diff --git a/R/abnormal.R b/R/abnormal.R index dab670140a..f09275681e 100644 --- a/R/abnormal.R +++ b/R/abnormal.R @@ -109,10 +109,15 @@ a_count_abnormal <- function(df, extra_afun_params <- retrieve_extra_afun_params(names(dots_extra_args$.additional_fun_parameters)) dots_extra_args$.additional_fun_parameters <- NULL + # Check for user-defined functions + default_and_custom_stats_list <- .split_std_from_custom_stats(.stats) + .stats <- default_and_custom_stats_list$all_stats + custom_stat_functions <- default_and_custom_stats_list$custom_stats + # Apply statistics function x_stats <- .apply_stat_functions( default_stat_fnc = s_count_abnormal, - custom_stat_fnc_list = NULL, + custom_stat_fnc_list = custom_stat_functions, args_list = c( df = list(df), extra_afun_params, @@ -121,7 +126,7 @@ a_count_abnormal <- function(df, ) # Fill in formatting defaults - .stats <- get_stats("abnormal", stats_in = .stats) + .stats <- get_stats("abnormal", stats_in = .stats, custom_stats_in = names(custom_stat_functions)) levels_per_stats <- lapply(x_stats, names) .formats <- get_formats_from_stats(.stats, .formats, levels_per_stats) .labels <- get_labels_from_stats(.stats, .labels, levels_per_stats) diff --git a/R/abnormal_by_baseline.R b/R/abnormal_by_baseline.R index 0262cf6465..de9802a62d 100644 --- a/R/abnormal_by_baseline.R +++ b/R/abnormal_by_baseline.R @@ -136,10 +136,15 @@ a_count_abnormal_by_baseline <- function(df, extra_afun_params <- retrieve_extra_afun_params(names(dots_extra_args$.additional_fun_parameters)) dots_extra_args$.additional_fun_parameters <- NULL + # Check for user-defined functions + default_and_custom_stats_list <- .split_std_from_custom_stats(.stats) + .stats <- default_and_custom_stats_list$all_stats + custom_stat_functions <- default_and_custom_stats_list$custom_stats + # Apply statistics function x_stats <- .apply_stat_functions( default_stat_fnc = s_count_abnormal_by_baseline, - custom_stat_fnc_list = NULL, + custom_stat_fnc_list = custom_stat_functions, args_list = c( df = list(df), extra_afun_params, @@ -148,7 +153,7 @@ a_count_abnormal_by_baseline <- function(df, ) # Fill in formatting defaults - .stats <- get_stats("abnormal_by_baseline", stats_in = .stats) + .stats <- get_stats("abnormal_by_baseline", stats_in = .stats, custom_stats_in = names(custom_stat_functions)) levels_per_stats <- lapply(x_stats, names) .formats <- get_formats_from_stats(.stats, .formats, levels_per_stats) .labels <- get_labels_from_stats( diff --git a/R/abnormal_by_marked.R b/R/abnormal_by_marked.R index faf959120d..717f0c2b72 100644 --- a/R/abnormal_by_marked.R +++ b/R/abnormal_by_marked.R @@ -120,10 +120,15 @@ a_count_abnormal_by_marked <- function(df, extra_afun_params <- retrieve_extra_afun_params(names(dots_extra_args$.additional_fun_parameters)) dots_extra_args$.additional_fun_parameters <- NULL + # Check for user-defined functions + default_and_custom_stats_list <- .split_std_from_custom_stats(.stats) + .stats <- default_and_custom_stats_list$all_stats + custom_stat_functions <- default_and_custom_stats_list$custom_stats + # Apply statistics function x_stats <- .apply_stat_functions( default_stat_fnc = s_count_abnormal_by_marked, - custom_stat_fnc_list = NULL, + custom_stat_fnc_list = custom_stat_functions, args_list = c( df = list(df), extra_afun_params, @@ -132,7 +137,7 @@ a_count_abnormal_by_marked <- function(df, ) # Fill in formatting defaults - .stats <- get_stats("abnormal_by_marked", stats_in = .stats) + .stats <- get_stats("abnormal_by_marked", stats_in = .stats, custom_stats_in = names(custom_stat_functions)) levels_per_stats <- lapply(x_stats, names) .formats <- get_formats_from_stats(.stats, .formats, levels_per_stats) .labels <- get_labels_from_stats(.stats, .labels, levels_per_stats) diff --git a/R/abnormal_by_worst_grade.R b/R/abnormal_by_worst_grade.R index 6470f3655b..a07407e879 100644 --- a/R/abnormal_by_worst_grade.R +++ b/R/abnormal_by_worst_grade.R @@ -107,10 +107,15 @@ a_count_abnormal_by_worst_grade <- function(df, extra_afun_params <- retrieve_extra_afun_params(names(dots_extra_args$.additional_fun_parameters)) dots_extra_args$.additional_fun_parameters <- NULL + # Check for user-defined functions + default_and_custom_stats_list <- .split_std_from_custom_stats(.stats) + .stats <- default_and_custom_stats_list$all_stats + custom_stat_functions <- default_and_custom_stats_list$custom_stats + # Apply statistics function x_stats <- .apply_stat_functions( default_stat_fnc = s_count_abnormal_by_worst_grade, - custom_stat_fnc_list = NULL, + custom_stat_fnc_list = custom_stat_functions, args_list = c( df = list(df), extra_afun_params, @@ -119,7 +124,7 @@ a_count_abnormal_by_worst_grade <- function(df, ) # Fill in formatting defaults - .stats <- get_stats("abnormal_by_worst_grade", stats_in = .stats) + .stats <- get_stats("abnormal_by_worst_grade", stats_in = .stats, custom_stats_in = names(custom_stat_functions)) levels_per_stats <- lapply(x_stats, names) .formats <- get_formats_from_stats(.stats, .formats, levels_per_stats) .labels <- get_labels_from_stats(.stats, .labels, levels_per_stats) diff --git a/R/abnormal_lab_worsen_by_baseline.R b/R/abnormal_lab_worsen_by_baseline.R index 45567526e9..a44e0188be 100644 --- a/R/abnormal_lab_worsen_by_baseline.R +++ b/R/abnormal_lab_worsen_by_baseline.R @@ -88,10 +88,15 @@ a_count_abnormal_lab_worsen_by_baseline <- function(df, extra_afun_params <- retrieve_extra_afun_params(names(dots_extra_args$.additional_fun_parameters)) dots_extra_args$.additional_fun_parameters <- NULL + # Check for user-defined functions + default_and_custom_stats_list <- .split_std_from_custom_stats(.stats) + .stats <- default_and_custom_stats_list$all_stats + custom_stat_functions <- default_and_custom_stats_list$custom_stats + # Apply statistics function x_stats <- .apply_stat_functions( default_stat_fnc = s_count_abnormal_lab_worsen_by_baseline, - custom_stat_fnc_list = NULL, + custom_stat_fnc_list = custom_stat_functions, args_list = c( df = list(df), extra_afun_params, @@ -100,7 +105,11 @@ a_count_abnormal_lab_worsen_by_baseline <- function(df, ) # Fill in formatting defaults - .stats <- get_stats("abnormal_lab_worsen_by_baseline", stats_in = .stats) + .stats <- get_stats( + "abnormal_lab_worsen_by_baseline", + stats_in = .stats, + custom_stats_in = names(custom_stat_functions) + ) levels_per_stats <- lapply(x_stats, names) .formats <- get_formats_from_stats(.stats, .formats, levels_per_stats) .labels <- get_labels_from_stats(.stats, .labels, levels_per_stats) diff --git a/R/summarize_ancova.R b/R/summarize_ancova.R index 82dda6f85b..40ce288081 100644 --- a/R/summarize_ancova.R +++ b/R/summarize_ancova.R @@ -237,7 +237,7 @@ a_ancova <- function(df, ) # Fill in formatting defaults - .stats <- c(get_stats("summarize_ancova", stats_in = .stats), names(custom_stat_functions)) + .stats <- get_stats("summarize_ancova", stats_in = .stats, custom_stats_in = names(custom_stat_functions)) x_stats <- x_stats[.stats] .formats <- get_formats_from_stats(.stats, .formats) .labels <- get_labels_from_stats( diff --git a/R/summarize_change.R b/R/summarize_change.R index fc86806952..f2f962e5a9 100644 --- a/R/summarize_change.R +++ b/R/summarize_change.R @@ -88,11 +88,7 @@ a_change_from_baseline <- function(df, ) # Fill in with formatting defaults if needed - .stats <- get_stats( - "analyze_vars_numeric", - stats_in = .stats, - custom_stats_in = names(custom_stat_functions), - ) + .stats <- get_stats("analyze_vars_numeric", stats_in = .stats, custom_stats_in = names(custom_stat_functions)) .formats <- get_formats_from_stats(.stats, .formats) .labels <- get_labels_from_stats(.stats, .labels) .indent_mods <- get_indents_from_stats(.stats, .indent_mods) diff --git a/R/summarize_glm_count.R b/R/summarize_glm_count.R index 95b4005bb6..cd6fc5d09d 100644 --- a/R/summarize_glm_count.R +++ b/R/summarize_glm_count.R @@ -303,7 +303,7 @@ a_glm_count <- function(df, ) # Fill in formatting defaults - .stats <- c(get_stats("summarize_glm_count", stats_in = .stats), names(custom_stat_functions)) + .stats <- get_stats("summarize_glm_count", stats_in = .stats, custom_stats_in = names(custom_stat_functions)) .formats <- get_formats_from_stats(.stats, .formats) .labels <- get_labels_from_stats(.stats, .labels) .indent_mods <- get_indents_from_stats(.stats, .indent_mods)