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. Repeat for all other generate / exclude map funs diff --git a/R/sysdata.rda b/R/sysdata.rda index e41f60b..f368e38 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/_targets.R b/_targets.R index 1cfb2c0..39fa921 100644 --- a/_targets.R +++ b/_targets.R @@ -65,9 +65,6 @@ list(tarchetypes::tar_file_read(name = euc_reviews, tarchetypes::tar_file_read(name = list_of_new_prediction_files, command = "data-raw/analyst_data/S2/list_of_new_csv_files.csv", read = readr::read_csv(!!.x)), - tarchetypes::tar_file_read(name = expert_subset, - command = "data-raw/metadata_and_key_data/Good_Statistician_ResponseIds.csv", - read = readr::read_csv(file = !!.x)), targets::tar_target(name = all_review_data, command = prepare_review_data(bt_reviews,euc_reviews)), targets::tar_target(ManyEcoEvo, @@ -79,7 +76,7 @@ list(tarchetypes::tar_file_read(name = euc_reviews, 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(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) }