fix rcmdcheck issues (#122)

R/process.R

@@ -208,14 +208,14 @@ dataset_process <- function(filename_data_raw,
         metadata[["exclude_observations"]] %>%
         traits.build::util_list_to_df2() %>%
         dplyr::mutate(
-          find = stringr::str_split(find, ", ")
+          find = stringr::str_split(.data$find, ", ")
           ) %>%
-        tidyr::unnest_longer(find) %>%
-        dplyr::filter(variable == "taxon_name")
+        tidyr::unnest_longer(.data$find) %>%
+        dplyr::filter(.data$variable == "taxon_name")
 
     taxonomic_updates <- 
       taxonomic_updates %>%
-      dplyr::filter(!aligned_name %in% taxa_to_exclude$find)
+      dplyr::filter(!.data$aligned_name %in% taxa_to_exclude$find)
   }
 
   ## A temporary dataframe created to generate and bind `method_id`,
@@ -263,7 +263,7 @@ dataset_process <- function(filename_data_raw,
     dplyr::select(dplyr::all_of(c("error")), everything()) %>%
     dplyr::select(-dplyr::all_of(c("unit_in"))),
     taxonomic_updates = taxonomic_updates %>%
-      dplyr::filter(aligned_name %in% traits$taxon_name),
+      dplyr::filter(.data$aligned_name %in% traits$taxon_name),
     taxa = taxonomic_updates %>%
       dplyr::select(dplyr::all_of(c(taxon_name = "aligned_name"))) %>%
       dplyr::distinct(),
@@ -1903,20 +1903,20 @@ build_update_taxonomy <- function(austraits_raw, taxa) {
         taxa$taxon_rank[match(.data$taxon_name, taxa$aligned_name)],
         .data$taxonomic_resolution),
       taxon_rank = .data$taxonomic_resolution,
-      name_to_match_to = taxon_name,
+      name_to_match_to = .data$taxon_name,
       # Create variable `name_to_match_to` which specifies the part of the taxon name to which matches can be made.
       # This step requires taxon_rank.
-      name_to_match_to = stringr::str_replace(taxon_name, " \\[.+",""),
-      name_to_match_to = ifelse(!taxon_rank %in% c("species", "subspecies", "series", "variety", "form"), 
-                                stringr::word(taxon_name,1), name_to_match_to)
+      name_to_match_to = stringr::str_replace(.data$taxon_name, " \\[.+",""),
+      name_to_match_to = ifelse(!.data$taxon_rank %in% c("species", "subspecies", "series", "variety", "form"), 
+                                stringr::word(.data$taxon_name,1), .data$name_to_match_to)
     ) %>%
     # Remove taxon_rank, as it is about to be merged back in, but matches will now be possible to more rows.
     select(-dplyr::any_of(c("taxon_rank", "taxonomic_resolution"))) %>%
     util_df_convert_character() %>%
     # Merge in all data from taxa.
     dplyr::left_join(by = c("taxon_name"),
       taxa %>% dplyr::select(-dplyr::any_of(dplyr::contains("align"))) %>%
-              dplyr::distinct(taxon_name, .keep_all = TRUE) %>%
+              dplyr::distinct(.data$taxon_name, .keep_all = TRUE) %>%
               util_df_convert_character()
     ) %>%
     dplyr::arrange(.data$taxon_name) %>%

R/setup.R

@@ -899,14 +899,14 @@ metadata_add_taxonomic_change <- function(dataset_id, find, replace, reason, tax
       } else {
         message(sprintf(red("Existing substitution will be overwritten for ") %+% green("'%s'"), find))     
         data <- data %>% 
-                  filter(find != to_add$find) %>%
+                  filter(.data$find != to_add$find) %>%
                   dplyr::bind_rows(to_add) %>%
-                  filter(!find == replace) %>%
+                  filter(!.data$find == replace) %>%
                   arrange(.data$find)
       }
     } else {
       data <- dplyr::bind_rows(data, to_add) %>%
-            filter(!find == replace) %>%
+            filter(!.data$find == replace) %>%
             arrange(.data$find)
     }
   }
@@ -971,7 +971,6 @@ metadata_add_taxonomic_changes_list <- function(dataset_id, taxonomic_updates) {
 
     # Read in dataframe of taxonomic changes, split into single-row lists, and add to metadata file
     metadata$taxonomic_updates <- taxonomic_updates %>% dplyr::filter(!.data$find == .data$replace)
-
   }
 
   # Write metadata