Merge pull request #135 from NIFU-NO/dev

Dev
NIFU-NO · Dec 27, 2024 · 5916266 · 5916266
2 parents dc2f88d + a28fef9
commit 5916266
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Showing 31 changed files with 818 additions and 649 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: saros.base
 Title: Base Tools for Semi-Automatic Reporting of Ordinary Surveys
-Version: 0.3.2
+Version: 0.4.0
 Authors@R: c(
     person(given = "Stephan", 
            family = "Daus", 

diff --git a/R/add_chapter_foldername_to_chapter_structure.R b/R/add_chapter_foldername_to_chapter_structure.R
@@ -1,29 +1,37 @@
 add_chapter_foldername_to_chapter_structure <-
   function(chapter_structure,
-           max_width_folder_name = 64)  {
-
+           max_width_folder_name = 64,
+           filename_prefix = "") {
     grouping_vars <- dplyr::group_vars(chapter_structure)
 
     # Handles NA acceptably, as these are converted to string
 
-    if(!is.null(chapter_structure$chapter)) {
-      chapter_structure$.chapter_number <- as.integer(as.factor(chapter_structure$chapter))
+    if (!is.null(chapter_structure$chapter)) {
+      chapter_structure$.chapter_number <-
+        as.integer(factor(chapter_structure$chapter,
+          levels = unique(chapter_structure$chapter),
+          exclude = character()
+        ))
 
-      digits <- floor(log10(length(unique(chapter_structure$chapter))))+1
-      chapter_number_text <- sprintf(paste0("%0", digits, "d"),
-                                     chapter_structure$.chapter_number)
+      digits <- floor(log10(length(unique(chapter_structure$chapter)))) + 1
+      chapter_number_text <- sprintf(
+        paste0("%0", digits, "d"),
+        chapter_structure$.chapter_number
+      )
 
       chapter_foldername_clean <-
         filename_sanitizer(as.character(chapter_structure$chapter),
-                           max_chars = max_width_folder_name,
-                           accept_hyphen = FALSE,
-                           make_unique = FALSE)
+          max_chars = max_width_folder_name,
+          accept_hyphen = FALSE,
+          make_unique = FALSE
+        )
 
       chapter_structure$.chapter_foldername <-
-        stringi::stri_c(chapter_number_text, "_", chapter_foldername_clean,
-                        ignore_null = TRUE)
-
+        stringi::stri_c(filename_prefix,
+          chapter_number_text, "_", chapter_foldername_clean,
+          ignore_null = TRUE
+        )
     }
     chapter_structure |>
-      dplyr::group_by(dplyr::pick(tidyselect::all_of(grouping_vars)))
+      dplyr::grouped_df(grouping_vars)
   }
diff --git a/R/add_n_cats_to_chapter_structure.R b/R/add_n_cats_to_chapter_structure.R
@@ -35,5 +35,5 @@ add_n_cats_to_chapter_structure <-
         }
       ) |>
       dplyr::bind_rows() |>
-      dplyr::group_by(dplyr::pick(tidyselect::all_of(dplyr::group_vars(chapter_structure))))
+      dplyr::grouped_df(dplyr::group_vars(chapter_structure))
   }
diff --git a/R/add_n_range_to_chapter_structure.R b/R/add_n_range_to_chapter_structure.R
@@ -24,32 +24,30 @@ add_n_range_to_chapter_structure <-
            glue_template_1 = "{n}",
            glue_template_2 = "[{n[1]}-{n[2]}]",
            variable_name = ".n_range") {
-
     chapter_structure |>
-      dplyr::group_map(.keep = TRUE, .f = ~{
+      dplyr::group_map(.keep = TRUE, .f = ~ {
         deps <- as.character(unique(.x$.variable_name_dep))
         deps <- deps[!is.na(deps)]
         n <-
           lapply(deps, function(v) {
             length(data[[v]][!is.na(data[[v]])])
           }) |>
           unlist()
-        if(!is.null(n)) {
+        if (!is.null(n)) {
           n <-
             range(n, na.rm = TRUE) |>
             unique()
-          if(all(is.na(n))) {
+          if (all(is.na(n))) {
             .x[[variable_name]] <- 0
           } else {
-            template <- if(length(n)==1) glue_template_1 else glue_template_2
-            tryCatch(.x[[variable_name]] <-  glue::glue(template),
-                     error = function(cnd) glue_err(cnd=cnd, arg_name="glue_template_*"))
+            template <- if (length(n) == 1) glue_template_1 else glue_template_2
+            tryCatch(.x[[variable_name]] <- glue::glue(template),
+              error = function(cnd) glue_err(cnd = cnd, arg_name = "glue_template_*")
+            )
           }
-
         }
         .x
       }) |>
       dplyr::bind_rows() |>
-      dplyr::group_by(dplyr::pick(tidyselect::all_of(dplyr::group_vars(chapter_structure))))
+      dplyr::grouped_df(dplyr::group_vars(chapter_structure))
   }
-
diff --git a/R/add_n_to_chapter_structure.R b/R/add_n_to_chapter_structure.R
@@ -4,7 +4,7 @@ add_n_to_chapter_structure <- function(chapter_structure,
   target_grouping_variables <- c(".variable_name_dep", ".variable_name_indep")
   out <-
     chapter_structure |>
-    dplyr::group_by(dplyr::pick(tidyselect::all_of(target_grouping_variables))) |>
+    dplyr::grouped_df(vars = target_grouping_variables) |>
     dplyr::group_map(.keep = TRUE, .f = ~ {
       target_grouping_variables_tmp <-
         lapply(target_grouping_variables, function(chapter_structure_col) {
@@ -38,7 +38,7 @@ add_n_to_chapter_structure <- function(chapter_structure,
   if (length(out) > 0) {
     out |>
       dplyr::bind_rows() |>
-      dplyr::group_by(dplyr::pick(tidyselect::all_of(dplyr::group_vars(chapter_structure))))
+      dplyr::grouped_df(vars = dplyr::group_vars(chapter_structure))
   } else {
     attr(out, "ptype")
   }

diff --git a/R/add_n_vars_to_chapter_structure.R b/R/add_n_vars_to_chapter_structure.R
@@ -2,23 +2,22 @@ add_n_vars_to_chapter_structure <-
   function(chapter_structure,
            target_variable = ".variable_name_dep",
            variable_name = ".n_dep") {
-
-
     grouping_structure <- dplyr::group_vars(chapter_structure)
 
     chapter_structure |>
-    dplyr::group_map(.keep = TRUE,
-        .f = ~{
+      dplyr::group_map(
+        .keep = TRUE,
+        .f = ~ {
           uniques <- as.character(unique(.x[[target_variable]]))
-          if(!is.na(length(uniques[!is.na(uniques)]))) {
+          if (!is.na(length(uniques[!is.na(uniques)]))) {
             .x[[variable_name]] <-
               length(uniques[!is.na(uniques)])
           } else {
             .x[[variable_name]] <- 0
           }
           .x
-        }) |>
+        }
+      ) |>
       dplyr::bind_rows() |>
-      dplyr::group_by(dplyr::pick(tidyselect::all_of(grouping_structure)))
-
+      dplyr::grouped_df(grouping_structure)
   }
diff --git a/R/add_obj_name_to_chapter_structure.R b/R/add_obj_name_to_chapter_structure.R
@@ -5,40 +5,43 @@ add_obj_name_to_chapter_structure <-
            max_width = 128,
            valid_obj = TRUE,
            make_unique = TRUE,
-           to_lower = TRUE
-  ) {
-
-
+           to_lower = TRUE) {
     grouping_structure_original <- dplyr::group_vars(chapter_structure)
     out <- replace_label_groups_with_name_groups(chapter_structure)
     grouping_structure_reduced <- dplyr::group_vars(out)
     grouping_structure_temporary <- ".variable_group_id"
 
     collapsed <-
       out |>
-      dplyr::group_by(dplyr::pick(tidyselect::all_of(c(grouping_structure_temporary)))) |>
-      dplyr::group_map(.keep = FALSE,
-                       .f = ~{
-
-                         .x[[variable_name]] <-
-                           get_common_names_from_data(.x[, grouping_structure_reduced],
-                                                      sep = sep,
-                                                      max_width = max_width)
-                         .x
-                       }) |>
+      dplyr::grouped_df(grouping_structure_temporary) |>
+      dplyr::group_map(
+        .keep = FALSE,
+        .f = ~ {
+          .x[[variable_name]] <-
+            get_common_names_from_data(.x[, grouping_structure_reduced],
+              sep = sep,
+              max_width = max_width
+            )
+          .x
+        }
+      ) |>
       dplyr::bind_rows() |>
       dplyr::distinct(dplyr::pick(tidyselect::all_of(c(grouping_structure_original, variable_name))))
 
     collapsed[[variable_name]] <-
-      filename_sanitizer(x = collapsed[[variable_name]],
-                         max_chars = max_width,
-                         sep = sep,
-                         valid_obj = valid_obj,
-                         to_lower = to_lower,
-                         make_unique = make_unique)
+      filename_sanitizer(
+        x = collapsed[[variable_name]],
+        max_chars = max_width,
+        sep = sep,
+        valid_obj = valid_obj,
+        to_lower = to_lower,
+        make_unique = make_unique
+      )
 
-    dplyr::left_join(x = out,
-                     y = collapsed,
-                     by = grouping_structure_original) |>
-      dplyr::group_by(dplyr::pick(tidyselect::all_of(grouping_structure_original)))
+    dplyr::left_join(
+      x = out,
+      y = collapsed,
+      by = grouping_structure_original
+    ) |>
+      dplyr::grouped_df(vars = grouping_structure_original)
   }
diff --git a/R/add_parsed_vars_to_chapter_structure.R b/R/add_parsed_vars_to_chapter_structure.R
@@ -1,30 +1,36 @@
 add_parsed_vars_to_chapter_structure <-
   function(chapter_structure,
            data) {
-
     chapter_structure$.variable_selection <-
       stringi::stri_replace_all_fixed(chapter_structure$.variable_selection,
-                                      pattern = '\"',
-                                      replacement = "'")
+        pattern = '\"',
+        replacement = "'"
+      )
     chapter_structure$.variable_selection <-
       stringi::stri_replace_all_regex(chapter_structure$.variable_selection,
-                                      pattern = '[[:space:],]+',
-                                      replacement = ",")
+        pattern = "[[:space:],]+",
+        replacement = ","
+      )
 
     chapter_structure$.cols <-
-      eval_cols(x = chapter_structure$.variable_selection,
-                data = data,
-                call = call)
+      eval_cols(
+        x = chapter_structure$.variable_selection,
+        data = data,
+        call = call
+      )
 
     chapter_structure <-
       tidyr::unnest_longer(chapter_structure,
-                           col = ".cols",
-                           values_to = ".variable_position",
-                           indices_to = ".variable_name")
+        col = ".cols",
+        values_to = ".variable_position",
+        indices_to = ".variable_name"
+      )
+    chapter_structure$.variable_position <- unname(chapter_structure$.variable_position)
     chapter_structure$.variable_name <-
       ifelse(chapter_structure$.variable_name %in% c("1", ""),
-             NA_character_,
-             chapter_structure$.variable_name)
+        NA_character_,
+        chapter_structure$.variable_name
+      )
 
     chapter_structure
   }