standardise pipes

Change all native pipes (|>) to %>% pipes

R/check_compatibility.R

@@ -24,7 +24,7 @@ check_compatibility <- function(database) {
     compiled_by_traits.build <-
       database$metadata$related_identifiers %>% 
       convert_list_to_df2() %>%
-      dplyr::filter(relation_type == "isCompiledBy") |> 
+      dplyr::filter(relation_type == "isCompiledBy") %>% 
       dplyr::filter(stringr::str_detect(identifier, "github.com/traitecoevo/traits.build"))
 
     if(is.null(compiled_by_traits.build) | nrow(compiled_by_traits.build) > 0) {

R/join_.R

@@ -279,10 +279,10 @@ join_contributors <- function(database,
   } else if (format == "single_column_json") {
 
     compacted_contributors_column <-
-      contributors_tmp |> 
-      tidyr::nest(-dplyr::all_of("dataset_id")) |>
-      dplyr::mutate(data_contributors = purrr::map_chr(data, jsonlite::toJSON)) |>
-      dplyr::select(-dplyr::any_of("data")) |>
+      contributors_tmp %>% 
+      tidyr::nest(-dplyr::all_of("dataset_id")) %>%
+      dplyr::mutate(data_contributors = purrr::map_chr(data, jsonlite::toJSON)) %>%
+      dplyr::select(-dplyr::any_of("data")) %>%
       dplyr::ungroup()
   }
 
@@ -383,10 +383,10 @@ join_location_properties <- function(database,
   } else if (format == "single_column_json") {
 
     compacted_locations_column <-
-      locations |> 
-      tidyr::nest(data = -dplyr::all_of(c("dataset_id", "location_id"))) |>
-      dplyr::mutate(location_properties = purrr::map_chr(data, jsonlite::toJSON)) |>
-      dplyr::select(-dplyr::any_of("data")) |>
+      locations %>% 
+      tidyr::nest(data = -dplyr::all_of(c("dataset_id", "location_id"))) %>%
+      dplyr::mutate(location_properties = purrr::map_chr(data, jsonlite::toJSON)) %>%
+      dplyr::select(-dplyr::any_of("data")) %>%
       dplyr::ungroup()
 
     database$traits <- database$traits %>%
@@ -481,13 +481,13 @@ join_context_properties <- function(database,
   } else if (format == "single_column_json") {
 
     contexts_tmp <-
-      contexts_tmp |> 
-      tidyr::separate_longer_delim(link_vals, ", ") |>
-      dplyr::distinct() |> 
-      dplyr::mutate(description = ifelse(!is.na(description) & include_description, description, NA)) |> 
-      tidyr::nest(data = -dplyr::all_of(c("dataset_id", "link_id", "link_vals"))) |> 
-      dplyr::mutate(value = purrr::map_chr(data, jsonlite::toJSON)) |>
-      dplyr::select(-dplyr::any_of("data")) |>
+      contexts_tmp %>% 
+      tidyr::separate_longer_delim(link_vals, ", ") %>%
+      dplyr::distinct() %>% 
+      dplyr::mutate(description = ifelse(!is.na(description) & include_description, description, NA)) %>% 
+      tidyr::nest(data = -dplyr::all_of(c("dataset_id", "link_id", "link_vals"))) %>% 
+      dplyr::mutate(value = purrr::map_chr(data, jsonlite::toJSON)) %>%
+      dplyr::select(-dplyr::any_of("data")) %>%
       dplyr::ungroup()
 
     pivot <- FALSE

R/load_austraits.R

@@ -62,7 +62,7 @@ load_austraits <- function(doi = NULL, version = NULL, path = "data/austraits",
   version_name <- paste0("v", version)
 
   # Getting specific version
-  id <- ret[which(ret$version == version), "id"] |> as.character()
+  id <- ret[which(ret$version == version), "id"] %>% as.character()
 
   target <- res$hits$hits$files[[version_name]]
 
@@ -119,15 +119,15 @@ load_json <- function(path, update){
 
 create_metadata <- function(res){
   # Version table
-  ret <- res$hits$hits$metadata |> 
-    dplyr::select(tidyselect::all_of(c("publication_date", "doi", "version"))) |>  
-    dplyr::mutate(version = gsub("v", "", version) |> numeric_version(),
+  ret <- res$hits$hits$metadata %>% 
+    dplyr::select(tidyselect::all_of(c("publication_date", "doi", "version"))) %>%  
+    dplyr::mutate(version = gsub("v", "", version) %>% numeric_version(),
                   id = stringr::str_remove_all(doi, stringr::fixed("10.5281/zenodo."))
-                  )|>  # set as numeric version for easier filtering
-    dplyr::filter(version >= "3.0.2") |> # exclude everything pre 3.0.2
+                  )%>%  # set as numeric version for easier filtering
+    dplyr::filter(version >= "3.0.2") %>% # exclude everything pre 3.0.2
     dplyr::mutate(version = as.character(version),
-                  publication_date = lubridate::ymd(publication_date)) |>  # change back as character
-    dplyr::tibble() |> 
+                  publication_date = lubridate::ymd(publication_date)) %>%  # change back as character
+    dplyr::tibble() %>% 
     dplyr::arrange(dplyr::desc(publication_date))
 
   ret
@@ -228,10 +228,10 @@ get_version_latest <- function(path = "data/austraits", update = TRUE){
   metadata <- create_metadata(res) 
 
   # Sort old to new
-  metadata <- metadata |> 
+  metadata <- metadata %>% 
   dplyr::arrange(dplyr::desc(publication_date))
 
   # Grab the first version
-  dplyr::first(metadata$version) |> as.character()
+  dplyr::first(metadata$version) %>% as.character()
 }
 

R/plot_locations.R

@@ -29,7 +29,7 @@ plot_locations <- function(database, feature="trait_name", ...){
 
     if( length(stringr::str_which(names(traits), "(deg)")) < 2 ){
       cli::cli_alert_info("Coordinate columns were not detected, joining location tables now.")
-      database <- database |> join_location_coordinates()
+      database <- database %>% join_location_coordinates()
       traits <- get_traits_table(database)
     }
   } else {
@@ -51,9 +51,9 @@ plot_locations2 <- function(database, feature, ...){
 
   #Create site data
   sites <-
-    database |> 
-    dplyr::select(!!feature, tidyselect::any_of(c("site_name", "location_name", "latitude (deg)", "longitude (deg)"))) |> 
-    tidyr::drop_na() |> 
+    database %>% 
+    dplyr::select(!!feature, tidyselect::any_of(c("site_name", "location_name", "latitude (deg)", "longitude (deg)"))) %>% 
+    tidyr::drop_na() %>% 
     dplyr::mutate(dplyr::across(c("longitude (deg)","latitude (deg)"), as.numeric)) %>% 
     dplyr::filter(
       `latitude (deg)` > (-45), `latitude (deg)` < (-9.5),

R/summarise_austraits.R

@@ -54,7 +54,7 @@ summarise_austraits_traits <-function(database, var) {
   ret <- dplyr::left_join(ret, sum_stats, by = "trait_name")
 
   # Organise
-  ret %>% dplyr::select(1, dplyr::starts_with("n_"), percent_total) |> tibble::tibble()
+  ret %>% dplyr::select(1, dplyr::starts_with("n_"), percent_total) %>% tibble::tibble()
 }
 
 #' @noRd
@@ -92,6 +92,6 @@ summarise_austraits_taxa <-function(database, var) {
   ret <- dplyr::left_join(ret, sum_stats, by = var)
 
   # Organise
-  ret %>% dplyr::select(1, dplyr::starts_with("n_"), percent_total) |> tibble::tibble()
+  ret %>% dplyr::select(1, dplyr::starts_with("n_"), percent_total) %>% tibble::tibble()
 
 }