fix bugs for testing

Author: halleeshearer

.github/workflows/R-CMD-check.yml

@@ -47,9 +47,7 @@ jobs:
           "graphics",
           "utils",
           "colorspace",
-          "png",
-          "ggpubr",
-          "devtools"
+          "png"
         ))
         remotes::install_deps(dependencies = TRUE)
       shell: Rscript {0}

R/create_plots.R

@@ -5,7 +5,7 @@
 #' @import ggplot2
 #' @importFrom ggplot2 element_text
 #' @param plot_data_list A list of lists containing effect size data for plotting:
-#'  - plot_data_list[i] = `plot_data`: contains:
+#'  - plot_data_list = `plot_data`: contains:
 #'    - `data`: A list containing sorted & downsampled effect size data & helpers: estimate, cons_estimate, lb, ub, below_cross_idx, and above_cross_idx
 #'    - `extra_study_details`: A list containing extra descriptive info: percent_not_zero, max_cons_effect, group_by_title, n_title, mv_estimate, and mv_ci
 #'    - `study_details`: A list of original study details: orig_stat_type, test_component_1, test_component_2, dataset, map_type, group, and ref
@@ -21,7 +21,9 @@
 #'
 #' @examples
 #' # Example usage
+#' \dontrun{
 #' create_plots(pd)
+#' }
 create_plots <- function(plot_data_list, plot_type = 'simci', effect_type = 'd', do_multivariate = FALSE, add_description = FALSE, do_minimal_title = FALSE, summary_info = NULL) {
 
   # General plot parameters

R/meta_analysis.R

@@ -14,7 +14,9 @@
 #'
 #' @examples
 #' # Example usage
+#' \dontrun{
 #' meta_analysis(v,v$brain_masks, "pooling.none.motion.none.mv.none")
+#' }
 meta_analysis <- function(v, brain_masks, combo_name, grouping_var = "category") {
 
   testing <- FALSE

R/plot_helpers.R

@@ -42,7 +42,9 @@
 #'
 #' @examples
 #' # Example usage
+#' \dontrun{
 #' plot_simci_panel(plot_data)
+#' }
 plot_simci_panel <- function(pp, plot_data_list) {
 
   if (length(plot_data_list) == 0) {
@@ -130,13 +132,16 @@ plot_simci_panel <- function(pp, plot_data_list) {
 #'  - `summary_info`: A list containing extra descriptive info: percent_not_zero, max_cons_effect, group_by_title, and n_title
 #'  - `mv_data`: A list containing multivariate effect size data: estimate, lb, and ub
 #'  - `study_details`: A list of original study details: orig_stat_type, test_component_1, test_component_2, dataset, map_type, group, and ref
+#' @param use_effect_size_bin Whether to bin effect sizes
 #'
 #' @return A ggplot object containing one or overlapping densities
 #' @export
 #'
 #' @examples
 #' # Example usage
+#' \dontrun{
 #' plot_density_panel(plot_data)
+#' }
 plot_density_panel <- function(pp, plot_data_list, use_effect_size_bin = FALSE) {
 
   # add density-specific plot params
@@ -306,7 +311,9 @@ plot_density_panel <- function(pp, plot_data_list, use_effect_size_bin = FALSE)
 #'
 #' @examples
 #' # Example usage
+#' \dontrun{
 #' plot_activation_maps(plot_data)
+#' }
 plot_activation_panel <- function(pp, plot_data_list, threshold_category = NA) {
 
   # add spatial map-specific plot params
@@ -552,7 +559,9 @@ colorbar_custom <- function(breaks, #the minimum and maximum z values for which
 #'
 #' @examples
 #' # Example usage
+#' \dontrun{
 #' plot_connectivity_panel(plot_data)
+#' }
 plot_connectivity_panel <- function(pp, plot_data_list, threshold_category = NA) {
 
   # add connectivity map-specific plot params
@@ -1018,7 +1027,9 @@ plot_power_panel <- function(pp, plot_data_list, output_type, use_category_bins
 #'
 #' @examples
 #' # Example usage
+#' \dontrun{
 #' get_summary_info(pp, study_details, extra_study_details)
+#' }
 get_summary_info <- function(study_details, extra_study_details) {
 
   summary_info <- list()
@@ -1122,7 +1133,9 @@ combine_summary_info <- function(summary_info) {
 #'
 #' @examples
 #' # Example usage
+#' \dontrun{
 #' add_plot_description(p, pp, study_details, extra_study_details)
+#' }
 add_plot_description <- function(p, pp, summary_info, add_extra_text, do_minimal_title) {
 
   # add description-specific plot params

R/prep_data_for_plot.R

@@ -16,11 +16,13 @@
 #'
 #' @examples
 #' # Example usage
+#' \dontrun{
 #' plot_info <- list(grouping_var = 'none', group_level = 'test', ref = 'atlas')
 #' pd <- prep_data_for_plot(data = v$data[[i]], study_details = v$study[i, ], 
 #' plot_info = plot_info, grouping_var='none', 
 #' combo_name = "pooling.none.motion.none.mv.none", 
 #' mv_combo_name = "pooling.none.motion.none.mv.multi")
+#' }
 prep_data_for_plot <- function(data, study_details, combo_name, mv_combo_name, estimate = 'd', plot_info = 'NA', prep_spatial = FALSE, brain_masks = NA) {
 
 

R/prep_data_for_spatial_plot.R

@@ -16,10 +16,13 @@
 #'
 #' @examples
 #' # Example usage
+#' \dontrun{
 #' pd <- prep_data_for_spatial_plot(data = v$data[[i]], 
-#' study_details = v$study[i, ], plot_info$grouping_var='none',
+#' brain_masks = brain_masks,
+#' study_details = v$study[i, ],
 #' combo_name = "pooling.none.motion.none.mv.none", 
 #' mv_combo_name = "pooling.none.motion.none.mv.multi")
+#' }
 prep_data_for_spatial_plot <- function(data, brain_masks, study_details, combo_name, mv_combo_name, estimate = 'd', plot_info = 'NA') {
 
   # Input validation

demo/00Index

@@ -1 +1 @@
-main_figure_generator    generates figures for BrainEffeX using utils package
+main_figure_generator    Example demonstration of package functions