,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,NA,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NA,NA,NA,NA,NA,Euc_canopy_cover,NA,euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,annual_precipitation,NA,NA,NA,NA,K_perc,Th_ppm,NA,SRad_Jan,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bundarra R_3oWTTWWo1e8y3jB,Bundeena-1-6-1,1,6,1,-0.36145,slope,321.03707,0.13658,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_3oWTTWWo1e8y3jB,ExoticPerennialGrass_cover,NA,0,generalised,standard,9,9,8,8,1,1,0,0,retain,retain,NA,Seedlings from 50 cm to 2 meters were negatively influenced only by Exotic Perennial Grass.,neg_c,R 3.6.1.,R,3.6.1,R,3.6.1,NA,NA,NA,Property,NA,NA,NA,NA,NA,NA,NA,NA,ExoticPerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),NA,NA,NA,NA,NA,NA,NA,MrVBF,K_perc,Th_ppm,U_ppm,NA,SRad_Jul,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bundeena R_3PBpbf5wxagIV7X,Bungonia-1-1-1,1,1,1,-0.6843,slope,341.50259,0.3055,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_3PBpbf5wxagIV7X,NA,NA,0,generalised,standard,4,NA,NA,NA,NA,NA,NA,NA,exclude,retain,NA,Grass cover does not influence the recruitment of Eucalyptus seedlings,none_c,R,R,NA,R,NA,NA,NA,NA,Property,Quadrat no,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bungonia R_3PBpbf5wxagIV7X,Bungonia-2-2-1,2,2,1,-0.3824,slope,341.50259,0.1882,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_3PBpbf5wxagIV7X,NA,NA,0,generalised,standard,4,NA,NA,NA,NA,NA,NA,NA,exclude,retain,NA,Grass cover does not influence the recruitment of Eucalyptus seedlings,none_c,R,R,NA,R,NA,NA,NA,NA,Property,Quadrat no,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Distance_to_Eucalypt_canopy(m),NA,euc_sdlgs50cm-2m,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bungonia -R_3pte7gGbO7GliHv,Busselto-1-1-1,1,1,1,-0.017444,slope,274.69649,0.006074,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),all 3 seedlings combined - data$tot_seedlings <- data$euc_sdlgs.2m + data$euc_sdlgs0_50cm + data$euc_sdlgs50cm.2m,euc_sdlgs_all,R_3pte7gGbO7GliHv,NativePerennialGrass_cover,NA,0,generalised,zero_inflated,11,11,10,10,1,1,0,0,retain,retain,NA,"Eucalyptus seedling recruitment was significantly negatively correlated with exotic annual grass cover (P<0.001) and native perennial grass cover (P=0.004), with exotic annual grass having a larger effect. Exotic perennial grass cover had a marginally nonsignificant (P=0.075) positive association with seedlings. - +R_3pte7gGbO7GliHv,Busselto-1-1-1,1,1,1,-0.017444,slope,274.69649,0.006074,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),all 3 seedlings combined - data$tot_seedlings <- data$euc_sdlgs.2m + data$euc_sdlgs0_50cm + data$euc_sdlgs50cm.2m,euc_sdlgs_all,R_3pte7gGbO7GliHv,NativePerennialGrass_cover,NA,0,generalised,zero_inflated,11,11,10,10,1,1,0,0,retain,retain,NA,"Eucalyptus seedling recruitment was significantly negatively correlated with exotic annual grass cover (P<0.001) and native perennial grass cover (P=0.004), with exotic annual grass having a larger effect. Exotic perennial grass cover had a marginally nonsignificant (P=0.075) positive association with seedlings. + Grass cover generally negatively impacts Eucalyptus seedling recruitment, although there is a slight positive association with exotic perennial grass cover.",mixed,R 3.5.3 - For everything,R,3.5.3,R,3.5.3,NA,NA,Season,Property,NA,NA,NA,Aspect,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NativePerennialFern_cover,NativePerennialGrass_cover,NA,NA,NA,NA,Litter_cover,NA,Rock_cover,NA,NA,NA,NA,NA,annual_precipitation,NA,NA,NA,NA,K_perc,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Busselto R_3qfD5ZHHdBbTgk3,Byrock-1-8-1,1,8,1,-0.06549,slope,458.3576,0.0141,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_3qfD5ZHHdBbTgk3,NA,3720,0,linear,standard,4,NA,NA,NA,NA,NA,NA,NA,exclude,retain,NA,"Sibling count had a statistically significant effect on both measures of nestling growth. The 0.065 g decrease in mass for each additional sibling represents only a 0.63% change from the mean mass of 10.276 g. The 0.020 mm decrease in tarsus length per additional sibling represents a 0.12 % change from the mean of 16.7276 mm. Given the range in brood size from 1 to 17, the difference in mass and tarsus length due to sibling competition could be as much as 10.08% and 1.92%, respectively, when comparing the extremes of the brood size range. This indicates a potentially biologically significant effect when considering the extremes of brood size, but minor changes in brood size are unlikely to have a biologically significant effect.",neg_c,All analyses were conducted using R version 3.6.1 (R Core Team 2019) within RStudio version 1.2.1335 (RStudio Team 2018). Linear mixed effects models were conducted using R package “nlme” version 3.1-147 (Pinheiro et al. 2020).,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,NA,NA,day_14_weight,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Byrock -R_3rIdpCqsQtsmgqT,Adelong-2-2-1,2,2,1,-0.29,slope,2188.18,0.00276,identity,identity,blue tit,1,z.score,z.score,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_tarsus_length,R_3rIdpCqsQtsmgqT,rear_Cs_at_start_of_rearing,3208,0,linear,standard,8,8,7,7,1,1,0,0,retain,retain,NA,nestlings had larger tarsus lengths when rearing brood size 14 days after hatching was larger,pos_c,"R, version 3.6.2",R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_CS,hatch_nest_OH,d0_hatch_nest_brood_size,NA,NA,NA,NA,NA,NA,rear_nest_trt,NA,NA,rear_nest_CS,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,relatedness,NA,NA,NA,NA,NA,NA,NA,NA,NA,Adelong +R_3rIdpCqsQtsmgqT,Adelong-2-2-1,2,2,1,-0.29,slope,2188.18,0.00276,identity,identity,blue tit,1,z.score,z.score,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_tarsus_length,R_3rIdpCqsQtsmgqT,rear_Cs_at_start_of_rearing,3208,0,linear,standard,8,8,7,7,1,1,0,0,retain,retain,NA,nestlings had larger tarsus lengths when rearing brood size 14 days after hatching was larger,pos_c,"R, version 3.6.2",R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_CS,hatch_nest_OH,d0_hatch_nest_brood_size,NA,NA,NA,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,relatedness,NA,NA,NA,NA,NA,NA,NA,NA,NA,Adelong R_3rIdpCqsQtsmgqT,Calliope-3-3-1,3,3,1,-0.5836,slope,326.7,0.4958,log,log,eucalyptus,1,z.score,z.score,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_3rIdpCqsQtsmgqT,ExoticPerennialGrass_cover,NA,0,generalised,standard,7,7,6,6,1,1,0,0,retain,retain,NA,No effect of exotic perennial grass cover on seedlings <50cm,none_c,"R, version 3.6.2",R,3.6.2,R,3.6.2,NA,NA,NA,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NativePerennialGraminoid_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,annual_precipitation,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,month,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Calliope R_3rIdpCqsQtsmgqT,Calliope-4-4-1,4,4,1,-0.42733,slope,322.1,0.24362,log,log,eucalyptus,1,z.score,z.score,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_3rIdpCqsQtsmgqT,ExoticPerennialGrass_cover,NA,0,generalised,standard,7,7,6,6,1,1,0,0,retain,retain,NA,weak effect of exotic perennial grass cover on the number of seedlings between 50-200 cm tall,neg_c,"R, version 3.6.2",R,3.6.2,R,3.6.2,NA,NA,NA,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NativePerennialGraminoid_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,annual_precipitation,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,month,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Calliope -R_3rIdpCqsQtsmgqT,Adelong-1-1-1,1,1,1,0.29,slope,1952.32,0.01675,identity,identity,blue tit,1,z.score,z.score,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_3rIdpCqsQtsmgqT,rear_Cs_at_start_of_rearing,3208,0,linear,standard,8,8,7,7,1,1,0,0,retain,retain,NA,nestlings were lighter when rearing brood size 14 days after hatching was larger,neg_c,"R, version 3.6.2",R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_CS,hatch_nest_OH,d0_hatch_nest_brood_size,NA,NA,NA,NA,NA,NA,rear_nest_trt,NA,NA,rear_nest_CS,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,relatedness,NA,NA,NA,NA,NA,NA,NA,NA,NA,Adelong +R_3rIdpCqsQtsmgqT,Adelong-1-1-1,1,1,1,0.29,slope,1952.32,0.01675,identity,identity,blue tit,1,z.score,z.score,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_3rIdpCqsQtsmgqT,rear_Cs_at_start_of_rearing,3208,0,linear,standard,8,8,7,7,1,1,0,0,retain,retain,NA,nestlings were lighter when rearing brood size 14 days after hatching was larger,neg_c,"R, version 3.6.2",R,3.6.2,R,3.6.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_CS,hatch_nest_OH,d0_hatch_nest_brood_size,NA,NA,NA,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,relatedness,NA,NA,NA,NA,NA,NA,NA,NA,NA,Adelong R_40VJPSNfIlSJGAV,Angasto-1-1-2,1,1,2,-0.29782521,control-enlarged,547.8151,0.0525173,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_40VJPSNfIlSJGAV,rear_nest_trt_C.E,3720,0,linear,standard,8,8,6,6,2,2,0,0,retain,retain,NA,"There was no interaction between between brood size and experimental treatment on tarsus length (parametric bootstrap p-value : p = 0.508). However, there was a negative effect of the Enlarged treatment on tarsus length as compared to the Control treatment (Table 1 ; Figure 1 ; p = 0.001), but no effect of body size (Table 1 ; p= 0.088).",neg_c,R,R,NA,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_OH,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,NA,NA,NA,day14_measurer,NA,NA,within-area_movement,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Angasto R_40VJPSNfIlSJGAV,Angasto-3-3-2,3,3,2,-0.211005222,control-enlarged,294.8284,0.08013358,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_40VJPSNfIlSJGAV,rear_nest_trt_C.E,2626,0,linear,standard,10,10,8,8,2,2,0,0,retain,retain,NA,"There was no 3-way interaction between between brood size, experimental treatment and chick sex on tarsus length (p = 0.323), or any other two-way interactions (brood size * treatment: p = 0.389, brood size * chick sex: p= 0.229, treatment * chick sex: p= 0.672). However, as found in the full dataset, there was an effect of experimental treatment (p = 0.001), with a reduced body size in the Enlarged treatment (Table 3), but no effect of body size (p= 0.619).",neg_c,R,R,NA,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_OH,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,rear_nest_trt,home_or_away,NA,NA,NA,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,within-area_movement,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Angasto R_40VJPSNfIlSJGAV,Angasto-1-1-1,1,1,1,-0.07273354,reduced-control,581.6741,0.05334864,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_40VJPSNfIlSJGAV,rear_nest_trt_R.C,3720,0,linear,standard,8,8,6,6,2,2,0,0,retain,retain,NA,"There was no interaction between between brood size and experimental treatment on tarsus length (parametric bootstrap p-value : p = 0.508). However, there was a negative effect of the Enlarged treatment on tarsus length as compared to the Control treatment (Table 1 ; Figure 1 ; p = 0.001), but no effect of body size (Table 1 ; p= 0.088).",neg_c,R,R,NA,R,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_OH,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,NA,NA,NA,day14_measurer,NA,NA,within-area_movement,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Angasto @@ -448,8 +448,8 @@ R_4ZWbwCKuORJbmMx,Antwerp-1-5-1,1,5,1,-1.07,control-enlarged,843.98863,0.0896,id R_4ZWbwCKuORJbmMx,Antwerp-1-5-2,1,5,2,-0.0147,reduced-control,871.332,0.0887,identity,identity,blue tit,1,NA,NA,original variable (transformed prior to analysis [not with a link function in analysis]),NA,day_14_weight,R_4ZWbwCKuORJbmMx,rear_nest_trt_R.C,3720,0,generalised,standard,6,6,2,2,4,4,0,0,retain,retain,NA,Brood size has a significant effect on sibling growth with reduced broods having longer tarsi and heavier bodies compared with controls while chicks in enlarged broods had shorter tarsi and lighter bodies.,neg_q,R version 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,hatch_mom_Ring,NA,NA,NA,NA,hatch_nest_LD,NA,NA,NA,NA,NA,rear_area,rear_Box,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Antwerp R_9FUOSSR4h4s5OlX,Canberra-1-1-1,1,1,1,0.05045,slope,339.37501,0.18504,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),euc_sdlgs0_50cm + euc_sdlgs50cm-2m,euc_sdlgs0_2m,R_9FUOSSR4h4s5OlX,ExoticPerennialGrass_cover,342,0,generalised,standard,5,5,4,4,1,1,0,0,retain,retain,NA,"The results of the analyses do not suggest an association between seedling recruitment and grass cover, irrespective of the grasses geographic origin.",none_c,R (version 3.6.3 (2020-02-29)),R,3.6.3,R,3.6.3,NA,NA,NA,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,NA,NA,ExoticPerennialGrass_cover,NA,NA,NativePerennialGrass_cover,NA,NativePerennialGraminoid_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Canberra R_9GOTiblKFa9C4x3,Capertee-1-1-1,1,1,1,-0.399331,slope,280.22552,0.195949,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_9GOTiblKFa9C4x3,all_exotic_grass,345,0,generalised,standard,11,11,10,10,1,1,0,0,retain,retain,NA,"Overall, the association between seedling recruitment and grass cover was weak and other factors are indicated to be more important for Eucalyptus seedling recruitment. For the initial seedling recruitment (size seedlings 0 – 0.5 m) no statistical clear association with either exotic or annual grass cover was found",none_q,R 4.0.0,R,4.0.0,R,4.0.0,NA,NA,NA,Property,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NativePerennialGrass_cover,NA,NA,NA,BareGround_cover,Litter_cover,NA,Rock_cover,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,annual_precipitation,NA,NA,NA,NA,NA,Th_ppm,NA,NA,NA,NA,all_exotic_grass,NA,NA,NA,NA,NA,NA,NA,all_exotic_herb,native_herb_fern_gram,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Capertee -R_9GOTiblKFa9C4x3,Capertee-2-2-1,2,2,1,-0.236116,slope,262.91434,0.248979,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_9GOTiblKFa9C4x3,all_exotic_grass,345,0,generalised,standard,11,11,10,10,1,1,0,0,retain,retain,NA,"Overall, the association between seedling recruitment and grass cover was weak and other factors are indicated to be more important for Eucalyptus seedling recruitment. later seedling recruitment (size seedlings 0.5 – 2 m) exotic grass cover showed a statistical clear association with decreasing number of seedlings. However, the estimated effects were smaller than for all other statistical clear association found, except distance to Eucalyputs spp. canopy. -The semi-explorative results of other included predictors show that for initial seedling recruitment, the only statistical clear effect was negative association with distance to Eucalyptus spp. canopy, suggesting that at this stage seedling recruitment is largely depend on seed sources rather than other factors. At later seedling recruitment distance to Eucalyptus spp. canopy still shows an negative association, but other abiotic and biotic factors are indicated to become increasingly important such as soil conditions (thorium), litter cover and competition with exotic species (exotic herb and grass cover). +R_9GOTiblKFa9C4x3,Capertee-2-2-1,2,2,1,-0.236116,slope,262.91434,0.248979,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_9GOTiblKFa9C4x3,all_exotic_grass,345,0,generalised,standard,11,11,10,10,1,1,0,0,retain,retain,NA,"Overall, the association between seedling recruitment and grass cover was weak and other factors are indicated to be more important for Eucalyptus seedling recruitment. later seedling recruitment (size seedlings 0.5 – 2 m) exotic grass cover showed a statistical clear association with decreasing number of seedlings. However, the estimated effects were smaller than for all other statistical clear association found, except distance to Eucalyputs spp. canopy. +The semi-explorative results of other included predictors show that for initial seedling recruitment, the only statistical clear effect was negative association with distance to Eucalyptus spp. canopy, suggesting that at this stage seedling recruitment is largely depend on seed sources rather than other factors. At later seedling recruitment distance to Eucalyptus spp. canopy still shows an negative association, but other abiotic and biotic factors are indicated to become increasingly important such as soil conditions (thorium), litter cover and competition with exotic species (exotic herb and grass cover). ",neg_q,R 4.0.0,R,4.0.0,R,4.0.0,NA,NA,NA,Property,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NativePerennialGrass_cover,NA,NA,NA,BareGround_cover,Litter_cover,NA,Rock_cover,NA,Distance_to_Eucalypt_canopy(m),NA,NA,NA,annual_precipitation,NA,NA,NA,NA,NA,Th_ppm,NA,NA,NA,NA,all_exotic_grass,NA,NA,NA,NA,NA,NA,NA,all_exotic_herb,native_herb_fern_gram,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Capertee R_9KB5LL2E99Hqfhn,Cardwell-1-1-1,1,1,1,NA,NA,NA,NA,logit,logit,eucalyptus,0,NA,NA,constructed variable (combining information from two or more original variables),"summed variables euc_sdlgs0_50cm, euc_sdlgs50cm-2m,euc_sdlgs>2m, and then manually converted to presence-absence data where 1 = present, 0 = absent",NA,R_9KB5LL2E99Hqfhn,NA,NA,0,generalised,standard,21,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,exclude,There was little evidence to suggest the presence or abundance of Eucalyptus spp. seedlings was influenced by exotic or native grass cover.,none_c,basic data manipulation - Microsoft Excel; assumption testing - IBM SPSS v25; ANOVA - Primer v6; DISTLM - Primer 6; binomial regression - IBM SPSS v25,Excel,NA,SPSS,25,NA,NA,Season,Property,NA,NA,NA,NA,NA,ExoticAnnualGrass_cover,ExoticAnnualHerb_cover,ExoticPerennialHerb_cover,ExoticPerennialGrass_cover,ExoticShrub_cover,NativePerennialFern_cover,NativePerennialGrass_cover,NativePerennialHerb_cover,NativePerennialGraminoid_cover,NativeShrub_cover,BareGround_cover,Litter_cover,MossLichen_cover,Rock_cover,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),euc_sdlgs0_50cm,euc_sdlgs50cm-2m,euc_sdlgs>2m,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Cardwell R_AzL6RdNTHtPjxzX,Carnarvo-1-1-1,1,1,1,-9.06E-04,slope,341,0.0048042,log,log,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),data$total_seedlings..temp.<- data$euc_sdlgs0_50cm+data$euc_sdlgs50cm.2m+data$euc_sdlgs.2m,euc_sdlgs_all,R_AzL6RdNTHtPjxzX,all_grass,349,0,generalised,standard,2,2,1,1,1,1,0,0,retain,retain,NA,Grass cover does not significantly influence Eucalyptus spp. seedling recruitment,none_c,R version 4.0.0,R,4.0.0,R,4.0.0,NA,NA,NA,Property,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Carnarvo @@ -467,28 +467,28 @@ R_CfUlQXg434XEESd,Arltung-2-2-1,2,2,1,-0.062585417,slope,163.6781411,0.005794606 R_CfUlQXg434XEESd,Arltung-3-3-1,3,3,1,-0.182253296,slope,216.021074,0.015059314,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_CfUlQXg434XEESd,net_rearing_manipulation,2550,0,linear,standard,10,10,3,3,7,7,0,0,retain,retain,NA,"An experimental decrease in sibling competition increased chick growth and decreased chick mortality (presumably because of improved nourishment), whereas experimental increase in sibling competition decreased chick growth and increase chick mortality.",neg_c,R 4.0.2.,R,4.0.2,R,4.0.2,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,hatch_mom_Ring,NA,NA,NA,genetic_dad_ring_(WP_or_EP),NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,NA,NA,NA,NA,rear_nest_OH,NA,NA,NA,net_rearing_manipulation,NA,NA,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,brood_sex_ratio,Arltung R_DoCdsvLclGEF14Z,Armadal-1-1-1,1,1,1,NA,NA,NA,NA,NA,NA,blue tit,0,check,check,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_DoCdsvLclGEF14Z,rear_Cs_at_start_of_rearing,NA,0,linear,standard,16,16,16,16,0,0,0,0,retain,exclude_all,exclude,"Sibling competition seemed to be an important factor, measured both by its statistical significance but also its effect size compared to other measured variables. However, it still only explained a minority of the observed variation in growth, and there are apparently other factors associated with the chick's parents or nest that determine growth more strongly.",neg_q,I performed all analysis in Python 3.6.9. I used pandas version 1.0.5 for initial reading and processing the data and scikit-learn version 0.23.1 for all analysis (which internally relied on NumPy version 1.19.0 and SciPy version 1.5.0).,Python,3.6.9,Python,3.6.9,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,hatch_Area,NA,NA,NA,NA,NA,NA,hatch_nest_LD,hatch_nest_CS,hatch_nest_OH,d0_hatch_nest_brood_size,NA,NA,rear_area,NA,NA,NA,rear_nest_trt,home_or_away,rear_nest_LD,rear_nest_CS,rear_nest_OH,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,number_chicks_fledged_from_rear_nest,NA,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Armadal R_eo0tGxxndcHxDJ7,Ashford-1-1-1,1,1,1,-0.29135,slope,413.85953,0.04679,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_eo0tGxxndcHxDJ7,d14_rear_nest_brood_size,NA,0,linear,standard,7,8,4,5,3,3,1,0,retain,retain,NA,"Chicks raised with larger broods had significantly smaller body weight at 14 days post hatching, relative to chicks raised in smaller broods(F = 38.679, df = 1, 411.7, p < 0.001). With each standard deviation increase in brood size (i.e. 3.25), there is an 0.29 ± 0.05 factor decrease in chick weight. Therefore, increased sibling competition has a negative effect on the growth of nestling blue tits (Cyanistes caeruleus).",neg_c,Data were analysed using R version 4.0.0 (R Development Core Team 2015).,R,4.0.0,R,4.0.0,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,NA,home_or_away,NA,NA,NA,NA,NA,NA,NA,NA,d14_rear_nest_brood_size,NA,NA,NA,NA,day14_measurer,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Ashford -R_eqzPwjXV6eOi2zv,Babinda-2-2-1,2,2,1,-0.385,slope,75.93552,0.0547,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_eqzPwjXV6eOi2zv,rear_Cs_at_start_of_rearing,NA,1,linear,standard,13,14,6,7,7,7,1,0,retain,retain,NA,"Tarsus length at day 14 was negatively affected by the number of siblings present in the nest at start of rearing (mean: -0.090, CI: -0.133 to -0.046), but positively by the number of siblings present in the nest at day 14 (mean: 0.088 CI: 0.028 to 0.148). +R_eqzPwjXV6eOi2zv,Babinda-2-2-1,2,2,1,-0.385,slope,75.93552,0.0547,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_eqzPwjXV6eOi2zv,rear_Cs_at_start_of_rearing,NA,1,linear,standard,13,14,6,7,7,7,1,0,retain,retain,NA,"Tarsus length at day 14 was negatively affected by the number of siblings present in the nest at start of rearing (mean: -0.090, CI: -0.133 to -0.046), but positively by the number of siblings present in the nest at day 14 (mean: 0.088 CI: 0.028 to 0.148). My conclusion is that growth of nestling blue tits seem to be reduced by competition with siblings when very young, and not affected by the number of siblings as eggs. It looks as if growth is promoted by having more siblings present at a later stage, which is the opposite from the effect of competition with siblings when younger. However, it is possible that the number of chicks present at day 14 is confounded with something else affecting their growth not accounted for by the model. In terms of body mass, females seem to be more affected by this positive effect compared to males.",mixed,"The statistical analyses were done in R (R Core Team 2019, version 3.6.2.) and all models were fit using Bayesian Hamiltonian Markov chain Monte Carlo in the rstanarm package (Goodrich et al 2019, version 2.19.2",R,3.6.2,"R, Stan","3.6.2,2.19.2",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,hatch_Area,NA,NA,NA,NA,NA,NA,NA,NA,NA,d0_hatch_nest_brood_size,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,NA,home_or_away,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,net_rearing_manipulation,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,Date_of_day14,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Babinda R_eqzPwjXV6eOi2zv,Babinda-1-1-1,1,1,1,-1.027,slope,56.60666,0.1293875,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_eqzPwjXV6eOi2zv,rear_Cs_at_start_of_rearing,NA,1,linear,standard,13,14,6,7,7,7,1,0,retain,retain,NA,"Body weight at day 14 was also negatively affected by the number of siblings present in the nest at start of rearing (mean: -0.250, CI: -0.342 to -0.153), and positively by the number of siblings present in the nest at day 14 (mean: 0.257, CI: 0.127 to 0.391). My conclusion is that growth of nestling blue tits seem to be reduced by competition with siblings when very young, and not affected by the number of siblings as eggs. It looks as if growth is promoted by having more siblings present at a later stage, which is the opposite from the effect of competition with siblings when younger. However, it is possible that the number of chicks present at day 14 is confounded with something else affecting their growth not accounted for by the model. In terms of body mass, females seem to be more affected by this positive effect compared to males.",mixed,"The statistical analyses were done in R (R Core Team 2019, version 3.6.2.) and all models were fit using Bayesian Hamiltonian Markov chain Monte Carlo in the rstanarm package (Goodrich et al 2019, version 2.19.2).",R,3.6.2,"R, Stan","3.6.2,2.19.2",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,hatch_nest_breed_ID,hatch_Area,NA,NA,NA,NA,NA,NA,NA,NA,NA,d0_hatch_nest_brood_size,NA,rear_nest_breed_ID,rear_area,NA,NA,NA,NA,home_or_away,NA,NA,NA,rear_d0_rear_nest_brood_size,NA,NA,net_rearing_manipulation,rear_Cs_at_start_of_rearing,d14_rear_nest_brood_size,NA,Date_of_day14,NA,NA,NA,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Babinda -R_es2jrrN9CTGwl5D,Balingu-1-1-1,1,1,1,NA,NA,NA,NA,NA,NA,blue tit,NA,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,NA,R_es2jrrN9CTGwl5D,NA,NA,CHECK,CHECK,CHECK,7,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"In conclusion, according to the results obtained in our study, blue tits growth is influenced by competition with siblings as it is evidenced in the enlarged nests. In fact, bigger nestlings are most likely to survive to the first breeding season. We rejected the changes in body mass to be due to genetic characteristics of males with which the female copulated. Although males were heavier with longer tarsi than females, survival to first breeding season is not influenced by sex. This suggests that sex is not related to competition with siblings. Even though weight presented more noticeable changes related to growth, tarsus length supports our analysis as well.",neg_q,"R 4.0.0 +R_es2jrrN9CTGwl5D,Balingu-1-1-1,1,1,1,NA,NA,NA,NA,NA,NA,blue tit,NA,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,NA,R_es2jrrN9CTGwl5D,NA,NA,CHECK,CHECK,CHECK,7,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"In conclusion, according to the results obtained in our study, blue tits growth is influenced by competition with siblings as it is evidenced in the enlarged nests. In fact, bigger nestlings are most likely to survive to the first breeding season. We rejected the changes in body mass to be due to genetic characteristics of males with which the female copulated. Although males were heavier with longer tarsi than females, survival to first breeding season is not influenced by sex. This suggests that sex is not related to competition with siblings. Even though weight presented more noticeable changes related to growth, tarsus length supports our analysis as well.",neg_q,"R 4.0.0 RStudio 1.2.5042",R,4.0.0,R,4.0.0,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,Extra-pair_paternity,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,net_rearing_manipulation,NA,NA,NA,NA,day_14_tarsus_length,day_14_weight,NA,chick_sex_molec,chick_survival_to_first_breed_season,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Balingu R_OHkieloS1B9JsC5,Ballina-1-1-1,1,1,1,-0.1666341,slope,3151.521,0.005495044,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_OHkieloS1B9JsC5,rear_Cs_at_start_of_rearing,3189,1,linear,standard,4,4,2,2,2,2,0,0,retain,retain,exclude,"Despite model poor predictive power, there is evidence for unambiguous, if small, negative impacts of increased competition on Blue Tit chick growth.",neg_c,"Extract from full text description: “I completed all analysis in R v.3.5.3 [1] and R Studio v.1.2.1335 [2]. I used dplyr v.0.8.4 [3], stringr v.1.4.0 [4], and tidybayes v.1.0.4 [5] for data manipulation; ggplot2 v.3.2.1 [6], ggpubr v.0.2 [7], ggridges v.0.5.1 [8], reshape2 v.1.4.3 [9], and scico v.1.1.0 [10] for data visualisation; brms v.2.8.0 [11, 12], and performance v.0.4.5 [13] for modelling and analysis.”",R,3.5.3,R,3.5.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,hatch_mom_Ring,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,home_or_away,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Ballina R_phpZePnRFCxhQFH,Cassilis-1-1-1,1,1,1,0.1374,slope,332.91,0.0316,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_phpZePnRFCxhQFH,ExoticPerennialGrass_cover,349,1,generalised,standard,2,2,1,1,1,1,0,0,retain,retain,NA,"when Eucalyptus seedlings were present, their abundance increased with cover of exotic perennial grass species",pos_q,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,Property,NA,NA,NA,NA,NA,NA,NA,NA,ExoticPerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Cassilis -R_PvSAhRE12PvmEJb,Bargara-3-3-1,3,3,1,NA,NA,55.44391,0.01823188,logit,logit,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,NA,R_PvSAhRE12PvmEJb,NA,NA,0,generalised,standard,8,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"Chicks that hatch earlier in the season and from smaller brood sizes are more likely to come back. This study does not make any difference between 1) chicks dying before and after fledgling or 2) between chicks that did not survive and chicks that survived but went breeding in another area. Therefore, this model is should be interpreted carefully.",NA,"All data processing: - -R version 3.6.1 (2019-07-05) -- ""Action of the Toes"" -Copyright (C) 2019 The R Foundation for Statistical Computing +R_PvSAhRE12PvmEJb,Bargara-3-3-1,3,3,1,NA,NA,55.44391,0.01823188,logit,logit,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,NA,R_PvSAhRE12PvmEJb,NA,NA,0,generalised,standard,8,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"Chicks that hatch earlier in the season and from smaller brood sizes are more likely to come back. This study does not make any difference between 1) chicks dying before and after fledgling or 2) between chicks that did not survive and chicks that survived but went breeding in another area. Therefore, this model is should be interpreted carefully.",NA,"All data processing: + +R version 3.6.1 (2019-07-05) -- ""Action of the Toes"" +Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit)",R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_LD,NA,NA,d0_hatch_nest_brood_size,NA,NA,rear_area,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,day_14_tarsus_length,NA,NA,chick_sex_molec,chick_survival_to_first_breed_season,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bargara -R_PvSAhRE12PvmEJb,Bargara-2-2-1,2,2,1,NA,NA,NA,0.02039768,logit,logit,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,NA,R_PvSAhRE12PvmEJb,NA,NA,0,generalised,standard,5,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"Mostly, the lay date was determinant for the number of fledglings but this may be due to predation pressure changing or parents condition evolving as they breed multiple times over the breeding season.",NA,"All data processing: - -R version 3.6.1 (2019-07-05) -- ""Action of the Toes"" -Copyright (C) 2019 The R Foundation for Statistical Computing +R_PvSAhRE12PvmEJb,Bargara-2-2-1,2,2,1,NA,NA,NA,0.02039768,logit,logit,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,NA,R_PvSAhRE12PvmEJb,NA,NA,0,generalised,standard,5,NA,NA,NA,NA,NA,NA,NA,exclude,exclude_all,NA,"Mostly, the lay date was determinant for the number of fledglings but this may be due to predation pressure changing or parents condition evolving as they breed multiple times over the breeding season.",NA,"All data processing: + +R version 3.6.1 (2019-07-05) -- ""Action of the Toes"" +Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit)",R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,NA,NA,rear_nest_LD,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,number_chicks_fledged_from_rear_nest,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bargara -R_PvSAhRE12PvmEJb,Bargara-1-1-1,1,1,1,-0.06508427,slope,1818.9243,0.018344004,identity,identity,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),"d_14_weight, d_14_tarsus_length were combined to build a mass index which is scaled for each sex separately.",SMI,R_PvSAhRE12PvmEJb,rear_Cs_at_start_of_rearing,NA,0,linear,standard,8,8,6,6,2,2,0,0,retain,retain,NA,"Model 1: Effect of brood size on chick body condition (SMI) -The larger the brood, the lower the Scaled Mass Index -> probably due to parents ability to feed larger broods as efficiently. -Females are in better condition than males (higher Scaled Mass Index -> Could be due to behavioral differences in begging, parents tendency to feed female chicks more or some physiological specificities of the sexes. -",neg_c,"R version 3.6.1 (2019-07-05) -- ""Action of the Toes"" -Copyright (C) 2019 The R Foundation for Statistical Computing +R_PvSAhRE12PvmEJb,Bargara-1-1-1,1,1,1,-0.06508427,slope,1818.9243,0.018344004,identity,identity,blue tit,1,NA,NA,constructed variable (combining information from two or more original variables),"d_14_weight, d_14_tarsus_length were combined to build a mass index which is scaled for each sex separately.",SMI,R_PvSAhRE12PvmEJb,rear_Cs_at_start_of_rearing,NA,0,linear,standard,8,8,6,6,2,2,0,0,retain,retain,NA,"Model 1: Effect of brood size on chick body condition (SMI) +The larger the brood, the lower the Scaled Mass Index -> probably due to parents ability to feed larger broods as efficiently. +Females are in better condition than males (higher Scaled Mass Index -> Could be due to behavioral differences in begging, parents tendency to feed female chicks more or some physiological specificities of the sexes. +",neg_c,"R version 3.6.1 (2019-07-05) -- ""Action of the Toes"" +Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit)",R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_year,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_LD,NA,NA,d0_hatch_nest_brood_size,NA,NA,rear_area,NA,NA,NA,NA,home_or_away,NA,NA,NA,NA,NA,NA,NA,rear_Cs_at_start_of_rearing,NA,NA,NA,NA,NA,day14_measurer,chick_sex_molec,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Bargara R_QhJspbYhGLOQVZD,Barooga-2-2-1,2,2,1,-0.035073,slope,426.2106,0.009129,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_tarsus_length,R_QhJspbYhGLOQVZD,rear_Cs_at_start_of_rearing,3145,0,linear,standard,5,5,1,1,4,4,0,0,retain,retain,NA,"The growth of nestling blue tits is influenced by competition with siblings. The relevant factor is not the absolute number of siblings, but the relative change in brood size compared to the expected brood size. It seems that parents ""decide"" to lay as many eggs as they can comfortably raise (a 'quality' confounder), but having fewer or more siblings respectively decreases or increases the intensity of sibling competition.Every 10% decrease in brood size compared to the number of hatched eggs increases the average tarsus length by 0.06mm. I am not sure why the relevant baseline is clutch size for weight and hatched clutch size for tarsus length; it may have something to do with the precise growth pattern (e.g. lengthening bones first, then putting on weight).",neg_q,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,hatch_mom_Ring,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,relative_CS,envir_rear,NA,NA,NA,NA,NA,NA,Barooga R_QhJspbYhGLOQVZD,Barooga-1-1-1,1,1,1,-1.8656,slope,303.4426,0.1368,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_QhJspbYhGLOQVZD,relative_CS,3145,0,linear,standard,5,5,1,1,4,4,0,0,retain,retain,NA,"The growth of nestling blue tits is influenced by competition with siblings. The relevant factor is not the absolute number of siblings, but the relative change in brood size compared to the expected brood size. It seems that parents ""decide"" to lay as many eggs as they can comfortably raise (a 'quality' confounder), but having fewer or more siblings respectively decreases or increases the intensity of sibling competition. Every 10% decrease in brood size compared to clutch size increases the average weight of nestlings by 0.18 grams.",neg_q,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,hatch_mom_Ring,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,relative_CS,envir_rear,NA,NA,NA,NA,NA,NA,Barooga @@ -517,6 +517,6 @@ R_vojH4E5b8mNOCU9,Charlton-1-1-1,1,1,1,-0.01685,slope,259.7297,0.19136,log,log,e R_x9Fs6DQf26tdSRr,Childers-1-1-1,1,1,1,0.26926,slope,294.39735,0.15161,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs0_50cm,R_x9Fs6DQf26tdSRr,all_exotic_grass,346,0,generalised,standard,6,6,4,4,2,2,0,0,retain,retain,NA,I conclude that grass cover of any type has little effect on 0 - 50 cm Eucalyptus spp. seedling recruitment,none_q,R version 3.6.0,R,3.6.0,R,3.6.0,NA,NA,NA,Property,Quadrat no,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),NA,NA,NA,annual_precipitation,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_exotic_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Childers R_x9Fs6DQf26tdSRr,Childers-2-2-1,2,2,1,0.267,slope,326.95399,0.0679,log,log,eucalyptus,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,euc_sdlgs50cm_2m,R_x9Fs6DQf26tdSRr,NativePerennialGrass_cover,346,0,generalised,standard,6,6,4,4,2,2,0,0,retain,retain,NA,native perennial grass cover has a positive effect on 50 cm - 2 m Eucalyptus spp. seedling recruitment.,pos_c,R version 3.6.0,R,3.6.0,R,3.6.0,NA,NA,NA,Property,Quadrat no,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NativePerennialGrass_cover,NA,NA,NA,NA,NA,NA,NA,Euc_canopy_cover,Distance_to_Eucalypt_canopy(m),NA,NA,NA,annual_precipitation,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Childers R_XQXeN7diZLPsRVv,Chiltern-1-1-1,1,1,1,NA,NA,3.536992,0.5756016,logit,logit,eucalyptus,1,NA,NA,constructed variable (combining information from two or more original variables),"Sum of ""euc_sdlgs0-50cm"", ""euc_sdlgs50cm-2m"", and ""euc_sdlgs>2m""",euc_sdlgs_all,R_XQXeN7diZLPsRVv,all_grass,300,0,generalised,zero_inflated,3,3,2,2,1,1,0,0,retain,exclude_all,exclude,"Three properties showed a positive relationship between grass cover and recruitment. In other words, higher grass cover was correlated with greater recruitment of seedlings across these three properties. However, the other 11 properties showed no directional relationship (95% confidence intervals all crossing zero), nor did the averaged estimate. Therefore, overall, we can conclude that there is weak to no evidence that grass cover has a measurable effect on eucalyptus recruitment across these properties in the Goulburn Broken Catchment, Australia.",none_q,Data cleaning (i.e. removing three properties) occurred in Excel before uploading the database in R. All analyses were conducted in R Version 3.6.3.,Excel,NA,R,3.6.3,NA,NA,NA,Property,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,annual_precipitation,NA,NA,NA,NA,NA,NA,NA,NA,NA,all_grass,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Chiltern -R_yZQkQmoW6cuEO09,Beverle-1-1-1,1,1,1,-1.08,reduced-enlarged,335.4,0.08793,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_yZQkQmoW6cuEO09,rear_nest_trt_R.E,3720,0,linear,standard,3,3,1,1,2,2,0,0,retain,retain,NA,"I conclude that there is some evidence that growth may be influenced by competition with siblings. Larger broods and experimentally enlarged nests were associated with smaller and lighter nestlings on day 14. Furthermore, there was more variation in nestling size and mass on day 14 in nests with experimentally increased brood sizes, which may indicate that some siblings were not able to compete effectively for resources in those broods. Those effects may also underestimate competition, since nestlings were also more likely to die before fledging (or measurement) in enlarged broods. - -However, most differences observed were driven by broods that were enlarged beyond the natural range of variation in brood size and there was less evidence that brood reduction resulted in a release from sibling competition. Therefore, it is somewhat unclear how big of a role sibling competition plays in driving variation in nestling growth under normal conditions and it may only be especially important at larger brood sizes or when resources are especially limited.",neg_q,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Beverle +R_yZQkQmoW6cuEO09,Beverle-1-1-1,1,1,1,-1.08,reduced-enlarged,335.4,0.08793,identity,identity,blue tit,1,NA,NA,"original variable (not transformed prior to analysis - if transformed with link function in analysis, click this option)",NA,day_14_weight,R_yZQkQmoW6cuEO09,rear_nest_trt_R.E,3720,0,linear,standard,3,3,1,1,2,2,0,0,retain,retain,NA,"I conclude that there is some evidence that growth may be influenced by competition with siblings. Larger broods and experimentally enlarged nests were associated with smaller and lighter nestlings on day 14. Furthermore, there was more variation in nestling size and mass on day 14 in nests with experimentally increased brood sizes, which may indicate that some siblings were not able to compete effectively for resources in those broods. Those effects may also underestimate competition, since nestlings were also more likely to die before fledging (or measurement) in enlarged broods. + +However, most differences observed were driven by broods that were enlarged beyond the natural range of variation in brood size and there was less evidence that brood reduction resulted in a release from sibling competition. Therefore, it is somewhat unclear how big of a role sibling competition plays in driving variation in nestling growth under normal conditions and it may only be especially important at larger brood sizes or when resources are especially limited.",neg_q,R 3.6.1,R,3.6.1,R,3.6.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,hatch_nest_breed_ID,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,rear_nest_breed_ID,NA,NA,NA,NA,rear_nest_trt,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Beverle \ No newline at end of file diff --git a/data-raw/create_internal_pkg_data.R b/data-raw/create_internal_pkg_data.R new file mode 100644 index 0000000..8772dc1 --- /dev/null +++ b/data-raw/create_internal_pkg_data.R @@ -0,0 +1,43 @@ +# ------- Create tibble of analysis IDs of analyses with collinear variables ------- + +library(tidyverse) +library(usethis) +library(ManyEcoEvo) + +collinearity_subset <- + tibble::tribble( + ~response_id, ~id_col, ~dataset, + "R_DoCdsvLclGEF14Z", "Armadal-1-1-1", "blue tit", + "R_eqzPwjXV6eOi2zv", "Babinda-1-1-1", "blue tit", + "R_eqzPwjXV6eOi2zv", "Babinda-2-2-1", "blue tit", + "R_2Tzp6JznvkvCY4h", "Barham-1-1-1", "blue tit", + "R_2Tzp6JznvkvCY4h", "Barham-2-2-1", "blue tit", + "R_126erjKKuN3IwSJ", "Bega-1-1-1", "blue tit", + "R_126erjKKuN3IwSJ", "Bega-1-1-2", "blue tit", + "R_126erjKKuN3IwSJ", "Bega-2-2-1", "blue tit", + "R_126erjKKuN3IwSJ", "Bega-2-2-2", "blue tit", + "R_210APF6gYFATf7Y", "Borde-1-1-1", "blue tit", + "R_1dzfML4yheLxG0D", "Bruc-1-1-1", "blue tit", + "R_3lMQ3NmmjrzpbM2", "Caigun-1-1-1", "blue tit", + "R_3lMQ3NmmjrzpbM2", "Caigun-2-2-1", "blue tit", + "R_3rIdpCqsQtsmgqT", "Adelong-1-1-1", "blue tit", + "R_3rIdpCqsQtsmgqT", "Adelong-2-2-1", "blue tit", + ) + +# ---- Make Parameter Tables for Standardising out-of-sample Predictions ---- + +#NOTE: relies on package being built after running `data-raw/osf_load_analyst_datasets.R` +# alternatively, devtools::load_all() is needed to access the fns to build `analysis_data_param_tables` +# devtools::load_all() #TODO + +analysis_data_param_tables <- + bind_rows( + make_param_table(ManyEcoEvo::blue_tit_data) %>% + mutate(dataset = "blue tit"), + make_param_table(ManyEcoEvo::euc_data) %>% + mutate(dataset = "eucalyptus") + ) + +# ------- Write data internally ------- + +usethis::use_data(analysis_data_param_tables, collinearity_subset, internal = TRUE, overwrite = TRUE) diff --git a/data-raw/tar_make.R b/data-raw/tar_make.R index 503ede8..23b69a7 100644 --- a/data-raw/tar_make.R +++ b/data-raw/tar_make.R @@ -18,11 +18,11 @@ tar_load(ManyEcoEvo_viz) tar_load(ManyEcoEvo_yi_viz) usethis::use_data(ManyEcoEvo, - ManyEcoEvo_yi, + ManyEcoEvo_yi, # consider making internal ManyEcoEvo_results, - ManyEcoEvo_yi_results, + ManyEcoEvo_yi_results, #consider making internal ManyEcoEvo_viz, - ManyEcoEvo_yi_viz, + ManyEcoEvo_yi_viz, #TODO consider making internal overwrite = TRUE) # TODO also need to add raw files to demonstrate pipeline / package functionality in package vignette and software manuscript. diff --git a/data/ManyEcoEvo.rda b/data/ManyEcoEvo.rda index 3867035..b4dd3d4 100644 Binary files a/data/ManyEcoEvo.rda and b/data/ManyEcoEvo.rda differ diff --git a/data/ManyEcoEvo_results.rda b/data/ManyEcoEvo_results.rda index 21122bf..6e0d4ec 100644 Binary files a/data/ManyEcoEvo_results.rda and b/data/ManyEcoEvo_results.rda differ diff --git a/data/ManyEcoEvo_viz.rda b/data/ManyEcoEvo_viz.rda index 02851cf..a4071fc 100644 Binary files a/data/ManyEcoEvo_viz.rda and b/data/ManyEcoEvo_viz.rda differ diff --git a/data/ManyEcoEvo_yi_results.rda b/data/ManyEcoEvo_yi_results.rda index bd5bc92..034bf8b 100644 Binary files a/data/ManyEcoEvo_yi_results.rda and b/data/ManyEcoEvo_yi_results.rda differ diff --git a/data/ManyEcoEvo_yi_viz.rda b/data/ManyEcoEvo_yi_viz.rda index 0cba26b..de459e9 100644 Binary files a/data/ManyEcoEvo_yi_viz.rda and b/data/ManyEcoEvo_yi_viz.rda differ diff --git a/man/apply_VZ_exclusions.Rd b/man/apply_VZ_exclusions.Rd index 9dd99eb..5519d13 100644 --- a/man/apply_VZ_exclusions.Rd +++ b/man/apply_VZ_exclusions.Rd @@ -26,10 +26,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, diff --git a/man/compute_MA_inputs.Rd b/man/compute_MA_inputs.Rd index 3b7803f..b9a0826 100644 --- a/man/compute_MA_inputs.Rd +++ b/man/compute_MA_inputs.Rd @@ -31,10 +31,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, diff --git a/man/cube_back.Rd b/man/cube_back.Rd index 65c53ea..bde7f6a 100644 --- a/man/cube_back.Rd +++ b/man/cube_back.Rd @@ -21,8 +21,8 @@ Back transform beta estimates for models with $x^3$-link } \seealso{ Other back transformation: -\code{\link{conversion_2}()}, \code{\link{conversion}()}, +\code{\link{conversion_2}()}, \code{\link{divide_back}()}, \code{\link{identity_back}()}, \code{\link{inverse_back}()}, diff --git a/man/divide_back.Rd b/man/divide_back.Rd index bdbe080..9149587 100644 --- a/man/divide_back.Rd +++ b/man/divide_back.Rd @@ -23,8 +23,8 @@ Back transform beta estimates or out-of-sample predictions from models whose res } \seealso{ Other back transformation: -\code{\link{conversion_2}()}, \code{\link{conversion}()}, +\code{\link{conversion_2}()}, \code{\link{cube_back}()}, \code{\link{identity_back}()}, \code{\link{inverse_back}()}, diff --git a/man/generate_collinearity_subset.Rd b/man/generate_collinearity_subset.Rd new file mode 100644 index 0000000..8ac4957 --- /dev/null +++ b/man/generate_collinearity_subset.Rd @@ -0,0 +1,42 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/generate_collinearity_subset.R +\name{generate_collinearity_subset} +\alias{generate_collinearity_subset} +\title{Generate Collinearity Data Subset} +\usage{ +generate_collinearity_subset(ManyEcoEvo, collinearity_subset) +} +\arguments{ +\item{ManyEcoEvo}{a ManyEcoEvo dataframe containing formatted raw \code{data}, formatted \code{diversity_data}, the \code{estimate_type}, \code{dataset}, \code{publishable_subset}, and \code{exclusion_set}. See details.} + +\item{collinearity_subset}{a dataframe containing the column \code{response_id} containing response ID's to be included in the expert subset} +} +\value{ +A ManyEcoEvo dataframe with added column \code{expertise_subset} with new subsets of \code{data} and \code{diversity_data} +} +\description{ +This function generates a subset of the data that is used to demonstrate the +effects of collinearity on regression models. The data is generated by +sampling from a multivariate normal distribution with a specified correlation +matrix. +} +\details{ +#' + +Note that this function needs to be run on \code{ManyEcoEvo} after the following functions have been run (See examples): +\itemize{ +\item \code{prepare_response_variables()} +\item \code{generate_exclusion_subsets()} +\item \code{generate_rating_subsets()} +} + +\code{generate_collinearity_subset()} only creates expertise subsets based on the full dataset where \code{exclusion_set == "complete"} and \code{publishable_subset == "All"} and \code{expertise_subset == "All"}. +} +\examples{ +ManyEcoEvo \%>\% +prepare_response_variables(estimate_type = "Zr") |> +generate_exclusion_subsets(estimate_type = "Zr") |> +generate_rating_subsets() |> +generate_expertise_subsets(expert_subset) |> +generate_collinearity_subset(collinearity_subset = collinearity_subset) +} diff --git a/man/generate_exclusion_subsets.Rd b/man/generate_exclusion_subsets.Rd index 4e0a7b4..a645d52 100644 --- a/man/generate_exclusion_subsets.Rd +++ b/man/generate_exclusion_subsets.Rd @@ -34,10 +34,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, diff --git a/man/generate_outlier_subsets.Rd b/man/generate_outlier_subsets.Rd index c3acff4..f4811c9 100644 --- a/man/generate_outlier_subsets.Rd +++ b/man/generate_outlier_subsets.Rd @@ -24,10 +24,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, @@ -38,10 +38,10 @@ Other Multi-dataset Wrapper Functions: Other targets-pipeline functions: \code{\link{generate_rating_subsets}()}, \code{\link{make_viz}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{prepare_review_data}()} } \concept{Multi-dataset Wrapper Functions} diff --git a/man/generate_rating_subsets.Rd b/man/generate_rating_subsets.Rd index 7bd5bd6..5e6dded 100644 --- a/man/generate_rating_subsets.Rd +++ b/man/generate_rating_subsets.Rd @@ -24,10 +24,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, @@ -38,10 +38,10 @@ Other Multi-dataset Wrapper Functions: Other targets-pipeline functions: \code{\link{generate_outlier_subsets}()}, \code{\link{make_viz}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{prepare_review_data}()} } \concept{Multi-dataset Wrapper Functions} diff --git a/man/generate_yi_subsets.Rd b/man/generate_yi_subsets.Rd index 3d328f2..5080504 100644 --- a/man/generate_yi_subsets.Rd +++ b/man/generate_yi_subsets.Rd @@ -27,10 +27,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_rating_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, diff --git a/man/identity_back.Rd b/man/identity_back.Rd index 2341d44..97263f0 100644 --- a/man/identity_back.Rd +++ b/man/identity_back.Rd @@ -21,8 +21,8 @@ Back transform beta estimates for models with identity-link } \seealso{ Other back transformation: -\code{\link{conversion_2}()}, \code{\link{conversion}()}, +\code{\link{conversion_2}()}, \code{\link{cube_back}()}, \code{\link{divide_back}()}, \code{\link{inverse_back}()}, diff --git a/man/inverse_back.Rd b/man/inverse_back.Rd index f125c0a..8e6c4ce 100644 --- a/man/inverse_back.Rd +++ b/man/inverse_back.Rd @@ -21,8 +21,8 @@ Back transform beta estimates for models with $1/x$ link } \seealso{ Other back transformation: -\code{\link{conversion_2}()}, \code{\link{conversion}()}, +\code{\link{conversion_2}()}, \code{\link{cube_back}()}, \code{\link{divide_back}()}, \code{\link{identity_back}()}, diff --git a/man/log_back.Rd b/man/log_back.Rd index be2cedf..8782cf8 100644 --- a/man/log_back.Rd +++ b/man/log_back.Rd @@ -21,8 +21,8 @@ Back transform beta estimates for models with log-link } \seealso{ Other back transformation: -\code{\link{conversion_2}()}, \code{\link{conversion}()}, +\code{\link{conversion_2}()}, \code{\link{cube_back}()}, \code{\link{divide_back}()}, \code{\link{identity_back}()}, diff --git a/man/logit_back.Rd b/man/logit_back.Rd index 60bab90..99d600a 100644 --- a/man/logit_back.Rd +++ b/man/logit_back.Rd @@ -21,8 +21,8 @@ Back transform beta estimates for models with logit-link } \seealso{ Other back transformation: -\code{\link{conversion_2}()}, \code{\link{conversion}()}, +\code{\link{conversion_2}()}, \code{\link{cube_back}()}, \code{\link{divide_back}()}, \code{\link{identity_back}()}, diff --git a/man/make_viz.Rd b/man/make_viz.Rd index ed535b9..789e041 100644 --- a/man/make_viz.Rd +++ b/man/make_viz.Rd @@ -19,10 +19,10 @@ Computes model summaries, tidy model summaries, model fit stats, funnel plots an Other targets-pipeline functions: \code{\link{generate_outlier_subsets}()}, \code{\link{generate_rating_subsets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{prepare_review_data}()} Other Multi-dataset Wrapper Functions: @@ -33,10 +33,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_rating_subsets}()}, \code{\link{generate_yi_subsets}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, diff --git a/man/meta_analyse_datasets.Rd b/man/meta_analyse_datasets.Rd index 81e77a4..89a558d 100644 --- a/man/meta_analyse_datasets.Rd +++ b/man/meta_analyse_datasets.Rd @@ -42,10 +42,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_rating_subsets}()}, \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, diff --git a/man/power_back.Rd b/man/power_back.Rd index 45492cd..2bf1178 100644 --- a/man/power_back.Rd +++ b/man/power_back.Rd @@ -23,8 +23,8 @@ Back transform beta estimates for models with power-link } \seealso{ Other back transformation: -\code{\link{conversion_2}()}, \code{\link{conversion}()}, +\code{\link{conversion_2}()}, \code{\link{cube_back}()}, \code{\link{divide_back}()}, \code{\link{identity_back}()}, diff --git a/man/prepare_ManyEcoEvo.Rd b/man/prepare_ManyEcoEvo.Rd index f4d4fae..ffb1ad7 100644 --- a/man/prepare_ManyEcoEvo.Rd +++ b/man/prepare_ManyEcoEvo.Rd @@ -30,8 +30,8 @@ Other Multi-dataset Wrapper Functions: \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, \code{\link{prepare_ManyEcoEvo_yi}()}, -\code{\link{prepare_response_variables_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, @@ -44,8 +44,8 @@ Other targets-pipeline functions: \code{\link{generate_rating_subsets}()}, \code{\link{make_viz}()}, \code{\link{prepare_ManyEcoEvo_yi}()}, -\code{\link{prepare_response_variables_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{prepare_review_data}()} } \concept{Multi-dataset Wrapper Functions} diff --git a/man/prepare_ManyEcoEvo_yi.Rd b/man/prepare_ManyEcoEvo_yi.Rd index aa37c00..4f9ef75 100644 --- a/man/prepare_ManyEcoEvo_yi.Rd +++ b/man/prepare_ManyEcoEvo_yi.Rd @@ -33,8 +33,8 @@ Other targets-pipeline functions: \code{\link{generate_rating_subsets}()}, \code{\link{make_viz}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{prepare_review_data}()} Other Multi-dataset Wrapper Functions: @@ -47,8 +47,8 @@ Other Multi-dataset Wrapper Functions: \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, diff --git a/man/prepare_response_variables.Rd b/man/prepare_response_variables.Rd index f154eb9..ff4d109 100644 --- a/man/prepare_response_variables.Rd +++ b/man/prepare_response_variables.Rd @@ -31,8 +31,8 @@ Other targets-pipeline functions: \code{\link{generate_outlier_subsets}()}, \code{\link{generate_rating_subsets}()}, \code{\link{make_viz}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables_yi}()}, \code{\link{prepare_review_data}()} @@ -45,8 +45,8 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, diff --git a/man/prepare_response_variables_yi.Rd b/man/prepare_response_variables_yi.Rd index ce710f7..cac4761 100644 --- a/man/prepare_response_variables_yi.Rd +++ b/man/prepare_response_variables_yi.Rd @@ -31,8 +31,8 @@ Other targets-pipeline functions: \code{\link{generate_outlier_subsets}()}, \code{\link{generate_rating_subsets}()}, \code{\link{make_viz}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, \code{\link{prepare_review_data}()} @@ -45,8 +45,8 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, diff --git a/man/prepare_review_data.Rd b/man/prepare_review_data.Rd index adc1820..34913a0 100644 --- a/man/prepare_review_data.Rd +++ b/man/prepare_review_data.Rd @@ -22,9 +22,9 @@ Other targets-pipeline functions: \code{\link{generate_outlier_subsets}()}, \code{\link{generate_rating_subsets}()}, \code{\link{make_viz}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, -\code{\link{prepare_response_variables}()} +\code{\link{prepare_ManyEcoEvo_yi}()}, +\code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()} } \concept{targets-pipeline functions} diff --git a/man/probit_back.Rd b/man/probit_back.Rd index 0f364fa..8f12ba9 100644 --- a/man/probit_back.Rd +++ b/man/probit_back.Rd @@ -21,8 +21,8 @@ Back transform beta estimates for models with probit-link } \seealso{ Other back transformation: -\code{\link{conversion_2}()}, \code{\link{conversion}()}, +\code{\link{conversion_2}()}, \code{\link{cube_back}()}, \code{\link{divide_back}()}, \code{\link{identity_back}()}, diff --git a/man/square_back.Rd b/man/square_back.Rd index fc32f72..f0d7f50 100644 --- a/man/square_back.Rd +++ b/man/square_back.Rd @@ -21,8 +21,8 @@ Back transform beta estimates for models with $x^2$-link } \seealso{ Other back transformation: -\code{\link{conversion_2}()}, \code{\link{conversion}()}, +\code{\link{conversion_2}()}, \code{\link{cube_back}()}, \code{\link{divide_back}()}, \code{\link{identity_back}()}, diff --git a/man/square_root_back.Rd b/man/square_root_back.Rd index bf8595d..c2ea0f5 100644 --- a/man/square_root_back.Rd +++ b/man/square_root_back.Rd @@ -21,8 +21,8 @@ Back transform beta estimates or out-of-sample predictions from models whose res } \seealso{ Other back transformation: -\code{\link{conversion_2}()}, \code{\link{conversion}()}, +\code{\link{conversion_2}()}, \code{\link{cube_back}()}, \code{\link{divide_back}()}, \code{\link{identity_back}()}, diff --git a/man/summarise_analysis_types.Rd b/man/summarise_analysis_types.Rd index f8b8b80..4979ec4 100644 --- a/man/summarise_analysis_types.Rd +++ b/man/summarise_analysis_types.Rd @@ -35,10 +35,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, \code{\link{summarise_reviews}()}, diff --git a/man/summarise_conclusions.Rd b/man/summarise_conclusions.Rd index 6f3539f..83a3805 100644 --- a/man/summarise_conclusions.Rd +++ b/man/summarise_conclusions.Rd @@ -35,10 +35,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_model_composition}()}, \code{\link{summarise_reviews}()}, diff --git a/man/summarise_model_composition.Rd b/man/summarise_model_composition.Rd index f72f8c2..1ce89d4 100644 --- a/man/summarise_model_composition.Rd +++ b/man/summarise_model_composition.Rd @@ -39,10 +39,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_reviews}()}, diff --git a/man/summarise_reviews.Rd b/man/summarise_reviews.Rd index 73365a8..bd9e6bb 100644 --- a/man/summarise_reviews.Rd +++ b/man/summarise_reviews.Rd @@ -32,10 +32,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, diff --git a/man/summarise_sorensen_index.Rd b/man/summarise_sorensen_index.Rd index 4303471..f10f17e 100644 --- a/man/summarise_sorensen_index.Rd +++ b/man/summarise_sorensen_index.Rd @@ -33,10 +33,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, diff --git a/man/summarise_variable_counts.Rd b/man/summarise_variable_counts.Rd index ad65cb9..8c87631 100644 --- a/man/summarise_variable_counts.Rd +++ b/man/summarise_variable_counts.Rd @@ -44,10 +44,10 @@ Other Multi-dataset Wrapper Functions: \code{\link{generate_yi_subsets}()}, \code{\link{make_viz}()}, \code{\link{meta_analyse_datasets}()}, -\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_ManyEcoEvo}()}, -\code{\link{prepare_response_variables_yi}()}, +\code{\link{prepare_ManyEcoEvo_yi}()}, \code{\link{prepare_response_variables}()}, +\code{\link{prepare_response_variables_yi}()}, \code{\link{summarise_analysis_types}()}, \code{\link{summarise_conclusions}()}, \code{\link{summarise_model_composition}()}, diff --git a/renv.lock b/renv.lock index 0ad97cb..b68b947 100644 --- a/renv.lock +++ b/renv.lock @@ -14,13 +14,6 @@ "Version": "1.84.0-0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "BH", - "RemoteRef": "BH", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.84.0-0", "Hash": "a8235afbcd6316e6e91433ea47661013" }, "DBI": { @@ -28,13 +21,6 @@ "Version": "1.2.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "DBI", - "RemoteRef": "DBI", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.2", "Requirements": [ "R", "methods" @@ -46,18 +32,24 @@ "Version": "1.1-3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "DEoptimR", - "RemoteRef": "DEoptimR", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1-3", "Requirements": [ "stats" ], "Hash": "72f87e0092e39384aee16df8d67d7410" }, + "EnvStats": { + "Package": "EnvStats", + "Version": "2.8.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "MASS", + "R", + "ggplot2", + "nortest" + ], + "Hash": "1b55a740dea99c9d226e75acc2c0a85e" + }, "KernSmooth": { "Package": "KernSmooth", "Version": "2.23-22", @@ -106,13 +98,6 @@ "Version": "0.5-3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "MatrixModels", - "RemoteRef": "MatrixModels", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.5-3", "Requirements": [ "Matrix", "R", @@ -126,13 +111,6 @@ "Version": "2.5.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "R6", - "RemoteRef": "R6", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.5.1", "Requirements": [ "R" ], @@ -143,13 +121,6 @@ "Version": "1.1-3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "RColorBrewer", - "RemoteRef": "RColorBrewer", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1-3", "Requirements": [ "R" ], @@ -160,13 +131,6 @@ "Version": "1.0.12", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "Rcpp", - "RemoteRef": "Rcpp", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.12", "Requirements": [ "methods", "utils" @@ -178,13 +142,6 @@ "Version": "0.12.8.3.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "RcppArmadillo", - "RemoteRef": "RcppArmadillo", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.12.8.3.0", "Requirements": [ "R", "Rcpp", @@ -199,13 +156,6 @@ "Version": "0.3.4.0.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "RcppEigen", - "RemoteRef": "RcppEigen", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.4.0.0", "Requirements": [ "R", "Rcpp", @@ -219,13 +169,6 @@ "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "RcppProgress", - "RemoteRef": "RcppProgress", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.2", "Hash": "1c0aa18b97e6aaa17f93b8b866c0ace5" }, "RcppRoll": { @@ -233,13 +176,6 @@ "Version": "0.3.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "RcppRoll", - "RemoteRef": "RcppRoll", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.0", "Requirements": [ "R", "Rcpp" @@ -251,13 +187,6 @@ "Version": "2021.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "SQUAREM", - "RemoteRef": "SQUAREM", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2021.1", "Requirements": [ "R" ], @@ -268,13 +197,6 @@ "Version": "1.81", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "SparseM", - "RemoteRef": "SparseM", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.81", "Requirements": [ "R", "graphics", @@ -289,13 +211,6 @@ "Version": "0.24.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "TTR", - "RemoteRef": "TTR", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.24.4", "Requirements": [ "curl", "xts", @@ -308,13 +223,6 @@ "Version": "1.4.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "UpSetR", - "RemoteRef": "UpSetR", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4.0", "Requirements": [ "R", "ggplot2", @@ -333,13 +241,6 @@ "Version": "4.4.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "V8", - "RemoteRef": "V8", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "4.4.2", "Requirements": [ "Rcpp", "curl", @@ -353,13 +254,6 @@ "Version": "1.4-5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "abind", - "RemoteRef": "abind", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4-5", "Requirements": [ "R", "methods", @@ -372,13 +266,6 @@ "Version": "0.3.9", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "anytime", - "RemoteRef": "anytime", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.9", "Requirements": [ "BH", "R", @@ -391,13 +278,6 @@ "Version": "5.8", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ape", - "RemoteRef": "ape", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "5.8", "Requirements": [ "R", "Rcpp", @@ -417,13 +297,6 @@ "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "askpass", - "RemoteRef": "askpass", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.0", "Requirements": [ "sys" ], @@ -434,13 +307,6 @@ "Version": "1.5.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "backports", - "RemoteRef": "backports", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.5.0", "Requirements": [ "R" ], @@ -451,13 +317,6 @@ "Version": "0.1-3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "base64enc", - "RemoteRef": "base64enc", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.1-3", "Requirements": [ "R" ], @@ -468,13 +327,6 @@ "Version": "1.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "base64url", - "RemoteRef": "base64url", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4", "Requirements": [ "backports" ], @@ -485,13 +337,6 @@ "Version": "0.13.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "bayestestR", - "RemoteRef": "bayestestR", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.13.2", "Requirements": [ "R", "datawizard", @@ -508,13 +353,6 @@ "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "beeswarm", - "RemoteRef": "beeswarm", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.0", "Requirements": [ "grDevices", "graphics", @@ -528,13 +366,6 @@ "Version": "1.6", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "betapart", - "RemoteRef": "betapart", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.6", "Requirements": [ "ape", "doSNOW", @@ -554,13 +385,6 @@ "Version": "0.2.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "bigD", - "RemoteRef": "bigD", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.2.0", "Requirements": [ "R" ], @@ -571,13 +395,6 @@ "Version": "4.0.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "bit", - "RemoteRef": "bit", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "4.0.5", "Requirements": [ "R" ], @@ -588,13 +405,6 @@ "Version": "4.0.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "bit64", - "RemoteRef": "bit64", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "4.0.5", "Requirements": [ "R", "bit", @@ -609,13 +419,6 @@ "Version": "1.0-7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "bitops", - "RemoteRef": "bitops", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0-7", "Hash": "b7d8d8ee39869c18d8846a184dd8a1af" }, "blastula": { @@ -623,13 +426,6 @@ "Version": "0.3.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "blastula", - "RemoteRef": "blastula", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.5", "Requirements": [ "R", "base64enc", @@ -657,13 +453,6 @@ "Version": "1.2.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "blob", - "RemoteRef": "blob", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.4", "Requirements": [ "methods", "rlang", @@ -695,13 +484,6 @@ "Version": "1.1.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "brio", - "RemoteRef": "brio", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.5", "Requirements": [ "R" ], @@ -712,13 +494,6 @@ "Version": "1.0.6", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "broom", - "RemoteRef": "broom", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.6", "Requirements": [ "R", "backports", @@ -739,13 +514,6 @@ "Version": "0.2.9.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "broom.mixed", - "RemoteRef": "broom.mixed", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.2.9.5", "Requirements": [ "broom", "coda", @@ -766,13 +534,6 @@ "Version": "0.7.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "bslib", - "RemoteRef": "bslib", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.7.0", "Requirements": [ "R", "base64enc", @@ -795,13 +556,6 @@ "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "cachem", - "RemoteRef": "cachem", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.0", "Requirements": [ "fastmap", "rlang" @@ -813,13 +567,6 @@ "Version": "3.7.6", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "callr", - "RemoteRef": "callr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.7.6", "Requirements": [ "R", "R6", @@ -833,13 +580,6 @@ "Version": "3.1-2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "car", - "RemoteRef": "car", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.1-2", "Requirements": [ "MASS", "R", @@ -864,13 +604,6 @@ "Version": "3.0-5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "carData", - "RemoteRef": "carData", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.0-5", "Requirements": [ "R" ], @@ -881,13 +614,6 @@ "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "cellranger", - "RemoteRef": "cellranger", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.0", "Requirements": [ "R", "rematch", @@ -913,13 +639,6 @@ "Version": "3.6.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "cli", - "RemoteRef": "cli", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.6.2", "Requirements": [ "R", "utils" @@ -931,13 +650,6 @@ "Version": "0.8.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "clipr", - "RemoteRef": "clipr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.8.0", "Requirements": [ "utils" ], @@ -948,13 +660,6 @@ "Version": "0.7.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "clock", - "RemoteRef": "clock", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.7.0", "Requirements": [ "R", "cli", @@ -985,13 +690,6 @@ "Version": "0.19-4.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "coda", - "RemoteRef": "coda", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.19-4.1", "Requirements": [ "R", "lattice" @@ -1013,13 +711,6 @@ "Version": "2.1-0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "colorspace", - "RemoteRef": "colorspace", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.1-0", "Requirements": [ "R", "grDevices", @@ -1034,13 +725,6 @@ "Version": "1.9.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "commonmark", - "RemoteRef": "commonmark", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.9.1", "Hash": "5d8225445acb167abf7797de48b2ee3c" }, "conflicted": { @@ -1048,13 +732,6 @@ "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "conflicted", - "RemoteRef": "conflicted", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.0", "Requirements": [ "R", "cli", @@ -1063,18 +740,27 @@ ], "Hash": "bb097fccb22d156624fd07cd2894ddb6" }, + "correlation": { + "Package": "correlation", + "Version": "0.8.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "bayestestR", + "datasets", + "datawizard", + "insight", + "parameters", + "stats" + ], + "Hash": "d8bd29a9abda6eed9aaab3ba5769f231" + }, "corrplot": { "Package": "corrplot", "Version": "0.92", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "corrplot", - "RemoteRef": "corrplot", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.92", "Hash": "fcf11a91936fd5047b2ee9bc00595e36" }, "cowplot": { @@ -1082,13 +768,6 @@ "Version": "1.1.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "cowplot", - "RemoteRef": "cowplot", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.3", "Requirements": [ "R", "ggplot2", @@ -1106,13 +785,6 @@ "Version": "0.4.7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "cpp11", - "RemoteRef": "cpp11", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.7", "Requirements": [ "R" ], @@ -1123,13 +795,6 @@ "Version": "1.5.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "crayon", - "RemoteRef": "crayon", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.5.2", "Requirements": [ "grDevices", "methods", @@ -1142,13 +807,6 @@ "Version": "2.0.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "credentials", - "RemoteRef": "credentials", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.1", "Requirements": [ "askpass", "curl", @@ -1163,13 +821,6 @@ "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "crosstalk", - "RemoteRef": "crosstalk", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.1", "Requirements": [ "R6", "htmltools", @@ -1183,13 +834,6 @@ "Version": "1.4.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "crul", - "RemoteRef": "crul", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4.2", "Requirements": [ "R6", "curl", @@ -1205,13 +849,6 @@ "Version": "5.2.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "curl", - "RemoteRef": "curl", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "5.2.1", "Requirements": [ "R" ], @@ -1222,13 +859,6 @@ "Version": "1.15.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "data.table", - "RemoteRef": "data.table", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.15.4", "Requirements": [ "R", "methods" @@ -1240,13 +870,6 @@ "Version": "0.10.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "datawizard", - "RemoteRef": "datawizard", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.10.0", "Requirements": [ "R", "insight", @@ -1260,13 +883,6 @@ "Version": "2.5.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "dbplyr", - "RemoteRef": "dbplyr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.5.0", "Requirements": [ "DBI", "R", @@ -1295,13 +911,6 @@ "Version": "1.4.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "desc", - "RemoteRef": "desc", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4.3", "Requirements": [ "R", "R6", @@ -1349,13 +958,6 @@ "Version": "1.6.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "diagram", - "RemoteRef": "diagram", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.6.5", "Requirements": [ "R", "graphics", @@ -1369,13 +971,6 @@ "Version": "0.3.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "diffobj", - "RemoteRef": "diffobj", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.5", "Requirements": [ "R", "crayon", @@ -1391,13 +986,6 @@ "Version": "0.6.35", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "digest", - "RemoteRef": "digest", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.6.35", "Requirements": [ "R", "utils" @@ -1409,13 +997,6 @@ "Version": "0.77-1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "diptest", - "RemoteRef": "diptest", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.77-1", "Requirements": [ "graphics", "stats" @@ -1427,13 +1008,6 @@ "Version": "1.0.20", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "doSNOW", - "RemoteRef": "doSNOW", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.20", "Requirements": [ "R", "foreach", @@ -1448,13 +1022,6 @@ "Version": "0.4.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "downlit", - "RemoteRef": "downlit", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.3", "Requirements": [ "R", "brio", @@ -1475,13 +1042,6 @@ "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "dplyr", - "RemoteRef": "dplyr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.4", "Requirements": [ "R", "R6", @@ -1505,13 +1065,6 @@ "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "dtplyr", - "RemoteRef": "dtplyr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3.1", "Requirements": [ "R", "cli", @@ -1526,18 +1079,28 @@ ], "Hash": "54ed3ea01b11e81a86544faaecfef8e2" }, + "effectsize": { + "Package": "effectsize", + "Version": "0.8.8", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "bayestestR", + "datawizard", + "insight", + "parameters", + "performance", + "stats", + "utils" + ], + "Hash": "6709e156cf7869d95d8fd6e365337d2c" + }, "ellipsis": { "Package": "ellipsis", "Version": "0.3.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ellipsis", - "RemoteRef": "ellipsis", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.2", "Requirements": [ "R", "rlang" @@ -1549,13 +1112,6 @@ "Version": "1.10.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "emmeans", - "RemoteRef": "emmeans", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.10.2", "Requirements": [ "R", "estimability", @@ -1573,13 +1129,6 @@ "Version": "1.5.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "estimability", - "RemoteRef": "estimability", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.5.1", "Requirements": [ "R", "stats" @@ -1591,13 +1140,6 @@ "Version": "0.23", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "evaluate", - "RemoteRef": "evaluate", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.23", "Requirements": [ "R", "methods" @@ -1609,13 +1151,6 @@ "Version": "1.0.6", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "fansi", - "RemoteRef": "fansi", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.6", "Requirements": [ "R", "grDevices", @@ -1628,13 +1163,6 @@ "Version": "2.1.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "farver", - "RemoteRef": "farver", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.1.2", "Hash": "680887028577f3fa2a81e410ed0d6e42" }, "fastmap": { @@ -1642,13 +1170,6 @@ "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "fastmap", - "RemoteRef": "fastmap", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.0", "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, "fastmatch": { @@ -1656,13 +1177,6 @@ "Version": "1.1-4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "fastmatch", - "RemoteRef": "fastmatch", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1-4", "Requirements": [ "R" ], @@ -1673,13 +1187,6 @@ "Version": "2.3-19", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "flexmix", - "RemoteRef": "flexmix", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.3-19", "Requirements": [ "R", "grDevices", @@ -1700,13 +1207,6 @@ "Version": "0.5.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "fontawesome", - "RemoteRef": "fontawesome", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.5.2", "Requirements": [ "R", "htmltools", @@ -1719,13 +1219,6 @@ "Version": "1.0.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "forcats", - "RemoteRef": "forcats", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.0", "Requirements": [ "R", "cli", @@ -1742,13 +1235,6 @@ "Version": "1.5.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "foreach", - "RemoteRef": "foreach", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.5.2", "Requirements": [ "R", "codetools", @@ -1762,13 +1248,6 @@ "Version": "8.22.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "forecast", - "RemoteRef": "forecast", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "8.22.0", "Requirements": [ "R", "Rcpp", @@ -1795,13 +1274,6 @@ "Version": "2.2-12", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "fpc", - "RemoteRef": "fpc", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.2-12", "Requirements": [ "MASS", "R", @@ -1827,13 +1299,6 @@ "Version": "1.5-3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "fracdiff", - "RemoteRef": "fracdiff", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.5-3", "Requirements": [ "stats" ], @@ -1844,13 +1309,6 @@ "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "fs", - "RemoteRef": "fs", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.6.4", "Requirements": [ "R", "methods" @@ -1862,13 +1320,6 @@ "Version": "0.3.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "furrr", - "RemoteRef": "furrr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.1", "Requirements": [ "R", "future", @@ -1885,13 +1336,6 @@ "Version": "1.33.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "future", - "RemoteRef": "future", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.33.2", "Requirements": [ "digest", "globals", @@ -1907,13 +1351,6 @@ "Version": "1.11.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "future.apply", - "RemoteRef": "future.apply", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.11.2", "Requirements": [ "R", "future", @@ -1928,13 +1365,6 @@ "Version": "1.5.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "gargle", - "RemoteRef": "gargle", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.5.2", "Requirements": [ "R", "cli", @@ -1957,13 +1387,6 @@ "Version": "0.1.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "generics", - "RemoteRef": "generics", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.1.3", "Requirements": [ "R", "methods" @@ -1975,13 +1398,6 @@ "Version": "0.4.7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "geometry", - "RemoteRef": "geometry", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.7", "Requirements": [ "R", "Rcpp", @@ -1997,13 +1413,6 @@ "Version": "2.0.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "gert", - "RemoteRef": "gert", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.1", "Requirements": [ "askpass", "credentials", @@ -2019,13 +1428,6 @@ "Version": "0.2-4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "getPass", - "RemoteRef": "getPass", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.2-4", "Requirements": [ "R", "rstudioapi", @@ -2038,13 +1440,6 @@ "Version": "0.7.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ggbeeswarm", - "RemoteRef": "ggbeeswarm", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.7.2", "Requirements": [ "R", "beeswarm", @@ -2060,13 +1455,6 @@ "Version": "1.6.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ggeffects", - "RemoteRef": "ggeffects", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.6.0", "Requirements": [ "R", "graphics", @@ -2081,13 +1469,6 @@ "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ggforce", - "RemoteRef": "ggforce", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.2", "Requirements": [ "MASS", "R", @@ -2152,13 +1533,6 @@ "Version": "3.5.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ggplot2", - "RemoteRef": "ggplot2", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.5.1", "Requirements": [ "MASS", "R", @@ -2184,13 +1558,6 @@ "Version": "0.1.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ggplotify", - "RemoteRef": "ggplotify", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.1.2", "Requirements": [ "R", "ggplot2", @@ -2207,13 +1574,6 @@ "Version": "0.6.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ggpubr", - "RemoteRef": "ggpubr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.6.0", "Requirements": [ "R", "cowplot", @@ -2243,13 +1603,6 @@ "Version": "0.9.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ggrepel", - "RemoteRef": "ggrepel", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.9.5", "Requirements": [ "R", "Rcpp", @@ -2266,13 +1619,6 @@ "Version": "3.1.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ggsci", - "RemoteRef": "ggsci", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.1.0", "Requirements": [ "R", "ggplot2", @@ -2286,13 +1632,6 @@ "Version": "0.6.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ggsignif", - "RemoteRef": "ggsignif", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.6.4", "Requirements": [ "ggplot2" ], @@ -2303,13 +1642,6 @@ "Version": "0.3.7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ggstance", - "RemoteRef": "ggstance", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.7", "Requirements": [ "R", "cli", @@ -2325,13 +1657,6 @@ "Version": "1.4.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "gh", - "RemoteRef": "gh", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4.1", "Requirements": [ "R", "cli", @@ -2350,13 +1675,6 @@ "Version": "0.1.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "gitcreds", - "RemoteRef": "gitcreds", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.1.2", "Requirements": [ "R" ], @@ -2367,13 +1685,6 @@ "Version": "0.16.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "globals", - "RemoteRef": "globals", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.16.3", "Requirements": [ "R", "codetools" @@ -2385,13 +1696,6 @@ "Version": "1.7.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "glue", - "RemoteRef": "glue", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.7.0", "Requirements": [ "R", "methods" @@ -2403,13 +1707,6 @@ "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "googledrive", - "RemoteRef": "googledrive", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.1.1", "Requirements": [ "R", "cli", @@ -2435,13 +1732,6 @@ "Version": "1.1.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "googlesheets4", - "RemoteRef": "googlesheets4", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.1", "Requirements": [ "R", "cellranger", @@ -2470,13 +1760,6 @@ "Version": "1.0.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "gower", - "RemoteRef": "gower", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.1", "Hash": "7a0051eef852c301b5efe2f7913dd45f" }, "gridExtra": { @@ -2484,13 +1767,6 @@ "Version": "2.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "gridExtra", - "RemoteRef": "gridExtra", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.3", "Requirements": [ "grDevices", "graphics", @@ -2505,13 +1781,6 @@ "Version": "0.5-1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "gridGraphics", - "RemoteRef": "gridGraphics", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.5-1", "Requirements": [ "grDevices", "graphics", @@ -2524,13 +1793,6 @@ "Version": "0.10.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "gt", - "RemoteRef": "gt", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.10.1", "Requirements": [ "R", "base64enc", @@ -2561,13 +1823,6 @@ "Version": "0.3.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "gtable", - "RemoteRef": "gtable", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.5", "Requirements": [ "R", "cli", @@ -2583,13 +1838,6 @@ "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "hardhat", - "RemoteRef": "hardhat", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3.1", "Requirements": [ "R", "cli", @@ -2605,13 +1853,6 @@ "Version": "2.5.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "haven", - "RemoteRef": "haven", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.5.4", "Requirements": [ "R", "cli", @@ -2633,13 +1874,6 @@ "Version": "1.0.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "here", - "RemoteRef": "here", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.1", "Requirements": [ "rprojroot" ], @@ -2650,13 +1884,6 @@ "Version": "0.10", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "highr", - "RemoteRef": "highr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.10", "Requirements": [ "R", "xfun" @@ -2668,13 +1895,6 @@ "Version": "1.1.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "hms", - "RemoteRef": "hms", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.3", "Requirements": [ "lifecycle", "methods", @@ -2689,13 +1909,6 @@ "Version": "0.5.8.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "htmltools", - "RemoteRef": "htmltools", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.5.8.1", "Requirements": [ "R", "base64enc", @@ -2712,13 +1925,6 @@ "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "htmlwidgets", - "RemoteRef": "htmlwidgets", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.6.4", "Requirements": [ "grDevices", "htmltools", @@ -2734,13 +1940,6 @@ "Version": "0.3.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "httpcode", - "RemoteRef": "httpcode", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.0", "Hash": "13641a1c6d2cc98801b76764078e17ea" }, "httpuv": { @@ -2763,13 +1962,6 @@ "Version": "1.4.7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "httr", - "RemoteRef": "httr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4.7", "Requirements": [ "R", "R6", @@ -2785,13 +1977,6 @@ "Version": "1.0.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "httr2", - "RemoteRef": "httr2", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.1", "Requirements": [ "R", "R6", @@ -2813,13 +1998,6 @@ "Version": "1.0.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ids", - "RemoteRef": "ids", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.1", "Requirements": [ "openssl", "uuid" @@ -2831,13 +2009,6 @@ "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "igraph", - "RemoteRef": "igraph", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.3", "Requirements": [ "Matrix", "R", @@ -2861,13 +2032,6 @@ "Version": "0.3.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ini", - "RemoteRef": "ini", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.1", "Hash": "6154ec2223172bce8162d4153cda21f7" }, "insight": { @@ -2875,13 +2039,6 @@ "Version": "0.19.11", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "insight", - "RemoteRef": "insight", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.19.11", "Requirements": [ "R", "methods", @@ -2895,13 +2052,6 @@ "Version": "0.9-14", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ipred", - "RemoteRef": "ipred", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.9-14", "Requirements": [ "MASS", "R", @@ -2918,13 +2068,6 @@ "Version": "0.2.7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "isoband", - "RemoteRef": "isoband", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.2.7", "Requirements": [ "grid", "utils" @@ -2936,13 +2079,6 @@ "Version": "1.0.14", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "iterators", - "RemoteRef": "iterators", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.14", "Requirements": [ "R", "utils" @@ -2954,13 +2090,6 @@ "Version": "0.1-3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "itertools", - "RemoteRef": "itertools", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.1-3", "Requirements": [ "R", "iterators", @@ -2973,13 +2102,6 @@ "Version": "0.1.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "jquerylib", - "RemoteRef": "jquerylib", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.1.4", "Requirements": [ "htmltools" ], @@ -2990,13 +2112,6 @@ "Version": "1.8.8", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "jsonlite", - "RemoteRef": "jsonlite", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.8.8", "Requirements": [ "methods" ], @@ -3007,13 +2122,6 @@ "Version": "0.1.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "juicyjuice", - "RemoteRef": "juicyjuice", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.1.0", "Requirements": [ "V8" ], @@ -3024,13 +2132,6 @@ "Version": "0.9-32", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "kernlab", - "RemoteRef": "kernlab", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.9-32", "Requirements": [ "R", "grDevices", @@ -3045,13 +2146,6 @@ "Version": "1.46", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "knitr", - "RemoteRef": "knitr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.46", "Requirements": [ "R", "evaluate", @@ -3068,13 +2162,6 @@ "Version": "0.4.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "labeling", - "RemoteRef": "labeling", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.3", "Requirements": [ "graphics", "stats" @@ -3086,13 +2173,6 @@ "Version": "1.3.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "later", - "RemoteRef": "later", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3.2", "Requirements": [ "Rcpp", "rlang" @@ -3104,13 +2184,6 @@ "Version": "0.9.6", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "latex2exp", - "RemoteRef": "latex2exp", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.9.6", "Requirements": [ "magrittr", "stringr" @@ -3137,13 +2210,6 @@ "Version": "1.8.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "lava", - "RemoteRef": "lava", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.8.0", "Requirements": [ "R", "SQUAREM", @@ -3165,13 +2231,6 @@ "Version": "0.2.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "lazyeval", - "RemoteRef": "lazyeval", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.2.2", "Requirements": [ "R" ], @@ -3182,13 +2241,6 @@ "Version": "1.0.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "lifecycle", - "RemoteRef": "lifecycle", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.4", "Requirements": [ "R", "cli", @@ -3202,13 +2254,6 @@ "Version": "0.9-4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "linprog", - "RemoteRef": "linprog", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.9-4", "Requirements": [ "R", "lpSolve" @@ -3220,13 +2265,6 @@ "Version": "0.9.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "listenv", - "RemoteRef": "listenv", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.9.1", "Requirements": [ "R" ], @@ -3237,13 +2275,6 @@ "Version": "1.1-35.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "lme4", - "RemoteRef": "lme4", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1-35.3", "Requirements": [ "MASS", "Matrix", @@ -3270,13 +2301,6 @@ "Version": "0.9-40", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "lmtest", - "RemoteRef": "lmtest", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.9-40", "Requirements": [ "R", "graphics", @@ -3290,13 +2314,6 @@ "Version": "5.6.20", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "lpSolve", - "RemoteRef": "lpSolve", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "5.6.20", "Hash": "2801c8082e89ed84cc0dbe43de850d31" }, "lubridate": { @@ -3304,13 +2321,6 @@ "Version": "1.9.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "lubridate", - "RemoteRef": "lubridate", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.9.3", "Requirements": [ "R", "generics", @@ -3324,13 +2334,6 @@ "Version": "1.6-1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "magic", - "RemoteRef": "magic", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.6-1", "Requirements": [ "R", "abind" @@ -3342,13 +2345,6 @@ "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "magrittr", - "RemoteRef": "magrittr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.3", "Requirements": [ "R" ], @@ -3359,13 +2355,6 @@ "Version": "1.12", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "markdown", - "RemoteRef": "markdown", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.12", "Requirements": [ "R", "commonmark", @@ -3379,13 +2368,6 @@ "Version": "1.6-0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "mathjaxr", - "RemoteRef": "mathjaxr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.6-0", "Hash": "87da6ccdcee6077a7d5719406bf3ae45" }, "mclust": { @@ -3393,13 +2375,6 @@ "Version": "6.1.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "mclust", - "RemoteRef": "mclust", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "6.1.1", "Requirements": [ "R", "grDevices", @@ -3414,13 +2389,6 @@ "Version": "2.0.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "memoise", - "RemoteRef": "memoise", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.1", "Requirements": [ "cachem", "rlang" @@ -3432,13 +2400,6 @@ "Version": "1.2-0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "metadat", - "RemoteRef": "metadat", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2-0", "Requirements": [ "R", "mathjaxr", @@ -3452,13 +2413,6 @@ "Version": "4.6-0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "metafor", - "RemoteRef": "metafor", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "4.6-0", "Requirements": [ "Matrix", "R", @@ -3480,13 +2434,6 @@ "Version": "0.3.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "metaviz", - "RemoteRef": "metaviz", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.1", "Requirements": [ "R", "RColorBrewer", @@ -3521,13 +2468,6 @@ "Version": "0.12", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "mime", - "RemoteRef": "mime", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.12", "Requirements": [ "tools" ], @@ -3550,13 +2490,6 @@ "Version": "1.2-4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "minpack.lm", - "RemoteRef": "minpack.lm", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2-4", "Hash": "0d04497c6553720b3f1c2ae373c57aa9" }, "minqa": { @@ -3564,30 +2497,35 @@ "Version": "1.2.7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "minqa", - "RemoteRef": "minqa", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.7", "Requirements": [ "Rcpp" ], "Hash": "aba060ef3c097b26a4d304ea39d87f32" }, + "modelbased": { + "Package": "modelbased", + "Version": "0.8.7", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "bayestestR", + "datawizard", + "effectsize", + "graphics", + "insight", + "parameters", + "performance", + "stats", + "utils" + ], + "Hash": "857859a5dd55f53a2c6ab14fbdb6acc1" + }, "modelenv": { "Package": "modelenv", "Version": "0.1.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "modelenv", - "RemoteRef": "modelenv", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.1.1", "Requirements": [ "glue", "rlang", @@ -3601,13 +2539,6 @@ "Version": "0.1.11", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "modelr", - "RemoteRef": "modelr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.1.11", "Requirements": [ "R", "broom", @@ -3626,13 +2557,6 @@ "Version": "0.2-23", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "modeltools", - "RemoteRef": "modeltools", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.2-23", "Requirements": [ "methods", "stats", @@ -3645,13 +2569,6 @@ "Version": "0.14.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "moments", - "RemoteRef": "moments", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.14.1", "Hash": "bb94fd8ee5f7f127eae2bddbff26864d" }, "munsell": { @@ -3659,13 +2576,6 @@ "Version": "0.5.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "munsell", - "RemoteRef": "munsell", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.5.1", "Requirements": [ "colorspace", "methods" @@ -3677,13 +2587,6 @@ "Version": "1.2-5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "mvtnorm", - "RemoteRef": "mvtnorm", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2-5", "Requirements": [ "R", "stats" @@ -3695,13 +2598,6 @@ "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "naniar", - "RemoteRef": "naniar", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.0", "Requirements": [ "R", "UpSetR", @@ -3743,13 +2639,6 @@ "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "nloptr", - "RemoteRef": "nloptr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.3", "Requirements": [ "testthat" ], @@ -3772,30 +2661,26 @@ "Version": "1.0-11.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "norm", - "RemoteRef": "norm", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0-11.1", "Requirements": [ "stats" ], "Hash": "82d9d75b78bc83553c034cd5c7ed2b3c" }, + "nortest": { + "Package": "nortest", + "Version": "1.0-4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "stats" + ], + "Hash": "e587e7a30c737ad415590976481332e4" + }, "nullabor": { "Package": "nullabor", "Version": "0.3.9", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "nullabor", - "RemoteRef": "nullabor", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.9", "Requirements": [ "MASS", "dplyr", @@ -3818,13 +2703,6 @@ "Version": "2016.8-1.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "numDeriv", - "RemoteRef": "numDeriv", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2016.8-1.1", "Requirements": [ "R" ], @@ -3835,13 +2713,6 @@ "Version": "2.2.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "openssl", - "RemoteRef": "openssl", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.2.0", "Requirements": [ "askpass" ], @@ -3884,13 +2755,6 @@ "Version": "0.2.9", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "osfr", - "RemoteRef": "osfr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.2.9", "Requirements": [ "R", "crul", @@ -3910,13 +2774,6 @@ "Version": "0.6.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "padr", - "RemoteRef": "padr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.6.2", "Requirements": [ "R", "Rcpp", @@ -3931,13 +2788,6 @@ "Version": "1.37.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "parallelly", - "RemoteRef": "parallelly", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.37.1", "Requirements": [ "parallel", "tools", @@ -3950,13 +2800,6 @@ "Version": "0.21.7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "parameters", - "RemoteRef": "parameters", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.21.7", "Requirements": [ "R", "bayestestR", @@ -3974,13 +2817,6 @@ "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "parsnip", - "RemoteRef": "parsnip", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.1", "Requirements": [ "R", "cli", @@ -4010,13 +2846,6 @@ "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "patchwork", - "RemoteRef": "patchwork", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.0", "Requirements": [ "cli", "ggplot2", @@ -4035,13 +2864,6 @@ "Version": "1.7-2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "pbapply", - "RemoteRef": "pbapply", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.7-2", "Requirements": [ "R", "parallel" @@ -4053,13 +2875,6 @@ "Version": "0.5.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "pbkrtest", - "RemoteRef": "pbkrtest", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.5.2", "Requirements": [ "MASS", "Matrix", @@ -4078,13 +2893,6 @@ "Version": "0.11.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "performance", - "RemoteRef": "performance", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.11.0", "Requirements": [ "R", "bayestestR", @@ -4100,13 +2908,6 @@ "Version": "0.9-7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "permute", - "RemoteRef": "permute", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.9-7", "Requirements": [ "R", "stats" @@ -4118,13 +2919,6 @@ "Version": "1.8.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "picante", - "RemoteRef": "picante", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.8.2", "Requirements": [ "ape", "methods", @@ -4138,13 +2932,6 @@ "Version": "1.9.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "pillar", - "RemoteRef": "pillar", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.9.0", "Requirements": [ "cli", "fansi", @@ -4162,13 +2949,6 @@ "Version": "1.4.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "pkgbuild", - "RemoteRef": "pkgbuild", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4.4", "Requirements": [ "R", "R6", @@ -4184,13 +2964,6 @@ "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "pkgconfig", - "RemoteRef": "pkgconfig", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.3", "Requirements": [ "utils" ], @@ -4201,13 +2974,6 @@ "Version": "2.0.9", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "pkgdown", - "RemoteRef": "pkgdown", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.9", "Requirements": [ "R", "bslib", @@ -4238,13 +3004,6 @@ "Version": "1.3.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "pkgload", - "RemoteRef": "pkgload", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3.4", "Requirements": [ "R", "cli", @@ -4266,13 +3025,6 @@ "Version": "4.10.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "plotly", - "RemoteRef": "plotly", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "4.10.4", "Requirements": [ "R", "RColorBrewer", @@ -4305,13 +3057,6 @@ "Version": "1.8.9", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "plyr", - "RemoteRef": "plyr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.8.9", "Requirements": [ "R", "Rcpp" @@ -4323,13 +3068,6 @@ "Version": "0.12.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "pointblank", - "RemoteRef": "pointblank", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.12.1", "Requirements": [ "DBI", "R", @@ -4360,13 +3098,6 @@ "Version": "1.10-6", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "polyclip", - "RemoteRef": "polyclip", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.10-6", "Requirements": [ "R" ], @@ -4377,13 +3108,6 @@ "Version": "1.4-1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "polynom", - "RemoteRef": "polynom", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4-1", "Requirements": [ "graphics", "stats" @@ -4395,13 +3119,6 @@ "Version": "2.3-3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "prabclus", - "RemoteRef": "prabclus", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.3-3", "Requirements": [ "MASS", "R", @@ -4414,13 +3131,6 @@ "Version": "2.4.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "pracma", - "RemoteRef": "pracma", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.4.4", "Requirements": [ "R", "grDevices", @@ -4435,13 +3145,6 @@ "Version": "1.0.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "praise", - "RemoteRef": "praise", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.0", "Hash": "a555924add98c99d2f411e37e7d25e9f" }, "prettyunits": { @@ -4449,13 +3152,6 @@ "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "prettyunits", - "RemoteRef": "prettyunits", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.0", "Requirements": [ "R" ], @@ -4466,13 +3162,6 @@ "Version": "3.8.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "processx", - "RemoteRef": "processx", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.8.4", "Requirements": [ "R", "R6", @@ -4486,13 +3175,6 @@ "Version": "2023.08.28", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "prodlim", - "RemoteRef": "prodlim", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2023.08.28", "Requirements": [ "KernSmooth", "R", @@ -4527,13 +3209,6 @@ "Version": "1.2.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "progress", - "RemoteRef": "progress", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.3", "Requirements": [ "R", "R6", @@ -4548,13 +3223,6 @@ "Version": "0.14.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "progressr", - "RemoteRef": "progressr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.14.0", "Requirements": [ "R", "digest", @@ -4567,13 +3235,6 @@ "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "promises", - "RemoteRef": "promises", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3.0", "Requirements": [ "R6", "Rcpp", @@ -4590,13 +3251,6 @@ "Version": "1.7.6", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ps", - "RemoteRef": "ps", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.7.6", "Requirements": [ "R", "utils" @@ -4608,13 +3262,6 @@ "Version": "1.0.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "purrr", - "RemoteRef": "purrr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.2", "Requirements": [ "R", "cli", @@ -4630,13 +3277,6 @@ "Version": "1.5-8", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "quadprog", - "RemoteRef": "quadprog", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.5-8", "Requirements": [ "R" ], @@ -4647,13 +3287,6 @@ "Version": "0.4.26", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "quantmod", - "RemoteRef": "quantmod", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.26", "Requirements": [ "R", "TTR", @@ -4670,13 +3303,6 @@ "Version": "5.97", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "quantreg", - "RemoteRef": "quantreg", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "5.97", "Requirements": [ "MASS", "Matrix", @@ -4695,13 +3321,6 @@ "Version": "1.3.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "ragg", - "RemoteRef": "ragg", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3.2", "Requirements": [ "systemfonts", "textshaping" @@ -4713,13 +3332,6 @@ "Version": "0.3.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rappdirs", - "RemoteRef": "rappdirs", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.3", "Requirements": [ "R" ], @@ -4730,13 +3342,6 @@ "Version": "1.6", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rcdd", - "RemoteRef": "rcdd", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.6", "Requirements": [ "R", "methods" @@ -4770,13 +3375,6 @@ "Version": "0.5.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "reactR", - "RemoteRef": "reactR", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.5.0", "Requirements": [ "htmltools" ], @@ -4787,13 +3385,6 @@ "Version": "0.4.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "reactable", - "RemoteRef": "reactable", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.4", "Requirements": [ "R", "digest", @@ -4809,13 +3400,6 @@ "Version": "2.1.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "readr", - "RemoteRef": "readr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.1.5", "Requirements": [ "R", "R6", @@ -4839,13 +3423,6 @@ "Version": "1.4.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "readxl", - "RemoteRef": "readxl", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4.3", "Requirements": [ "R", "cellranger", @@ -4861,13 +3438,6 @@ "Version": "1.0.10", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "recipes", - "RemoteRef": "recipes", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.10", "Requirements": [ "Matrix", "R", @@ -4901,13 +3471,6 @@ "Version": "2.0.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rematch", - "RemoteRef": "rematch", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.0", "Hash": "cbff1b666c6fa6d21202f07e2318d4f1" }, "rematch2": { @@ -4915,13 +3478,6 @@ "Version": "2.1.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rematch2", - "RemoteRef": "rematch2", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.1.2", "Requirements": [ "tibble" ], @@ -4943,26 +3499,24 @@ }, "renv": { "Package": "renv", - "Version": "1.0.7", - "Source": "Repository", - "Repository": "CRAN", + "Version": "0.17.3-62", + "Source": "GitHub", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "rstudio", + "RemoteRepo": "renv", + "RemoteRef": "0.17.3-62", + "RemoteSha": "bdafa4033ec3166aa1f36a4f02db8e3d09ca4ae0", "Requirements": [ "utils" ], - "Hash": "397b7b2a265bc5a7a06852524dabae20" + "Hash": "0eec72194bf21b1fb3d2ecf09cf64b0f" }, "reprex": { "Package": "reprex", "Version": "2.1.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "reprex", - "RemoteRef": "reprex", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.1.0", "Requirements": [ "R", "callr", @@ -4985,13 +3539,6 @@ "Version": "1.1.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rlang", - "RemoteRef": "rlang", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.3", "Requirements": [ "R", "utils" @@ -5003,13 +3550,6 @@ "Version": "2.27", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rmarkdown", - "RemoteRef": "rmarkdown", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.27", "Requirements": [ "R", "bslib", @@ -5033,13 +3573,6 @@ "Version": "0.99-2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "robustbase", - "RemoteRef": "robustbase", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.99-2", "Requirements": [ "DEoptimR", "R", @@ -5094,13 +3627,6 @@ "Version": "2.0.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rprojroot", - "RemoteRef": "rprojroot", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.4", "Requirements": [ "R" ], @@ -5111,13 +3637,6 @@ "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rsample", - "RemoteRef": "rsample", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.1", "Requirements": [ "R", "cli", @@ -5143,13 +3662,6 @@ "Version": "0.7.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rstatix", - "RemoteRef": "rstatix", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.7.2", "Requirements": [ "R", "broom", @@ -5173,13 +3685,6 @@ "Version": "0.16.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rstudioapi", - "RemoteRef": "rstudioapi", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.16.0", "Hash": "96710351d642b70e8f02ddeb237c46a7" }, "rticles": { @@ -5187,13 +3692,6 @@ "Version": "0.27", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rticles", - "RemoteRef": "rticles", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.27", "Requirements": [ "knitr", "lifecycle", @@ -5222,13 +3720,6 @@ "Version": "1.0.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "rvest", - "RemoteRef": "rvest", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.0.4", "Requirements": [ "R", "cli", @@ -5248,13 +3739,6 @@ "Version": "1.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "sae", - "RemoteRef": "sae", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3", "Requirements": [ "MASS", "lme4", @@ -5267,13 +3751,6 @@ "Version": "0.4.9", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "sass", - "RemoteRef": "sass", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.9", "Requirements": [ "R6", "fs", @@ -5288,13 +3765,6 @@ "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "scales", - "RemoteRef": "scales", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3.0", "Requirements": [ "R", "R6", @@ -5315,30 +3785,38 @@ "Version": "0.5.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "secretbase", - "RemoteRef": "secretbase", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.5.0", "Requirements": [ "R" ], "Hash": "c476c18b22b21849c9f4d29b3cd720a5" }, + "see": { + "Package": "see", + "Version": "0.8.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "bayestestR", + "correlation", + "datawizard", + "effectsize", + "ggplot2", + "grDevices", + "graphics", + "insight", + "modelbased", + "parameters", + "performance", + "stats" + ], + "Hash": "3d2fd0b72314499e6af4fd20d39309dc" + }, "selectr": { "Package": "selectr", "Version": "0.4-2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "selectr", - "RemoteRef": "selectr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4-2", "Requirements": [ "R", "R6", @@ -5365,13 +3843,6 @@ "Version": "1.4.6.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "shape", - "RemoteRef": "shape", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.4.6.1", "Requirements": [ "R", "grDevices", @@ -5418,13 +3889,6 @@ "Version": "0.3.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "slider", - "RemoteRef": "slider", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.1", "Requirements": [ "R", "cli", @@ -5439,13 +3903,6 @@ "Version": "0.4-4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "snow", - "RemoteRef": "snow", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4-4", "Requirements": [ "R", "utils" @@ -5467,13 +3924,6 @@ "Version": "1.8.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "stringi", - "RemoteRef": "stringi", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.8.4", "Requirements": [ "R", "stats", @@ -5487,13 +3937,6 @@ "Version": "1.5.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "stringr", - "RemoteRef": "stringr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.5.1", "Requirements": [ "R", "cli", @@ -5527,13 +3970,6 @@ "Version": "3.4.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "sys", - "RemoteRef": "sys", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.4.2", "Hash": "3a1be13d68d47a8cd0bfd74739ca1555" }, "systemfonts": { @@ -5541,13 +3977,6 @@ "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "systemfonts", - "RemoteRef": "systemfonts", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.0", "Requirements": [ "R", "cpp11", @@ -5560,13 +3989,6 @@ "Version": "0.9.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tarchetypes", - "RemoteRef": "tarchetypes", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.9.0", "Requirements": [ "R", "dplyr", @@ -5588,13 +4010,6 @@ "Version": "1.7.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "targets", - "RemoteRef": "targets", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.7.0", "Requirements": [ "R", "R6", @@ -5623,13 +4038,6 @@ "Version": "3.2.1.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "testthat", - "RemoteRef": "testthat", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.2.1.1", "Requirements": [ "R", "R6", @@ -5659,13 +4067,6 @@ "Version": "0.3.7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "textshaping", - "RemoteRef": "textshaping", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.7", "Requirements": [ "R", "cpp11", @@ -5678,13 +4079,6 @@ "Version": "3.2.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tibble", - "RemoteRef": "tibble", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.2.1", "Requirements": [ "R", "fansi", @@ -5704,13 +4098,6 @@ "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tidyr", - "RemoteRef": "tidyr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3.1", "Requirements": [ "R", "cli", @@ -5734,13 +4121,6 @@ "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tidyselect", - "RemoteRef": "tidyselect", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.1", "Requirements": [ "R", "cli", @@ -5757,13 +4137,6 @@ "Version": "2.0.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tidyverse", - "RemoteRef": "tidyverse", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.0", "Requirements": [ "R", "broom", @@ -5804,13 +4177,6 @@ "Version": "4032.109", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "timeDate", - "RemoteRef": "timeDate", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "4032.109", "Requirements": [ "R", "graphics", @@ -5825,13 +4191,6 @@ "Version": "0.3.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "timechange", - "RemoteRef": "timechange", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.3.0", "Requirements": [ "R", "cpp11" @@ -5843,13 +4202,6 @@ "Version": "2.9.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "timetk", - "RemoteRef": "timetk", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.9.0", "Requirements": [ "R", "anytime", @@ -5885,13 +4237,6 @@ "Version": "0.51", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tinytex", - "RemoteRef": "tinytex", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.51", "Requirements": [ "xfun" ], @@ -5902,13 +4247,6 @@ "Version": "0.4.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "triebeard", - "RemoteRef": "triebeard", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.1", "Requirements": [ "Rcpp" ], @@ -5919,13 +4257,6 @@ "Version": "0.10-56", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tseries", - "RemoteRef": "tseries", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.10-56", "Requirements": [ "R", "graphics", @@ -5943,13 +4274,6 @@ "Version": "1.1.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tsfeatures", - "RemoteRef": "tsfeatures", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.1", "Requirements": [ "R", "RcppRoll", @@ -5970,13 +4294,6 @@ "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tsibble", - "RemoteRef": "tsibble", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.4", "Requirements": [ "R", "anytime", @@ -5998,13 +4315,6 @@ "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tweenr", - "RemoteRef": "tweenr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.0.3", "Requirements": [ "R", "cpp11", @@ -6020,13 +4330,6 @@ "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "tzdb", - "RemoteRef": "tzdb", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.0", "Requirements": [ "R", "cpp11" @@ -6038,13 +4341,6 @@ "Version": "1.3-3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "urca", - "RemoteRef": "urca", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3-3", "Requirements": [ "R", "graphics", @@ -6073,13 +4369,6 @@ "Version": "1.7.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "urltools", - "RemoteRef": "urltools", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.7.3", "Requirements": [ "R", "Rcpp", @@ -6093,13 +4382,6 @@ "Version": "2.2.3", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "usethis", - "RemoteRef": "usethis", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.2.3", "Requirements": [ "R", "cli", @@ -6131,13 +4413,6 @@ "Version": "1.2.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "utf8", - "RemoteRef": "utf8", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2.4", "Requirements": [ "R" ], @@ -6148,13 +4423,6 @@ "Version": "1.2-0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "uuid", - "RemoteRef": "uuid", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.2-0", "Requirements": [ "R" ], @@ -6165,13 +4433,6 @@ "Version": "0.6.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "vctrs", - "RemoteRef": "vctrs", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.6.5", "Requirements": [ "R", "cli", @@ -6186,13 +4447,6 @@ "Version": "2.6-6.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "vegan", - "RemoteRef": "vegan", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.6-6.1", "Requirements": [ "MASS", "R", @@ -6208,13 +4462,6 @@ "Version": "0.4.7", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "vipor", - "RemoteRef": "vipor", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.7", "Requirements": [ "R", "graphics", @@ -6227,13 +4474,6 @@ "Version": "0.6.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "viridis", - "RemoteRef": "viridis", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.6.5", "Requirements": [ "R", "ggplot2", @@ -6247,13 +4487,6 @@ "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "viridisLite", - "RemoteRef": "viridisLite", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.2", "Requirements": [ "R" ], @@ -6264,13 +4497,6 @@ "Version": "0.6.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "visdat", - "RemoteRef": "visdat", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.6.0", "Requirements": [ "R", "cli", @@ -6293,13 +4519,6 @@ "Version": "1.6.5", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "vroom", - "RemoteRef": "vroom", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.6.5", "Requirements": [ "R", "bit64", @@ -6326,13 +4545,6 @@ "Version": "0.5.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "waldo", - "RemoteRef": "waldo", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.5.2", "Requirements": [ "R", "cli", @@ -6351,13 +4563,6 @@ "Version": "0.2.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "warp", - "RemoteRef": "warp", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.2.1", "Requirements": [ "R" ], @@ -6368,13 +4573,6 @@ "Version": "0.4.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "whisker", - "RemoteRef": "whisker", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.4.1", "Hash": "c6abfa47a46d281a7d5159d0a8891e88" }, "withr": { @@ -6382,13 +4580,6 @@ "Version": "3.0.0", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "withr", - "RemoteRef": "withr", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "3.0.0", "Requirements": [ "R", "grDevices", @@ -6401,13 +4592,6 @@ "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "workflows", - "RemoteRef": "workflows", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.1.4", "Requirements": [ "R", "cli", @@ -6428,13 +4612,6 @@ "Version": "0.44", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "xfun", - "RemoteRef": "xfun", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.44", "Requirements": [ "grDevices", "stats", @@ -6447,13 +4624,6 @@ "Version": "1.3.6", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "xml2", - "RemoteRef": "xml2", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.3.6", "Requirements": [ "R", "cli", @@ -6490,13 +4660,6 @@ "Version": "0.13.2", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "xts", - "RemoteRef": "xts", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.13.2", "Requirements": [ "R", "methods", @@ -6516,13 +4679,6 @@ "Version": "0.1.4", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "yulab.utils", - "RemoteRef": "yulab.utils", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "0.1.4", "Requirements": [ "cli", "digest", @@ -6540,13 +4696,6 @@ "Version": "2.3.1", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "zip", - "RemoteRef": "zip", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "2.3.1", "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" }, "zoo": { @@ -6554,13 +4703,6 @@ "Version": "1.8-12", "Source": "Repository", "Repository": "CRAN", - "RemoteType": "standard", - "RemotePkgRef": "zoo", - "RemoteRef": "zoo", - "RemoteRepos": "https://cran.rstudio.com", - "RemoteReposName": "CRAN", - "RemotePkgPlatform": "aarch64-apple-darwin20", - "RemoteSha": "1.8-12", "Requirements": [ "R", "grDevices", diff --git a/renv/activate.R b/renv/activate.R index 8fb55fb..37be925 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,10 +2,28 @@ local({ # the requested version of renv - version <- "1.0.7" + version <- "0.17.3-62" + attr(version, "sha") <- "bdafa4033ec3166aa1f36a4f02db8e3d09ca4ae0" # the project directory - project <- getwd() + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } # figure out whether the autoloader is enabled enabled <- local({ @@ -15,6 +33,14 @@ local({ if (!is.null(override)) return(override) + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + # next, check environment variables # TODO: prefer using the configuration one in the future envvars <- c( @@ -34,9 +60,22 @@ local({ }) - if (!enabled) + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + return(FALSE) + } + # avoid recursion if (identical(getOption("renv.autoloader.running"), TRUE)) { warning("ignoring recursive attempt to run renv autoloader") @@ -60,25 +99,90 @@ local({ # load bootstrap tools `%||%` <- function(x, y) { - if (is.environment(x) || length(x)) x else y + if (is.null(x)) y else x } - `%??%` <- function(x, y) { - if (is.null(x)) y else x + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix } bootstrap <- function(version, library) { + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + # attempt to download renv - tarball <- tryCatch(renv_bootstrap_download(version), error = identity) - if (inherits(tarball, "error")) - stop("failed to download renv ", version) + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) # now attempt to install - status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) - if (inherits(status, "error")) - stop("failed to install renv ", version) + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + return(invisible()) } renv_bootstrap_tests_running <- function() { @@ -108,13 +212,6 @@ local({ if (!inherits(repos, "error") && length(repos)) return(repos) - # if we're testing, re-use the test repositories - if (renv_bootstrap_tests_running()) { - repos <- getOption("renv.tests.repos") - if (!is.null(repos)) - return(repos) - } - # retrieve current repos repos <- getOption("repos") @@ -158,33 +255,34 @@ local({ renv_bootstrap_download <- function(version) { - # if the renv version number has 4 components, assume it must - # be retrieved via github - nv <- numeric_version(version) - components <- unclass(nv)[[1]] - - # if this appears to be a development version of 'renv', we'll - # try to restore from github - dev <- length(components) == 4L - - # begin collecting different methods for finding renv - methods <- c( - renv_bootstrap_download_tarball, - if (dev) - renv_bootstrap_download_github - else c( - renv_bootstrap_download_cran_latest, - renv_bootstrap_download_cran_archive + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) ) - ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } for (method in methods) { - path <- tryCatch(method(version), error = identity) + path <- tryCatch(method(), error = identity) if (is.character(path) && file.exists(path)) return(path) } - stop("failed to download renv ", version) + stop("All download methods failed") } @@ -248,8 +346,6 @@ local({ type <- spec$type repos <- spec$repos - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - baseurl <- utils::contrib.url(repos = repos, type = type) ext <- if (identical(type, "source")) ".tar.gz" @@ -266,13 +362,10 @@ local({ condition = identity ) - if (inherits(status, "condition")) { - message("FAILED") + if (inherits(status, "condition")) return(FALSE) - } # report success and return - message("OK (downloaded ", type, ")") destfile } @@ -329,8 +422,6 @@ local({ urls <- file.path(repos, "src/contrib/Archive/renv", name) destfile <- file.path(tempdir(), name) - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - for (url in urls) { status <- tryCatch( @@ -338,14 +429,11 @@ local({ condition = identity ) - if (identical(status, 0L)) { - message("OK") + if (identical(status, 0L)) return(destfile) - } } - message("FAILED") return(FALSE) } @@ -368,7 +456,7 @@ local({ if (!file.exists(tarball)) { # let the user know we weren't able to honour their request - fmt <- "* RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." msg <- sprintf(fmt, tarball) warning(msg) @@ -377,10 +465,7 @@ local({ } - fmt <- "* Bootstrapping with tarball at path '%s'." - msg <- sprintf(fmt, tarball) - message(msg) - + catf("- Using local tarball '%s'.", tarball) tarball } @@ -407,8 +492,6 @@ local({ on.exit(do.call(base::options, saved), add = TRUE) } - message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) - url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) name <- sprintf("renv_%s.tar.gz", version) destfile <- file.path(tempdir(), name) @@ -418,26 +501,105 @@ local({ condition = identity ) - if (!identical(status, 0L)) { - message("FAILED") + if (!identical(status, 0L)) return(FALSE) - } - message("OK") + renv_bootstrap_download_augment(destfile) + return(destfile) } + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + renv_bootstrap_install <- function(version, tarball, library) { # attempt to install it into project library - message("* Installing renv ", version, " ... ", appendLF = FALSE) dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { # invoke using system2 so we can capture and report output bin <- R.home("bin") exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" - r <- file.path(bin, exe) + R <- file.path(bin, exe) args <- c( "--vanilla", "CMD", "INSTALL", "--no-multiarch", @@ -445,19 +607,7 @@ local({ shQuote(path.expand(tarball)) ) - output <- system2(r, args, stdout = TRUE, stderr = TRUE) - message("Done!") - - # check for successful install - status <- attr(output, "status") - if (is.numeric(status) && !identical(status, 0L)) { - header <- "Error installing renv:" - lines <- paste(rep.int("=", nchar(header)), collapse = "") - text <- c(header, lines, output) - writeLines(text, con = stderr()) - } - - status + system2(R, args, stdout = TRUE, stderr = TRUE) } @@ -498,6 +648,9 @@ local({ # if the user has requested an automatic prefix, generate it auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + if (auto %in% c("TRUE", "True", "true", "1")) return(renv_bootstrap_platform_prefix_auto()) @@ -667,34 +820,61 @@ local({ } - renv_bootstrap_validate_version <- function(version) { + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") - loadedversion <- utils::packageDescription("renv", fields = "Version") - if (version == loadedversion) + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) return(TRUE) - # assume four-component versions are from GitHub; - # three-component versions are from CRAN - components <- strsplit(loadedversion, "[.-]")[[1]] - remote <- if (length(components) == 4L) - paste("rstudio/renv", loadedversion, sep = "@") + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") else - paste("renv", loadedversion, sep = "@") + paste("renv", description[["Version"]], sep = "@") - fmt <- paste( - "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", - sep = "\n" + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] ) - msg <- sprintf(fmt, loadedversion, version, remote) - warning(msg, call. = FALSE) + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) FALSE } + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + renv_bootstrap_hash_text <- function(text) { hashfile <- tempfile("renv-hash-") @@ -718,7 +898,7 @@ local({ hooks <- getHook("renv::autoload") for (hook in hooks) if (is.function(hook)) - tryCatch(hook(), error = warning) + tryCatch(hook(), error = warnify) # load the project renv::load(project) @@ -859,6 +1039,40 @@ local({ } + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } renv_json_read <- function(file = NULL, text = NULL) { @@ -867,7 +1081,7 @@ local({ # if jsonlite is loaded, use that instead if ("jsonlite" %in% loadedNamespaces()) { - json <- catch(renv_json_read_jsonlite(file, text)) + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -876,7 +1090,7 @@ local({ } # otherwise, fall back to the default JSON reader - json <- catch(renv_json_read_default(file, text)) + json <- tryCatch(renv_json_read_default(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -889,14 +1103,14 @@ local({ } renv_json_read_jsonlite <- function(file = NULL, text = NULL) { - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } renv_json_read_default <- function(file = NULL, text = NULL) { # find strings in the JSON - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' locs <- gregexpr(pattern, text, perl = TRUE)[[1]] @@ -944,14 +1158,14 @@ local({ map <- as.list(map) # remap strings in object - remapped <- renv_json_remap(json, map) + remapped <- renv_json_read_remap(json, map) # evaluate eval(remapped, envir = baseenv()) } - renv_json_remap <- function(json, map) { + renv_json_read_remap <- function(json, map) { # fix names if (!is.null(names(json))) { @@ -978,7 +1192,7 @@ local({ # recurse if (is.recursive(json)) { for (i in seq_along(json)) { - json[i] <- list(renv_json_remap(json[[i]], map)) + json[i] <- list(renv_json_read_remap(json[[i]], map)) } } @@ -998,35 +1212,9 @@ local({ # construct full libpath libpath <- file.path(root, prefix) - # attempt to load - if (renv_bootstrap_load(project, libpath, version)) - return(TRUE) - - # load failed; inform user we're about to bootstrap - prefix <- paste("# Bootstrapping renv", version) - postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "") - header <- paste(prefix, postfix) - message(header) - - # perform bootstrap - bootstrap(version, libpath) - - # exit early if we're just testing bootstrap - if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) - return(TRUE) - - # try again to load - if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { - message("* Successfully installed and loaded renv ", version, ".") - return(renv::load()) - } - - # failed to download or load renv; warn the user - msg <- c( - "Failed to find an renv installation: the project will not be loaded.", - "Use `renv::activate()` to re-initialize the project." - ) + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) - warning(paste(msg, collapse = "\n"), call. = FALSE) + invisible() })