Cleanup doc warnings in iidda package

R/iidda/R/data_frame_tools.R

@@ -1,3 +1,9 @@
+#' Set IIDDA Column Types
+#'
+#' Deprecated -- iidda.api package is not more robust.
+#'
+#' @param data Dataset from IIDDA Api
+#'
 #' @export
 set_iidda_col_types = function(data) {
   if (names(data)[1] == 'Internal Server Error') {

R/iidda/R/historical_normalization.R

@@ -17,6 +17,12 @@ normalize_diseases = function(diseases) {
   )
 }
 
+#' Two Field Format
+#'
+#' Attempt to automatically convert a dataset from `disease{|_subclass|_family}`
+#' format of disease ID to the `{|nesting_}disease` format.
+#'
+#' @param dataset A tidy data set with `disease{|_subclass|_family}` columns.
 #' @export
 two_field_format = function(dataset) {
   (dataset

R/iidda/R/metadata_tools.R

@@ -1,3 +1,9 @@
+#' Read Tracking Tables
+#'
+#' Read metadata tracking tables for an IIDDA project.
+#'
+#' @param path Path containing tracking tables.
+#'
 #' @export
 read_tracking_tables = function(path) {
   valid_colnames = c("access_script", "disease_family", "disease", "disease_subclass", "icd_7", "icd_9",
@@ -12,13 +18,20 @@ read_tracking_tables = function(path) {
     "staging_url_prefix", "scan", "access_script", "prep_script"
   )
   paths = file.path(path, list.files(path, pattern = '.csv'))
-  (paths
+  output = (paths
     %>% lapply(read.csv, check.names = FALSE)
     %>% setNames(tools::file_path_sans_ext(basename(paths)))
-    %>% lapply(function(x) select(x, any_of(valid_colnames)))
+    #%>% lapply(function(x) select(x, any_of(valid_colnames)))
     #%>% lapply(drop_empty_cols)
     %>% lapply(drop_empty_rows)
   )
+  valid_tabs = vapply(output, \(tab) all(names(tab) %in% valid_colnames), logical(1L))
+  if (any(!valid_tabs)) {
+    for (tnm in names(output)[!valid_tabs]) {
+      warn_msg = sprintf("Tracking table %s has invalid column names. Valid column names include:\n   %s", tnm, paste0(valid_colnames, collapse = ", "))
+      warning(warn_msg)
+    }
+  }
 }
 
 #' Read Tracking Metadata
@@ -189,6 +202,10 @@ get_tracking_metadata = function(tidy_dataset, digitization, tracking_path, orig
   metadata
 }
 
+#' Which Tracking Tables have a Particular Column
+#'
+#' @param metadata Output of \code{\link{read_tracking_tables}}.
+#' @param col_nm Name of a column.
 #' @export
 tracking_tables_with_column = function(metadata, col_nm) {
   (metadata
@@ -200,6 +217,8 @@ tracking_tables_with_column = function(metadata, col_nm) {
   )
 }
 
+#' Tracking Table Keys
+#'
 #' @export
 tracking_table_keys = list(
   organization = list(
@@ -225,6 +244,11 @@ tracking_table_keys = list(
 )
 
 
+#' Melt Tracking Table Keys (Deprecated)
+#'
+#' To be used in conjunction with \code{\link{tracking_table_keys}}.
+#'
+#' @param keys Character vector of
 #' @export
 melt_tracking_table_keys = function(keys) {
   (keys
@@ -233,15 +257,10 @@ melt_tracking_table_keys = function(keys) {
   )
 }
 
-#' Check Tracking Table Consistency
+#' Write Local Data Dictionaries
 #'
-#' @param path path to tracking tables
-check_tracking_tables = function(path) {
-  d = read_tracking_tables(path)
-
-}
-
-
+#' @param metadata Output of \code{\link{read_tracking_tables}}.
+#' @param path Path to a new JSON file.
 #' @importFrom tibble rownames_to_column
 #' @importFrom jsonlite write_json
 #' @export

R/iidda/R/missing_value_config.R

@@ -1,3 +1,16 @@
+#' Missing Handlers
+#'
+#' Construct an object with functions for handling missing values.
+#'
+#' @param unclear Character vector giving values corresponding to numbers
+#' that were unclear to data enterers.
+#' @param not_reported Character vector giving values corresponding to
+#' numbers that were not reported in the original source.
+#' @param zeros Character vector giving values corresponding to
+#' `0` but that were entered as another character to resemble the original
+#' source.
+#'
+#' @returns An environment with functions for handling missing values.
 #' @export
 MissingHandlers = function(
       unclear = c("Unclear", "unclear", "uncleaar", "uncelar", "r")

R/iidda/R/readme_templates.R

@@ -1,3 +1,7 @@
+#' README File Template
+#'
+#' (Deprecated)
+#'
 #' @export
 readme_classic_iidda = "# %{new_data_name}s
 

R/iidda/R/repo_paths.R

@@ -77,7 +77,7 @@ list_file_id = function(..., ext, root) {
 #' List Resources IDs
 #'
 #' @param source Source ID.
-#' @param type Type of resouce.
+#' @param type Type of resource.
 #' @param root Path to the root of the repository.
 #'
 #' @export
@@ -90,6 +90,13 @@ list_resource_ids = function(source
   read.csv(file.path(pipeline_dir, source, "tracking", file))[[1L]]
 }
 
+#' List Dependency IDs
+#'
+#' @param source Source ID.
+#' @param dataset Dataset ID.
+#' @param type Type of resource.
+#' @param root Path to the root of the repository.
+#'
 #' @export
 list_dependency_ids = function(source, dataset
     , type = c("PrepScripts", "Scans", "Digitizations", "AccessScripts")
@@ -107,6 +114,13 @@ list_dependency_ids = function(source, dataset
   tracking[[1L]][tracking[[2L]] == dataset]
 }
 
+#' List Dependency Paths
+#'
+#' @param source Source ID.
+#' @param dataset dataset ID.
+#' @param type Type of resource.
+#' @param root Path to the root of the repository.
+#'
 #' @export
 list_dependency_paths = function(source, dataset
     , type = c("PrepScripts", "Scans", "Digitizations", "AccessScripts")
@@ -120,9 +134,15 @@ list_dependency_paths = function(source, dataset
   vapply(strip_blob_github(urls), add_root_and_check, character(1L), USE.NAMES = FALSE)
 }
 
+#' List Source IDs
+#'
+#' @param root Path to the root of the repository.
 #' @export
 list_source_ids = function(root) list.files(add_root_and_check("pipelines", root))
 
+#' List Dataset IDs by Source
+#'
+#' @param root Path to the root of the repository.
 #' @export
 list_dataset_ids_by_source = function(root) {
   sources = list_source_ids(root)
@@ -133,16 +153,33 @@ list_dataset_ids_by_source = function(root) {
   )
 }
 
+#' List Dataset IDs
+#'
+#' @param source Source ID.
+#' @param root Path to the root of the repository.
+#'
 #' @export
 list_dataset_ids = function(source, root) {
   list_resource_ids(source, "TidyDatasets", root)
 }
 
+#' List Prep Script IDs
+#'
+#' @param source Source ID.
+#' @param root Path to the root of the repository.
+#'
 #' @export
 list_prep_script_ids = function(source, root) {
   list_resource_ids(source, "PrepScripts", root)
 }
 
+
+#' Get Main Script
+#'
+#' @param source Source ID.
+#' @param dataset dataset ID.
+#' @param root Path to the root of the repository.
+#'
 #' @export
 get_main_script = function(source, dataset, root) {
   assert_string(
@@ -151,6 +188,12 @@ get_main_script = function(source, dataset, root) {
   )
 }
 
+#' Get all Dependencies
+#'
+#' @param source Source ID.
+#' @param dataset dataset ID.
+#' @param root Path to the root of the repository.
+#'
 #' @export
 get_all_dependencies = function(source, dataset, root) {
   unlist(lapply(c("PrepScripts", "Scans", "Digitizations", "AccessScripts")
@@ -161,6 +204,13 @@ get_all_dependencies = function(source, dataset, root) {
   ))
 }
 
+#' Get Dataset path
+#'
+#' @param source Source ID.
+#' @param dataset dataset ID.
+#' @param root Path to the root of the repository.
+#' @param ext Dataset file extension.
+#'
 #' @export
 get_dataset_path = function(source, dataset, root, ext = "csv") {
   path = file.path(
@@ -175,6 +225,11 @@ get_dataset_path = function(source, dataset, root, ext = "csv") {
   add_root(path, root)
 }
 
+#' Get Source Path
+#'
+#' @param source Source ID.
+#' @param root Path to the root of the repository.
+#'
 #' @export
 get_source_path = function(source, root) {
   add_root(

R/iidda/R/string_tools.R

@@ -159,16 +159,25 @@ vsub = function(pattern, replacement, x, ...) {
   x
 }
 
-#' Remove Trailing Slash
+#' Remove Trailing / Leading Slash
 #'
-#' @param x Character vector with paths
-#' @return Character vector without trailing slash
+#' @param x Character vector with paths.
+#' @return Character vector without trailing/leading slash.
 #' @export
 rm_trailing_slash = function(x) sub('/$', '', x)
 
+#' @rdname rm_trailing_slash
 #' @export
 rm_leading_slash = function(x) sub('^/', '', x)
 
+#' Or Pattern
+#'
+#' Construct regex for Boolean-or.
+#'
+#' @param x Character vector of alternative patterns.
+#' @param at_start Match only at the start of strings.
+#' @param at_end Match only at the end of strings.
+#'
 #' @export
 or_pattern = function(x, at_start = TRUE, at_end = TRUE) {
   x = "(" %+% paste0(x, collapse = "|") %+% ")"

R/iidda/R/xlsx_diff.R

@@ -73,6 +73,12 @@ cp_git_version = function(file, version_hash) {
   temp
 }
 
+#' Excel to CSV
+#'
+#' Convert an Excel file to a CSV file.
+#'
+#' @param xlsx_path Path to an Excel file.
+#' @param csv_path Path to a new CSV file.
 #' @importFrom tidyxl xlsx_cells
 #' @importFrom readr write_csv
 #' @export