diff --git a/DESCRIPTION b/DESCRIPTION index 2f8c032e..1e29d3c7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,7 +19,6 @@ Imports: readr, purrr, forcats, - tibble, dplyr, stringr, stringi, diff --git a/NAMESPACE b/NAMESPACE index e2e58bfc..0c1bad02 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -12,5 +12,3 @@ export(state_diversity_counts) export(strip_names) export(strip_names_extra) export(update_taxonomy) -import(dplyr) -import(stringr) diff --git a/R/align_taxa.R b/R/align_taxa.R index fbe89bfa..3e991c26 100644 --- a/R/align_taxa.R +++ b/R/align_taxa.R @@ -107,7 +107,7 @@ align_taxa <- function(original_name, } else { taxa_raw <- - tibble::tibble( + dplyr::tibble( original_name = character(0L), cleaned_name = character(0L), aligned_name = character(0L), @@ -124,7 +124,7 @@ align_taxa <- function(original_name, taxa[["tocheck"]] <- dplyr::bind_rows( taxa_raw, - tibble::tibble( + dplyr::tibble( original_name = # only include new names subset(original_name, @@ -198,8 +198,8 @@ align_taxa <- function(original_name, if (!all(taxa$tocheck$checked)) { perfect_matches <- taxa$tocheck %>% - filter(original_name %in% resources$`APC list (accepted)`$canonical_name) %>% - distinct(original_name) %>% + dplyr::filter(original_name %in% resources$`APC list (accepted)`$canonical_name) %>% + dplyr::distinct(original_name) %>% nrow() if(!quiet) diff --git a/R/load_taxonomic_resources.R b/R/load_taxonomic_resources.R index 8a2e5ae0..ca1d31e9 100644 --- a/R/load_taxonomic_resources.R +++ b/R/load_taxonomic_resources.R @@ -17,8 +17,6 @@ #' @examples #' \donttest{load_taxonomic_resources(stable_or_current_data="stable",version="0.0.2.9000")} #' -#' @import dplyr -#' load_taxonomic_resources <- function(stable_or_current_data = "stable", @@ -53,7 +51,7 @@ load_taxonomic_resources <- zzz <- "zzzz zzzz" taxonomic_resources$APC <- taxonomic_resources$APC %>% - rename( + dplyr::rename( taxon_ID = .data$taxonID, taxon_rank = .data$taxonRank, name_type = .data$nameType, @@ -72,13 +70,13 @@ load_taxonomic_resources <- nomenclatural_code = .data$nomenclaturalCode, dataset_name = .data$datasetName ) %>% - mutate( + dplyr::mutate( genus = extract_genus(canonical_name), taxon_rank = standardise_taxon_rank(taxon_rank) ) taxonomic_resources$APNI <- taxonomic_resources$APNI %>% - rename( + dplyr::rename( name_type = .data$nameType, taxonomic_status = .data$taxonomicStatus, taxon_rank = .data$taxonRank, @@ -91,7 +89,7 @@ load_taxonomic_resources <- dataset_name = .data$datasetName, name_element = .data$nameElement ) %>% - mutate( + dplyr::mutate( genus = extract_genus(canonical_name), taxon_rank = standardise_taxon_rank(taxon_rank) ) diff --git a/R/match_taxa.R b/R/match_taxa.R index 3c82b058..c2d0a256 100644 --- a/R/match_taxa.R +++ b/R/match_taxa.R @@ -60,7 +60,7 @@ match_taxa <- function( if (APNI_matches == TRUE) { resources$genera_all2 <- resources$genera_all } else { - resources$genera_all2 <- resources$genera_all %>% filter(taxonomic_dataset != "APNI") + resources$genera_all2 <- resources$genera_all %>% dplyr::filter(taxonomic_dataset != "APNI") } ## Repeatedly used identifier strings are created. @@ -108,7 +108,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (accepted)`$taxon_rank[ii], aligned_name = resources$`APC list (accepted)`$canonical_name[ii], @@ -139,7 +139,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (known names)`$taxon_rank[ii], aligned_name = resources$`APC list (known names)`$canonical_name[ii], @@ -169,7 +169,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (accepted)`$taxon_rank[ii], aligned_name = resources$`APC list (accepted)`$canonical_name[ii], @@ -199,7 +199,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (known names)`$taxon_rank[ii], aligned_name = resources$`APC list (known names)`$canonical_name[ii], @@ -233,7 +233,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = resources$genera_all2$taxonomic_dataset[ii], taxon_rank = "genus", aligned_name_tmp = paste0(resources$genera_all2$genus[ii], " sp."), @@ -286,7 +286,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = resources$genera_accepted$taxonomic_dataset[ii], taxon_rank = "genus", aligned_name_tmp = @@ -325,7 +325,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = resources$genera_synonym$taxonomic_dataset[ii], taxon_rank = "genus", aligned_name_tmp = paste0(resources$genera_synonym$genus[ii], " sp."), @@ -356,7 +356,7 @@ match_taxa <- function( word(taxa$tocheck$cleaned_name, 2) %in% c("sp.") taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "family", aligned_name = ifelse(is.na(identifier_string), @@ -391,7 +391,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = resources$genera_all2$taxonomic_dataset[ii], taxon_rank = "genus", aligned_name_tmp = paste0(resources$genera_all2$genus[ii], " sp. [", cleaned_name), @@ -425,7 +425,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus, " sp. [", cleaned_name), @@ -457,7 +457,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus_synonym, " sp. [", cleaned_name), @@ -489,7 +489,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APNI", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus_APNI, " sp. [", cleaned_name), @@ -521,7 +521,7 @@ match_taxa <- function( !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = NA_character_, taxon_rank = NA, aligned_name_tmp = paste0(word(cleaned_name,1), " sp. [", cleaned_name), @@ -563,7 +563,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = resources$genera_all2$taxonomic_dataset[ii], taxon_rank = "genus", aligned_name_tmp = paste0(resources$genera_all2$genus[ii], " sp. [", cleaned_name), @@ -604,7 +604,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus, " sp. [", cleaned_name), @@ -643,7 +643,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus_synonym, " sp. [", cleaned_name), @@ -682,7 +682,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APNI", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus_APNI, " sp. [", cleaned_name), @@ -723,7 +723,7 @@ match_taxa <- function( !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = NA_character_, taxon_rank = NA, aligned_name_tmp = paste0(word(cleaned_name,1), " sp. [", cleaned_name), @@ -767,7 +767,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (accepted)`$taxon_rank[ii], aligned_name = resources$`APC list (accepted)`$canonical_name[ii], @@ -808,7 +808,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (known names)`$taxon_rank[ii], aligned_name = resources$`APC list (known names)`$canonical_name[ii], @@ -839,7 +839,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APNI", taxon_rank = resources$`APNI names`$taxon_rank[ii], aligned_name = resources$`APNI names`$canonical_name[ii], @@ -881,7 +881,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = resources$genera_all2$taxonomic_dataset[ii], taxon_rank = "genus", aligned_name_tmp = paste0(resources$genera_all2$genus[ii], " sp. [", cleaned_name), @@ -919,7 +919,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus, " sp. [", cleaned_name), @@ -955,7 +955,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus_synonym, " sp. [", cleaned_name), @@ -992,7 +992,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APNI", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus_APNI, " sp. [", cleaned_name), @@ -1030,7 +1030,7 @@ match_taxa <- function( !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = NA_character_, taxon_rank = NA, aligned_name_tmp = paste0(word(cleaned_name,1), " sp. [", cleaned_name), @@ -1076,7 +1076,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (accepted)`$taxon_rank[ii], aligned_name = resources$`APC list (accepted)`$canonical_name[ii], @@ -1122,7 +1122,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (known names)`$taxon_rank[ii], aligned_name = resources$`APC list (known names)`$canonical_name[ii], @@ -1158,7 +1158,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = resources$genera_all2$taxonomic_dataset[ii], taxon_rank = "genus", aligned_name_tmp = paste0(resources$genera_all2$genus[ii], " x [", cleaned_name), @@ -1193,7 +1193,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus, " x [", cleaned_name), @@ -1226,7 +1226,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus_synonym, " x [", cleaned_name), @@ -1260,7 +1260,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APNI", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus_APNI, " x [", cleaned_name), @@ -1294,7 +1294,7 @@ match_taxa <- function( !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = NA_character_, taxon_rank = NA, aligned_name_tmp = paste0(word(cleaned_name,1), " x [", cleaned_name), @@ -1329,7 +1329,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (accepted)`$taxon_rank[ii], aligned_name = resources$`APC list (accepted)`$canonical_name[ii], @@ -1363,7 +1363,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (known names)`$taxon_rank[ii], aligned_name = resources$`APC list (known names)`$canonical_name[ii], @@ -1410,7 +1410,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (accepted)`$taxon_rank[ii], aligned_name = resources$`APC list (accepted)`$canonical_name[ii], @@ -1457,7 +1457,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (known names)`$taxon_rank[ii], aligned_name = resources$`APC list (known names)`$canonical_name[ii], @@ -1493,7 +1493,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (accepted)`$taxon_rank[ii], aligned_name = resources$`APC list (accepted)`$canonical_name[ii], @@ -1528,7 +1528,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (known names)`$taxon_rank[ii], aligned_name = resources$`APC list (known names)`$canonical_name[ii], @@ -1578,7 +1578,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (accepted)`$taxon_rank[ii], aligned_name = resources$`APC list (accepted)`$canonical_name[ii], @@ -1628,7 +1628,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = resources$`APC list (known names)`$taxon_rank[ii], aligned_name = resources$`APC list (known names)`$canonical_name[ii], @@ -1676,7 +1676,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APNI", taxon_rank = resources$`APNI names`$taxon_rank[ii], aligned_name = resources$`APNI names`$canonical_name[ii], @@ -1723,7 +1723,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APNI", taxon_rank = resources$`APNI names`$taxon_rank[ii], aligned_name = resources$`APNI names`$canonical_name[ii], @@ -1759,7 +1759,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APNI", taxon_rank = resources$`APNI names`$taxon_rank[ii], aligned_name = resources$`APNI names`$canonical_name[ii], @@ -1796,7 +1796,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APNI", taxon_rank = resources$`APNI names`$taxon_rank[ii], aligned_name = resources$`APNI names`$canonical_name[ii], @@ -1828,7 +1828,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(resources$genera_accepted$genus[ii], " sp. [", cleaned_name), @@ -1863,7 +1863,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(resources$genera_synonym$genus[ii], " sp. [", cleaned_name), @@ -1899,7 +1899,7 @@ match_taxa <- function( ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APNI", taxon_rank = "genus", aligned_name_tmp = paste0(resources$genera_APNI$genus[ii], " sp. [", cleaned_name), @@ -1931,7 +1931,7 @@ match_taxa <- function( taxa$tocheck$genus %in% resources$family_accepted$canonical_name taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "family", aligned_name_tmp = paste0(genus, " sp. [", cleaned_name), @@ -1962,7 +1962,7 @@ match_taxa <- function( taxa$tocheck$genus %in% resources$family_synonym$canonical_name taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "family", aligned_name_tmp = paste0(genus, " sp. [", cleaned_name), @@ -1992,7 +1992,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus, " sp. [", cleaned_name), @@ -2022,7 +2022,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "genus", aligned_name_tmp = paste0(fuzzy_match_genus_synonym, " sp. [", cleaned_name), @@ -2062,7 +2062,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_family %in% resources$family_accepted$canonical_name taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "family", aligned_name_tmp = paste0(fuzzy_match_family, " sp. [", cleaned_name), @@ -2092,7 +2092,7 @@ match_taxa <- function( taxa$tocheck$fuzzy_match_family_synonym %in% resources$family_synonym$canonical_name taxa$tocheck[i,] <- taxa$tocheck[i,] %>% - mutate( + dplyr::mutate( taxonomic_dataset = "APC", taxon_rank = "family", aligned_name_tmp = paste0(fuzzy_match_family_synonym, " sp. [", cleaned_name), diff --git a/R/native_anywhere_in_australia.R b/R/native_anywhere_in_australia.R index bc0aff73..23ca9acf 100644 --- a/R/native_anywhere_in_australia.R +++ b/R/native_anywhere_in_australia.R @@ -37,7 +37,7 @@ native_anywhere_in_australia <- function(species, resources = load_taxonomic_res fulllist <- species %in% full_lookup$species # Create output tibble - result <- tibble( + result <- dplyr::tibble( species = species, native_anywhere_in_aus = dplyr::case_when( natives & fulllist ~ "native", diff --git a/R/standardise_names.R b/R/standardise_names.R index 1f135082..9f6207f6 100644 --- a/R/standardise_names.R +++ b/R/standardise_names.R @@ -136,14 +136,14 @@ extract_genus <- function(taxon_name) { taxon_name <- standardise_names(taxon_name) - genus <- str_split_i(taxon_name, " |\\/", 1) %>% stringr::str_to_sentence() + genus <- stringr::str_split_i(taxon_name, " |\\/", 1) %>% stringr::str_to_sentence() # Deal with names that being with x, # e.g."x Taurodium x toveyanum" or "x Glossadenia tutelata" i <- !is.na(genus) & genus =="X" genus[i] <- - str_split_i(taxon_name[i], " |\\/", 2) %>% stringr::str_to_sentence() %>% paste("x", .) + stringr::str_split_i(taxon_name[i], " |\\/", 2) %>% stringr::str_to_sentence() %>% paste("x", .) genus } diff --git a/R/state_diversity_counts.R b/R/state_diversity_counts.R index 36c169b7..78d61f93 100644 --- a/R/state_diversity_counts.R +++ b/R/state_diversity_counts.R @@ -51,7 +51,7 @@ state_diversity_counts <- function(state, create_species_state_origin_matrix(resources = resources) test2 <- test[test[[state]] != "not present", ] state_table <- table(test2[[state]]) - return(tibble( + return(dplyr::tibble( origin = names(state_table), state = state, num_species = state_table @@ -63,11 +63,11 @@ state_diversity_counts <- function(state, #' @noRd get_apc_genus_family_lookup <- function(resources = load_taxonomic_resources()) { - apc_s <- filter(resources$APC, + apc_s <- dplyr::filter(resources$APC, taxon_rank == "species") - tibble(genus = word(apc_s$scientific_name, 1, 1), + dplyr::tibble(genus = word(apc_s$scientific_name, 1, 1), family = apc_s$family) %>% - distinct() -> lu + dplyr::distinct() -> lu return(lu) } diff --git a/R/update_taxonomy.R b/R/update_taxonomy.R index de6f2e7d..3dabefdd 100644 --- a/R/update_taxonomy.R +++ b/R/update_taxonomy.R @@ -54,7 +54,7 @@ #' @examples #' # Update taxonomy for two plant names and print the result #' \donttest{update_taxonomy( -#' tibble::tibble( +#' dplyr::tibble( #' original_name = c("Dryandra preissii", "Banksia acuminata"), #' aligned_name = c("Dryandra preissii", "Banksia acuminata"), #' taxon_rank = c("species", "species"), @@ -117,7 +117,7 @@ update_taxonomy <- function(aligned_data, ## create a blank tibble with all columns, for taxon lists where some columns aren't created in any of the individual tibbles taxa_blank <- - tibble::tibble( + dplyr::tibble( original_name = character(0L), aligned_name = character(0L), accepted_name = character(0L), diff --git a/R/word.R b/R/word.R index cba74f34..78f45b6e 100644 --- a/R/word.R +++ b/R/word.R @@ -8,17 +8,16 @@ #' @param sep Separator between words. Defaults to single space. #' @return A character vector with the same length as `string`/`start`/`end`. #' -#' @import stringr #' @examples #' spp <- c("Banksia serrata", "Actinotus helanthii") #' APCalign:::word(spp, 1) #' APCalign:::word(spp, 2) word <- function(string, start = 1L, end = start, sep = " ") { if(end == start) { - str_split_i(string, " ", start) + stringr::str_split_i(string, " ", start) } else if(end == start+1) { - w1 <- str_split_i(string, sep, start) - w2 <- str_split_i(string, sep, start+1) + w1 <- stringr::str_split_i(string, sep, start) + w2 <- stringr::str_split_i(string, sep, start+1) out <- paste(w1, w2) out[is.na(w2)] <- NA_character_ @@ -26,9 +25,9 @@ word <- function(string, start = 1L, end = start, sep = " ") { return(out) } else if(end == start+2) { - w1 <- str_split_i(string, sep, start) - w2 <- str_split_i(string, sep, start+1) - w3 <- str_split_i(string, sep, start+2) + w1 <- stringr::str_split_i(string, sep, start) + w2 <- stringr::str_split_i(string, sep, start+1) + w3 <- stringr::str_split_i(string, sep, start+2) out <- paste(w1, w2, w3) out[is.na(w2) | is.na(w3)] <- NA_character_ @@ -37,7 +36,7 @@ word <- function(string, start = 1L, end = start, sep = " ") { } else { i <- seq(start, end) - txt <- str_split(string, sep) + txt <- stringr::str_split(string, sep) out <- purrr::map(txt, ~paste(.x[i], collapse = sep)) lngth <- purrr::map_int(txt, length) diff --git a/man/update_taxonomy.Rd b/man/update_taxonomy.Rd index 71feb47b..0b33a033 100644 --- a/man/update_taxonomy.Rd +++ b/man/update_taxonomy.Rd @@ -65,7 +65,7 @@ The aligned name is a plant name that has been aligned to a taxon name in the AP \examples{ # Update taxonomy for two plant names and print the result \donttest{update_taxonomy( - tibble::tibble( + dplyr::tibble( original_name = c("Dryandra preissii", "Banksia acuminata"), aligned_name = c("Dryandra preissii", "Banksia acuminata"), taxon_rank = c("species", "species"), diff --git a/tests/testthat/test-functions-standardise_names.R b/tests/testthat/test-functions-standardise_names.R index 06d66c5b..a8e9fc5b 100644 --- a/tests/testthat/test-functions-standardise_names.R +++ b/tests/testthat/test-functions-standardise_names.R @@ -29,7 +29,7 @@ test_that("Standardise names names", { readr::read_csv("benchmarks/standardise_names.csv", show_col_types = FALSE) out <- - tibble(taxon_names = expected$taxon_names, + dplyr::tibble(taxon_names = expected$taxon_names, standardised_names = standardise_names(taxon_names), genus = extract_genus(standardised_names), stripped_names = strip_names(standardised_names), diff --git a/tests/testthat/test-operation_executes.R b/tests/testthat/test-operation_executes.R index a0e5c021..fdace06f 100644 --- a/tests/testthat/test-operation_executes.R +++ b/tests/testthat/test-operation_executes.R @@ -241,7 +241,7 @@ test_that("handles APNI taxa and genus level IDs",{ expect_gte(nrow(out1), 4) - expect_false(any(str_detect(out2$suggested_name, "NA sp."))) + expect_false(any(stringr::str_detect(out2$suggested_name, "NA sp."))) expect_equal(out2$accepted_name, rep(NA_character_, nrow(out2))) }) diff --git a/tests/testthat/test-operation_outputs.R b/tests/testthat/test-operation_outputs.R index d3f16e57..7daeabb5 100644 --- a/tests/testthat/test-operation_outputs.R +++ b/tests/testthat/test-operation_outputs.R @@ -54,7 +54,7 @@ test_that("taxon name splits and complex taxonomic status values work as expecte # Compare results to a table of values that have been closely scrutinised benchmarks <- readr::read_csv("benchmarks/test_splits_synonyms.csv", show_col_types = FALSE) %>% - arrange(original_name, accepted_name_usage_ID, taxonomic_status) + dplyr::arrange(original_name, accepted_name_usage_ID, taxonomic_status) out1 <- create_taxonomic_update_lookup( @@ -64,7 +64,7 @@ test_that("taxon name splits and complex taxonomic status values work as expecte full = TRUE, quiet = TRUE ) %>% - arrange(original_name, taxon_ID, taxonomic_status) + dplyr::arrange(original_name, taxon_ID, taxonomic_status) expect_equal(benchmarks$original_name, out1$original_name) #expect_equal(benchmarks$accepted_name_usage_ID, out1$taxon_ID) @@ -78,7 +78,7 @@ test_that("taxon name splits and complex taxonomic status values work as expecte full = TRUE, quiet = TRUE ) %>% - arrange(original_name, taxon_ID, taxonomic_status) + dplyr::arrange(original_name, taxon_ID, taxonomic_status) expect_gte(nrow(out2), 60) expect_contains(out2$original_name, benchmarks$original_name) @@ -91,12 +91,12 @@ test_that("taxon name splits and complex taxonomic status values work as expecte resources = resources, full = TRUE, quiet = TRUE) %>% - arrange(original_name, taxon_ID, taxonomic_status) %>% - mutate(number_of_collapsed_taxa = ifelse(is.na(number_of_collapsed_taxa), 1, number_of_collapsed_taxa)) + dplyr::arrange(original_name, taxon_ID, taxonomic_status) %>% + dplyr::mutate(number_of_collapsed_taxa = ifelse(is.na(number_of_collapsed_taxa), 1, number_of_collapsed_taxa)) - rows_gt_1 <- out3 %>% filter(number_of_collapsed_taxa > 1) - rows_end_sp <- out3 %>% filter(stringr::str_detect(suggested_name, "sp.")) - rows_alt_names <- out3 %>% filter(stringr::str_detect(suggested_name, "collapsed names:")) + rows_gt_1 <- out3 %>% dplyr::filter(number_of_collapsed_taxa > 1) + rows_end_sp <- out3 %>% dplyr::filter(stringr::str_detect(suggested_name, "sp.")) + rows_alt_names <- out3 %>% dplyr::filter(stringr::str_detect(suggested_name, "collapsed names:")) expect_equal(nrow(out1), nrow(out3)) @@ -112,7 +112,7 @@ test_that("taxon name splits and complex taxonomic status values work as expecte fuzzy_matches = FALSE, full = TRUE, quiet = TRUE) %>% - arrange(original_name, taxon_ID, taxonomic_status) + dplyr::arrange(original_name, taxon_ID, taxonomic_status) expect_equal(out1, out4) @@ -171,7 +171,7 @@ test_that("taxon name alignment matches and updates work as expected", { output_updates <- output_updates %>% dplyr::left_join(by = "original_name", - benchmarks %>% select(original_name, updated_name, updated_name_passes), + benchmarks %>% dplyr::select(original_name, updated_name, updated_name_passes), ) %>% # Make a logical to see if the suggested name matches the updated_name in the spreadsheet # We don't expect all of these to match perfectly. diff --git a/tests/testthat/test-state_diversity.R b/tests/testthat/test-state_diversity.R index 3500c9ff..b207f831 100644 --- a/tests/testthat/test-state_diversity.R +++ b/tests/testthat/test-state_diversity.R @@ -11,7 +11,7 @@ test_that("state_diversity() works", { sd <- readr::read_csv("benchmarks/state_diversity.csv", show_col_types = FALSE) - ss_subset <- filter(ss, ss$species %in% sd$species) + ss_subset <- dplyr::filter(ss, ss$species %in% sd$species) expect_equal(ss_subset[1:200,], sd[1:200,]) })