edits to df_to_list and list_to_df functions

- rename all with `convert_` instead of `util_`
- add `convert_list_to_df1` from traits.build, so all 3 functions in one location

NAMESPACE

@@ -5,6 +5,9 @@ export("%>%")
 export(as_wide_table)
 export(bind_databases)
 export(bind_trait_values)
+export(convert_df_to_list)
+export(convert_list_to_df1)
+export(convert_list_to_df2)
 export(extract_data)
 export(extract_dataset)
 export(extract_taxa)
@@ -31,8 +34,6 @@ export(summarise_austraits)
 export(summarise_trait_means)
 export(trait_pivot_longer)
 export(trait_pivot_wider)
-export(util_df_to_list)
-export(util_list_to_df2)
 import(RefManageR)
 importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")

R/bind_databases.R

@@ -60,7 +60,7 @@ bind_databases <- function(database_1, ...) {
     dplyr::select(-dplyr::any_of(c("dataset_id", "additional_role"))) %>%
     dplyr::distinct() %>%
     dplyr::arrange(.data$last_name, .data$given_name) %>%
-    util_df_to_list()
+    convert_df_to_list()
 
   ret <- list(traits = combine("traits", databases) %>% dplyr::arrange(.data$dataset_id, .data$observation_id, .data$trait_name),
               locations = combine("locations", databases) %>% dplyr::arrange(.data$dataset_id, .data$location_id),

R/check_compatibility.R

@@ -23,7 +23,7 @@ check_compatibility <- function(austraits) {
 
     compiled_by_traits.build <-
       austraits$metadata$related_identifiers %>% 
-      util_list_to_df2() %>%
+      convert_list_to_df2() %>%
       dplyr::filter(relation_type == "isCompiledBy") |> 
       dplyr::filter(stringr::str_detect(identifier, "github.com/traitecoevo/traits.build"))
 

R/utils.R

@@ -1,18 +1,43 @@
-#'  Convert dataframe to list
+#' Convert dataframe to list
 #'
-#'  Convert a dataframe to a named list, useful when converting to yaml.
+#' @description Convert a dataframe to a named list, 
+#' useful when converting a datafreme a to yaml.
 #'
 #' @param df A dataframe
 #' @return A (yaml) list
 #' @export
-#' @examples util_df_to_list(dplyr::starwars)
-util_df_to_list <- function(df) {
+#' @examples convert_df_to_list(dplyr::starwars)
+convert_df_to_list <- function(df) {
   attr(df, "out.attrs") <- NULL
   unname(lapply(split(df, seq_len(nrow(df))), as.list))
 }
 
+#' Convert list with single entries to dataframe
+#' 
+#' @description Convert a list with a single level of entries to a dataframe, 
+#' useful when converting a yaml into a dataframe.
+#'
+#' @param my_list A list with single entries
+#' @return A tibble with two columns
+#' @export
+#' @examples \dontrun{
+#' convert_list_to_df1(as.list(dplyr::starwars)[2])
+#' }
+convert_list_to_df1 <- function(my_list) {
+
+  for (f in names(my_list)) {
+    if (is.null(my_list[[f]]))
+      my_list[[f]] <- NA
+  }
+
+  tibble::tibble(key = names(my_list), value = unname(unlist(my_list)))
+}
 
-#' Convert a list of lists to dataframe; requires that every list have same named elements.
+#' Convert list of lists to dataframe
+#' 
+#' @description Convert a list of lists to a dataframe, 
+#' useful when converting a multi-level yaml into a dataframe.
+#' Function required that every list have same named elements.
 #'
 #' @param my_list A list of lists to dataframe
 #' @param as_character A logical value, indicating whether the values are read as character
@@ -22,9 +47,9 @@ util_df_to_list <- function(df) {
 #' @examples demo_list1 <- list(word1 = "this", word2 = "is", word3 = "an", word4 = "example", word5 = "list")
 #' demo_list2 <- list(word1 = "and", word2 = "a", word3 = "second", word4 = "list", word5 = "also")
 #' combined_list <- list(demo_list1, demo_list2)
-#' util_list_to_df2(combined_list)
+#' convert_list_to_df2(combined_list)
 
-util_list_to_df2 <- function(my_list, as_character = TRUE, on_empty = NA) {
+convert_list_to_df2 <- function(my_list, as_character = TRUE, on_empty = NA) {
 
   if (is.null(my_list) || any(is.na(my_list)) || length(my_list) == 0)
     return(on_empty)
@@ -35,7 +60,6 @@ util_list_to_df2 <- function(my_list, as_character = TRUE, on_empty = NA) {
   dplyr::bind_rows(lapply(my_list, tibble::as_tibble))
 }
 
-
 #' Notify user the function they are using is no longer support
 #'
 #' @param austraits