Merge pull request #151 from sunroofgod/v2023.9.12

v2023.9.12 as per CRAN

R/002_df_for_plots.R

@@ -1,32 +1,17 @@
-#' Helper functions that generate dfs for tuftelines plot
-#'
-#' @noRd
-#'
+#' Generates the dataframe requires for the tufte lines plot component in raw plots. 
+#' 
+#' This function returns a dataframe with summary statistics, such as mean, standard
+#' deviation and quantiles (depending on the effect size) based on the input dataset. 
+#' 
 #' @param raw_data The tidy dataset passed to [load()] that was cleaned and altered for plotting.
 #' @param enquo_x Quosure of x as initially passed to [load()].
 #' @param enquo_y Quosure of y as initially passed to [load()].
 #' @param proportional Boolean value as initially passed to [load()].
-#' @param float_contrast Default TRUE. If TRUE, a Gardner-Altman plot will be produced.
-#' If FALSE, a Cumming estimation plot will be produced.
-#' @param enquo_id_col Quosure of id_col as initially passed to [load()].
-#' @param idx The list of control-test groupings as initially passed to [load()].
-#' @param tufte_lines_df Dataset for the creation of tufte lines.
-#' @param proportional_data List of calculations related to the plotting of proportion plots.
-#' @param scale_factor_sig Decimal value ranging from 0 to 1 which determines the significance of the scale factor.
-#' @param bar_width Numeric value determining the width of the bar in the sankey diagram or proportion plots.
-#' @param gap Numeric value determining the space between the bars in the sankey diagram or proportion plots.
-#' @param sankey Boolean value determining if the flows between the bar charts will be plotted.
-#' @param flow Boolean value determining whether the bars will be plotted in pairs.
-#' @param N The number of rows in the proportional dataset.
-#' @param proportion_success The proportion or ratio of values that are 1.
-#' @param boots Boot result obtained from boot.ci
-#' @param x_idx_position Numeric value determining the position of the plots on the x-axis.
+#' @param gap Integer value specifying the amount of gap for each tufte line.
+#' @param effsize_type String value specifying type of effect size.
 #'
-#' @details
-#' Contains functions `df_for_tufte`, `create_dfs_for_sankey`, `create_dfs_for_xaxis_redraw`, `create_dfs_for_proportion_bar` for generation of dfs.
-#'
-#' @return
-#' Various dfs which is required for the plotting functions to obtain a complete dabest plot.
+#' @returns a dataframe for plotting of the tufte lines plot component.
+#' @noRd
 create_df_for_tufte <- function(raw_data, enquo_x, enquo_y, proportional, gap, effsize_type) {
   tufte_lines_df <- raw_data %>%
     dplyr::group_by(!!enquo_x) %>%
@@ -67,8 +52,19 @@ create_df_for_tufte <- function(raw_data, enquo_x, enquo_y, proportional, gap, e
 
   return(tufte_lines_df)
 }
-
-# Function for creation of df for flow = FALSE plot
+#' Generates df for tufte lines plot component for raw plot WITH flow = FALSE.
+#' 
+#' This function rearranges and duplicates rows in a given dataframe (containing
+#' summary statistics) in the order of the unlisted given list of vectors.   
+#'
+#' @param idx List of vectors of control-test groupings that determines the arrangement
+#' of the final dataframe output.
+#' @param tufte_lines_df dataframe for plotting of the tufte lines plot component as 
+#' generated by [create_df_for_tufte()].
+#' @param enquo_x Quosure of x as initially passed to [load()].
+#' 
+#' @returns dataframe
+#' @noRd
 create_dfs_for_nonflow_tufte_lines <- function(idx,
                                                tufte_lines_df,
                                                enquo_x) {

cran-comments.md

@@ -1,3 +1,8 @@
+## Resubmission
+This is a resubmission. In this version I have:
+
+* Contacted the maintainers of affected package(s) >= 2 weeks ago.
+
 ## R CMD check results
 
 0 errors | 0 warnings | 3 note
@@ -42,4 +47,4 @@ Issues with CRAN packages are summarised below.
 
 * permubiome (NA)
 
-Maintainers of affected package(s) above have been informed for >= 2 weeks. No further changes to be made.
+Maintainers of affected package(s) above have been informed for >= 2 weeks ago. No further changes to be made.