From f93c497f75a0e97f67488843653046d5b13f60e1 Mon Sep 17 00:00:00 2001 From: egouldo Date: Fri, 14 Jun 2024 10:47:45 +1000 Subject: [PATCH] fix #41 mv expert_subset into pkg internals: echo E63AF5C2 && echo ignoreboth && /usr/bin/env && echo 5673D7C1 --- R/generate_collinearity_subset.R | 2 +- R/generate_expertise_subsets.R | 4 +--- R/sysdata.rda | Bin 2546 -> 4133 bytes _targets.R | 5 +---- data-raw/create_internal_pkg_data.R | 14 ++++++++++++-- man/generate_collinearity_subset.Rd | 2 +- man/generate_expertise_subsets.Rd | 4 +--- 7 files changed, 17 insertions(+), 14 deletions(-) diff --git a/R/generate_collinearity_subset.R b/R/generate_collinearity_subset.R index 34159af..060f439 100644 --- a/R/generate_collinearity_subset.R +++ b/R/generate_collinearity_subset.R @@ -27,7 +27,7 @@ #' prepare_response_variables(estimate_type = "Zr") |> #' generate_exclusion_subsets(estimate_type = "Zr") |> #' generate_rating_subsets() |> -#' generate_expertise_subsets(expert_subset) |> +#' generate_expertise_subsets(ManyEcoEvo:::expert_subset) |> #' generate_collinearity_subset(collinearity_subset = collinearity_subset) generate_collinearity_subset <- function(ManyEcoEvo, collinearity_subset) { # Check if the inputs are a dataframe diff --git a/R/generate_expertise_subsets.R b/R/generate_expertise_subsets.R index 173be3d..3e0ff93 100644 --- a/R/generate_expertise_subsets.R +++ b/R/generate_expertise_subsets.R @@ -16,13 +16,11 @@ #' library(ManyEcoEvo) #' library(tidyverse) #' library(targets) -#' targets::tar_load(ManyEcoEvo) -#' targets::tar_load(expert_subset) #' ManyEcoEvo %>% #' prepare_response_variables(estimate_type = "Zr") |> #' generate_exclusion_subsets(estimate_type = "Zr") |> #' generate_rating_subsets() |> -#' generate_expertise_subsets(expert_subset) +#' generate_expertise_subsets(ManyEcoEvo:::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. 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z(kH&KQcuwS(Ct}Kpq(vK@3H_zn}ItOx{0+)H~D^kolT6M>Dlz#k;7z{nl+IqMPL_( zYkyWuRO3xVM}TY9oS-AUBNJ-~QLx}0myw+6ScI*qaqiwFrkDhXFrx^P=qiF+!~L1c z>Uti)a3jrhhC|Z9%UH5~rD+)mXG8I>h$3M8X1?O-oIs)?R!TrT7uRF$BvsGNX|_o{ z+LZ;3+NkM~Y%=$Jy?Zrm8`09#5*yb|_#pX45BxxFG>t#4Jq`w-qxad%3|>JN1K&@ z-H>*if2ShO@)jHsfeu&d+fcZU7o)%B)UvpPQ=aVfP8V`x<;~!P=K~!j9LZTQ&AN!PWoXElZ;qw8X}Mlo9m zjZlFTBOg6gzEamsDp+O;LtFWSs+gu|D!&bn#e>1&{U3RIfhY#WYd+drCHU?H-r4G8 z*RF)Np`>KL#c|Fo)N7Lreo%9d%HfE=bLP2;JvQ zlX~2EDjCQwT^>BbUf^I+1=Djm2)4yJdH9RB#Bga{HuV@>W;fSt;$^$BUy_h6MwJrb zmJ7!>2mw^Y?96-zZRb;uTnJAm%J_|6O7bxBqT{y*eCJR?B8cA(HU`v#n zv2hqAdT)|VjRAvK@JW1XMtO5)Z7A$=xpbsu^z>j&qios&Txuw4rTeN2c71h_vBTr8 z3}Ht1MDk7;)!n78=U0@`R=R!;Ie6-lUPoJQNek(%?>beNuz9C)AW3+*Nl&u$)fDa3 z1R8lM4 generate_exclusion_subsets(estimate_type = "Zr") |> generate_rating_subsets() |> - generate_expertise_subsets(expert_subset) |> + generate_expertise_subsets(ManyEcoEvo:::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!! diff --git a/data-raw/create_internal_pkg_data.R b/data-raw/create_internal_pkg_data.R index 8772dc1..3bc5b00 100644 --- a/data-raw/create_internal_pkg_data.R +++ b/data-raw/create_internal_pkg_data.R @@ -1,9 +1,17 @@ # ------- Create tibble of analysis IDs of analyses with collinear variables ------- - +library(here) library(tidyverse) library(usethis) library(ManyEcoEvo) +# ----- Load Expert Subset ----- + +expert_subset <- readr::read_csv(here::here("data-raw", + "metadata_and_key_data", + "Good_Statistician_ResponseIds.csv")) + +# ------- Create tibble of analysis IDs of analyses with highly collinear variables ------- + collinearity_subset <- tibble::tribble( ~response_id, ~id_col, ~dataset, @@ -30,6 +38,8 @@ collinearity_subset <- # alternatively, devtools::load_all() is needed to access the fns to build `analysis_data_param_tables` # devtools::load_all() #TODO +#TODO consider moving *_data creation into this script to avoid dependence on pkg before built.. + analysis_data_param_tables <- bind_rows( make_param_table(ManyEcoEvo::blue_tit_data) %>% @@ -40,4 +50,4 @@ analysis_data_param_tables <- # ------- Write data internally ------- -usethis::use_data(analysis_data_param_tables, collinearity_subset, internal = TRUE, overwrite = TRUE) +usethis::use_data(expert_subset, analysis_data_param_tables, collinearity_subset, internal = TRUE, overwrite = TRUE) diff --git a/man/generate_collinearity_subset.Rd b/man/generate_collinearity_subset.Rd index 8ac4957..520625f 100644 --- a/man/generate_collinearity_subset.Rd +++ b/man/generate_collinearity_subset.Rd @@ -37,6 +37,6 @@ ManyEcoEvo \%>\% prepare_response_variables(estimate_type = "Zr") |> generate_exclusion_subsets(estimate_type = "Zr") |> generate_rating_subsets() |> -generate_expertise_subsets(expert_subset) |> +generate_expertise_subsets(ManyEcoEvo:::expert_subset) |> generate_collinearity_subset(collinearity_subset = collinearity_subset) } diff --git a/man/generate_expertise_subsets.Rd b/man/generate_expertise_subsets.Rd index e25cd90..513c8bd 100644 --- a/man/generate_expertise_subsets.Rd +++ b/man/generate_expertise_subsets.Rd @@ -31,11 +31,9 @@ Note that this function needs to be run on \code{ManyEcoEvo} after the following library(ManyEcoEvo) library(tidyverse) library(targets) -targets::tar_load(ManyEcoEvo) -targets::tar_load(expert_subset) ManyEcoEvo \%>\% prepare_response_variables(estimate_type = "Zr") |> generate_exclusion_subsets(estimate_type = "Zr") |> generate_rating_subsets() |> -generate_expertise_subsets(expert_subset) +generate_expertise_subsets(ManyEcoEvo:::expert_subset) }