Remove mesos entirely from saros.base

R/attach_chapter_dataset.R

@@ -2,7 +2,6 @@ attach_chapter_dataset <- function(chapter_structure_chapter,
                                    data,
                                    path,
                                    chapter_foldername_clean,
-                                   mesos_var,
                                    auxiliary_variables,
                                    serialized_format = "rds") {
 
@@ -19,7 +18,6 @@ attach_chapter_dataset <- function(chapter_structure_chapter,
 
   data_chapter <- data[, names(data) %in% unique(c(dep_vars,
                                                    indep_vars,
-                                                   mesos_var,
                                                    auxiliary_variables)), drop = FALSE]
 
   filename_chapter_dataset <-

R/draft_report.R

@@ -188,7 +188,6 @@ draft_report <-
            title = "Report",
            authors = NULL,
            authors_col = "author",
-           mesos_var = NULL,
 
            chapter_yaml_file = NULL,
            chapter_qmd_start_section_filepath = NULL,
@@ -245,91 +244,50 @@ draft_report <-
 
     all_authors <- get_authors(data = chapter_structure, col=args$authors_col)
 
-    if(!is_string(args$mesos_var)) {
 
-      uniques <- NA_character_
+    chapter_filepaths <-
+      rlang::exec(
+        gen_qmd_chapters,
+        chapter_structure = chapter_structure,
+        data = data,
+        path = path,
+        !!!args[!names(args) %in% .saros.env$ignore_args])
 
-    } else {
-      # Mesos reports
-      uniques <- pull_uniques(data[[args$mesos_var]])
-    }
-
-    report_foldername_clean <- filename_sanitizer(uniques, max_chars = args$max_clean_folder_name)
-
-    index_filepath <-
-      lapply(X =
-               cli::cli_progress_along(uniques, # Not working well
-                                       format = "Generating mesos report for... {uniques[cli::pb_current]}",
-                                       clear = FALSE,
-                                       auto_terminate = FALSE),
-             FUN = function(.x) {
-
-
-               if(is.na(uniques[.x])) { # Macro
-
-                 mesos_group <- NULL
-
-
-               } else {  # Mesos
 
-                 mesos_group <- uniques[.x]
-                 path <- file.path(path, report_foldername_clean[.x])
-                 args$title <- stringi::stri_c(if(!is.na(args$title)) args$title,
-                                               if(!is.na(uniques[.x])) uniques[.x],
-                                          ignore_null=TRUE)
 
 
-               }
+    if(isTRUE(args$combined_report)) {
 
+      report_filepath <-
+        gen_qmd_file(
+          path = path,
+          filename = args$report_filename,
+          yaml_file = args$report_yaml_file,
+          qmd_start_section_filepath = args$report_qmd_start_section_filepath,
+          qmd_end_section_filepath = args$report_qmd_end_section_filepath,
+          title = args$title,
+          authors = all_authors,
+          output_formats = NULL,
+          output_filename = NULL,
+          call = rlang::caller_env())
+    }
 
-               chapter_filepaths <-
-                 rlang::exec(
-                   gen_qmd_chapters,
-                   chapter_structure = chapter_structure,
-                   data = data,
-                   mesos_group = mesos_group,
-                   path = path,
-                   !!!args[!names(args) %in% .saros.env$ignore_args])
-
-
-
-
-               if(isTRUE(args$combined_report)) {
-
-                 report_filepath <-
-                     gen_qmd_file(
-                       path = path,
-                       filename = args$report_filename,
-                       yaml_file = args$report_yaml_file,
-                       qmd_start_section_filepath = args$report_qmd_start_section_filepath,
-                       qmd_end_section_filepath = args$report_qmd_end_section_filepath,
-                       title = args$title,
-                       authors = all_authors,
-                       output_formats = NULL,
-                       output_filename = NULL,
-                       call = rlang::caller_env())
-               }
-
-               index_filepath <-
-                   gen_qmd_file(
-                   path = path,
-                   filename = args$index_filename,
-                   yaml_file = args$index_yaml_file,
-                   qmd_start_section_filepath = args$index_qmd_start_section_filepath,
-                   qmd_end_section_filepath = args$index_qmd_end_section_filepath,
-                   title = args$title,
-                   authors = all_authors,
-                   output_formats = if(!is.null(args$report_yaml_file)) find_yaml_formats(args$report_yaml_file),
-                   output_filename = args$report_filename,
-                   call = rlang::caller_env())
-
-               index_filepath
+    index_filepath <-
+      gen_qmd_file(
+        path = path,
+        filename = args$index_filename,
+        yaml_file = args$index_yaml_file,
+        qmd_start_section_filepath = args$index_qmd_start_section_filepath,
+        qmd_end_section_filepath = args$index_qmd_end_section_filepath,
+        title = args$title,
+        authors = all_authors,
+        output_formats = if(!is.null(args$report_yaml_file)) find_yaml_formats(args$report_yaml_file),
+        output_filename = args$report_filename,
+        call = rlang::caller_env())
 
-             })
 
-    index_filepath <- as.character(unlist(index_filepath))
 
-    validate_path_lengths_on_win(path = path,
+    validate_path_lengths_on_win(path = index_filepath,
                                  max_path_warning_threshold = max_path_warning_threshold)
 
 

R/gen_qmd_chapters.R

@@ -12,28 +12,20 @@
 #' main question, and being of the same data type.
 #'
 #' @inheritParams draft_report
-#' @param mesos_group *Specific group to compare with*
-#'
-#'   `scalar<character>` // *Default:* `NULL` (`optional`)
-#'
-#'   Both the absolute and relative folder paths are required, as strings.
-#'
 #'
 #' @return Side-effects: qmd-files generated in the specified working directory.
 #' @keywords internal
 #'
 gen_qmd_chapters <-
   function(chapter_structure,
            data,
-           mesos_group = NULL,
            authors_col = "author",
            ...,
            call = rlang::caller_env()
   ) {
 
     dots <- rlang::list2(...)
 
-    check_string(mesos_group, n=1, null.ok=TRUE, call = call)
 
     path <- fs::as_fs_path(dots$path)
     dir.create(path = path, recursive = TRUE, showWarnings = FALSE)
@@ -100,7 +92,6 @@ gen_qmd_chapters <-
               gen_qmd_structure,
               data = data,
               chapter_structure = chapter_structure_chapter,
-              mesos_group = mesos_group,
               chapter_folderpath_absolute = chapter_folderpath_absolute,
               chapter_foldername = chapter_foldername_clean,
               !!!dots#[!names(dots) %in% c("chapter_structure", "call")]
@@ -130,7 +121,6 @@ gen_qmd_chapters <-
                                      chapter_structure_chapter = chapter_structure_chapter,
                                      chapter_foldername_clean = chapter_foldername_clean,
                                      path = path,
-                                     mesos_var = dots$mesos_var,
                                      auxiliary_variables = dots$auxiliary_variables,
                                      serialized_format = dots$serialized_format)
             }
@@ -157,7 +147,7 @@ gen_qmd_chapters <-
 
     chapter_filepaths <- unlist(chapter_filepaths)
 
-    cli::cli_process_done(msg_done = "Completed report{if(is_string(mesos_group)) paste0(' for ', mesos_group)}.")
+    cli::cli_process_done(msg_done = "Completed report.")
 
 
     chapter_filepaths

R/gen_qmd_structure.R

@@ -120,12 +120,6 @@ gen_qmd_structure <-
       return(output)
     }
 
-    # chapter_structure <- remove_empty_col_for_mesos_group(data = data,
-    #                                                      chapter_structure = chapter_structure,
-    #                                                      mesos_group = mesos_group,
-    #                                                      mesos_var = dots$mesos_var,
-    #                                                      hide_chunk_if_n_below = dots$hide_chunk_if_n_below)
-
     grouping_structure <- dplyr::group_vars(chapter_structure)
     non_grouping_vars <- colnames(chapter_structure)[!colnames(chapter_structure) %in% grouping_structure]
 

R/log_unused_variables.R

@@ -1,13 +1,11 @@
 log_unused_variables <- function(data,
                                  chapter_structure,
                                  auxiliary_variables = NULL,
-                                 mesos_var = NULL,
                                  log_file = NULL) {
   used_vars <-
     unique(c(as.character(chapter_structure$.variable_name_dep),
              as.character(chapter_structure$.variable_name_indep),
-             auxiliary_variables,
-             mesos_var))
+             auxiliary_variables))
   not_used_vars <- colnames(data)[!colnames(data) %in% used_vars]
   if(length(not_used_vars)>0) {
     cli::cli_inform("Not using the following variables in {.arg data}: {.var {not_used_vars}}.")

R/refine_chapter_overview.R

@@ -107,7 +107,7 @@
 #'
 #'  `scalar<integer>` // *default:* `10` (`optional`)
 #'
-#'  Whether to hide result if N for a given datasets (or mesos group) is below
+#'  Whether to hide result if N for a given dataset is below
 #'  this value. NOTE: Exceptions will be made to chr_table and chr_plot as these are
 #'  typically exempted in the first place. This might change in the future with
 #'  a separate argument.
@@ -116,15 +116,15 @@
 #'
 #'   `scalar<logical>` // *default:* `TRUE` (`optional`)
 #'
-#'   For mesos reports using the element "chr_table", open responses are
-#'   displayed for also the entire sample (`FALSE`) or only for the mesos
+#'   MOVE TO saros.contents: For reports using the element "chr_table", open responses are
+#'   displayed for also the entire sample (`FALSE`) or only for the target
 #'   group to ensure data privacy (`TRUE`).
 #'
 #' @param hide_variable_if_all_na *Hide variable from outputs if containing all NA*
 #'
 #'   `scalar<boolean>` // *default:* `TRUE` (`optional`)
 #'
-#'   Whether to remove all variables (in particular useful for mesos) if all values are NA
+#'   Whether to remove variables if all values are NA.
 #'
 #' @param max_width_obj,max_width_chunk,max_width_file *Maximum object width*
 #'
@@ -161,13 +161,6 @@
 #'   Column names in `data` that should always be included in datasets for
 #'   chapter qmd-files, if `attach_chapter_dataset=TRUE`. Not publicly available.
 #'
-#' @param mesos_var *Variable in ´data´ indicating groups to tailor reports for*
-#'
-#'   `scalar<character>` // *default:* `NULL` (`optional`)
-#'
-#'   Column name in data indicating the groups for which mesos reports will be produced.
-#'
-#'
 #' @param variable_group_dep *Name for the variable_group_dep column*
 #'
 #'   `scalar<string>` // *default:* `".variable_group_dep"`
@@ -247,8 +240,6 @@ refine_chapter_overview <-
            sep_file = "-",
            max_clean_folder_name = 12,  # Tidy up argument name: max_width_clean_folder_name
 
-           # MESOS AND OTHER FEATURES
-           mesos_var = NULL, # Not in use yet
            auxiliary_variables = NULL, # Not in use yet
            ...,
            progress = TRUE,
@@ -344,7 +335,6 @@ refine_chapter_overview <-
         log_unused_variables(chapter_structure = out,
                              data = data,
                              auxiliary_variables = auxiliary_variables,
-                             mesos_var = mesos_var,
                              log_file = log_file)
         # if(!is.factor(out$.variable_name_dep)) browser()
 

R/validate_draft_report_args.R

@@ -30,7 +30,6 @@ validate_draft_report_args <- function(params) {
       chapter_structure = list(fun = function(x) validate_chapter_structure(x, core_chapter_structure_cols = core_chapter_structure_cols)),
 
       # Character vectors (not enums)
-      mesos_var = list(fun = function(x) is.null(x) || is_string(x)),
       auxiliary_variables = list(fun = function(x) is.null(x) || (is.character(x) && all(x %in% colnames(params$data)))),
       path = list(fun = function(x) is_string(x)),
 
@@ -74,17 +73,6 @@ validate_draft_report_args <- function(params) {
   params$tabular_format <- params$tabular_format[1]
   params$serialized_format <- params$serialized_format[1]
 
-  if(is_string(params$mesos_var)) {
-    if(!any(colnames(params$data) == params$mesos_var)) {
-      cli::cli_abort("{.arg mesos_var}: {.arg {params$mesos_var}} not found in data.")
-    }
-    if(all(is.na(params$data[[params$mesos_var]]))) {
-      cli::cli_abort("{.arg mesos_var}: All mesos_var entries are NA.")
-    }
-  }
-
-
-
 
   pkg <- switch(params$tabular_format,
                 "delim" = "utils",

R/validate_refine_chapter_overview_args.R

@@ -34,7 +34,6 @@ validate_refine_chapter_overview_args <- function(params) {
       sep_obj = list(fun = function(x) is_string(x)),
       sep_chunk = list(fun = function(x) is_string(x)),
       sep_file = list(fun = function(x) is_string(x)),
-      mesos_var = list(fun = function(x) is.null(x) || is_string(x)),
       auxiliary_variables = list(fun = function(x) is.null(x) || (is.character(x) && all(x %in% colnames(params$data)))),
       always_show_bi_for_indep = list(fun = function(x) is.null(x) || (is.character(x) && all(x %in% colnames(params$data)))),
       variables_show_bi_for_by = list(fun = function(x) is.null(x) || (is.character(x) && all(x %in% colnames(params$data)))),
@@ -79,15 +78,6 @@ validate_refine_chapter_overview_args <- function(params) {
 
   params$chunk_templates <- validate_chunk_templates(params$chunk_templates)
 
-  if(is_string(params$mesos_var)) {
-    if(!any(colnames(params$data) == params$mesos_var)) {
-      cli::cli_abort("{.arg mesos_var}: {.arg {params$mesos_var}} not found in data.")
-    }
-    if(all(is.na(params$data[[params$mesos_var]]))) {
-      cli::cli_abort("{.arg mesos_var}: All mesos_var entries are NA.")
-    }
-  }
-
 
   if(!all(c("chapter", ".template_name") %in% params$organize_by)) {
     cli::cli_abort(c("{.arg organize_by} must contain both {.var {c('chapter', '.template_name')}}.",