From 3fcc6a399b0c19c85f0a937f35bc3357cec18d32 Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Wed, 7 Feb 2024 07:55:49 +1100 Subject: [PATCH] Bug fix, re-number match algorithms (#179) - re-number match algorithms in online table to be identical to manuscript - edit function extract_genus to make genus uppercase - edit match algorithms to ensure genus names match equivalent columns in resources and submitted names; previously comparing canonical names from resources with genus from submitted name derivations. Changes to extract_genus function probably good enough, but this should be standardised anyway - replace APC-known with APC-synonyms - bug fix to avoid genus-level phrase names that begin with a "family name" from being added to the list of genera --- R/APCalign-package.R | 2 +- R/align_taxa.R | 20 +- R/create_taxonomic_update_lookup.R | 2 +- R/load_taxonomic_resources.R | 7 +- R/match_taxa.R | 320 ++++++------- R/standardise_names.R | 6 +- R/update_taxonomy.R | 2 +- .../APCalign_outputs_documentation.csv | 2 +- inst/extdata/match_taxa_documentation.csv | 82 ++-- man/align_taxa.Rd | 10 +- man/create_taxonomic_update_lookup.Rd | 2 +- man/update_taxonomy.Rd | 2 +- .../test_matches_alignments_updates.csv | 448 +++++++++--------- vignettes/articles/function_notes.Rmd | 2 +- 14 files changed, 455 insertions(+), 452 deletions(-) diff --git a/R/APCalign-package.R b/R/APCalign-package.R index ac8eef5f..38b2b88a 100644 --- a/R/APCalign-package.R +++ b/R/APCalign-package.R @@ -53,7 +53,7 @@ utils::globalVariables( "family", "fuzzy_match_genus", "fuzzy_match_genus_APNI", - "fuzzy_match_genus_known", + "fuzzy_match_genus_synonym", "genus", "genus_accepted", "known", diff --git a/R/align_taxa.R b/R/align_taxa.R index 158a373c..90c2fcb0 100644 --- a/R/align_taxa.R +++ b/R/align_taxa.R @@ -35,16 +35,16 @@ #' - binomial: the first two words in `stripped_name2`, required for matches that ignore all other text in the original_name; improves phrase name matches. #' - genus: the first two words in `cleaned_name`; required for genus-rank matches and reprocessing of genus-rank names. #' - fuzzy_match_genus: fuzzy match of genus column to best match among APC-accepted names; required for fuzzy matches of genus-rank names. -#' - fuzzy_match_genus_known: fuzzy match of genus column to best match among APC-known names, only considering different matches to those documented under APC-accepted genera; required for fuzzy matches of genus-rank names. +#' - fuzzy_match_genus_synonym: fuzzy match of genus column to best match among APC-known names, only considering different matches to those documented under APC-accepted genera; required for fuzzy matches of genus-rank names. #' - fuzzy_match_genus_APNI: fuzzy match of genus column to best match among APNI names, only considering different matches to those documented under APC-accepted and APC-known genera; required for fuzzy matches of genus-rank names. #' - fuzzy_match_cleaned_APC: fuzzy match of stripped_name to APC-accepted names; created for yet-to-be-aligned names at the match step 07a in the function `match_taxa`. -#' - fuzzy_match_cleaned_APC_known: fuzzy match of stripped_name to APC-known names; created for yet-to-be-aligned names at the match step 07b in the function `match_taxa`. +#' - fuzzy_match_cleaned_APC_synonym: fuzzy match of stripped_name to APC-known names; created for yet-to-be-aligned names at the match step 07b in the function `match_taxa`. #' - fuzzy_match_cleaned_APC_imprecise: imprecise fuzzy match of stripped_name to APC-accepted names; created for yet-to-be-aligned names at the match step 10a in the function `match_taxa`. -#' - fuzzy_match_cleaned_APC_known_imprecise: imprecise fuzzy match of stripped_name to APC-accepted names; created for yet-to-be-aligned names at the match step 10b in the function `match_taxa`. +#' - fuzzy_match_cleaned_APC_synonym_imprecise: imprecise fuzzy match of stripped_name to APC-accepted names; created for yet-to-be-aligned names at the match step 10b in the function `match_taxa`. #' - fuzzy_match_binomial: fuzzy match of binomial column to best match among APC-accepted names; created for yet-to-be-aligned names at match step 15a in the function `match_taxa`. -#' - fuzzy_match_binomial_APC_known: fuzzy match of binomial column to best match among APC-known names; created for yet-to-be-aligned names at match step 15a in the function `match_taxa`. +#' - fuzzy_match_binomial_APC_synonym: fuzzy match of binomial column to best match among APC-known names; created for yet-to-be-aligned names at match step 15a in the function `match_taxa`. #' - fuzzy_match_trinomial: fuzzy match of trinomial column to best match among APC-accepted names; created for yet-to-be-aligned names at match step 16a in the function `match_taxa`. -#' - fuzzy_match_trinomial_known: fuzzy match of trinomial column to best match among APC-known names; created for yet-to-be-aligned names at match step 16b in the function `match_taxa`. +#' - fuzzy_match_trinomial_synonym: fuzzy match of trinomial column to best match among APC-known names; created for yet-to-be-aligned names at match step 16b in the function `match_taxa`. #' - fuzzy_match_cleaned_APNI: fuzzy match of stripped_name to APNI names; created for yet-to-be-aligned names at the match step 16a in the function `match_taxa`. #' - fuzzy_match_cleaned_APNI_imprecise: imprecise fuzzy match of stripped_name to APNI names; created for yet-to-be-aligned names at the match step 17a in the function `match_taxa`. #' @@ -127,17 +127,17 @@ align_taxa <- function(original_name, aligned_name = NA_character_, aligned_reason = NA_character_, fuzzy_match_genus = NA_character_, - fuzzy_match_genus_known = NA_character_, + fuzzy_match_genus_synonym = NA_character_, fuzzy_match_genus_APNI = NA_character_, fuzzy_match_binomial = NA_character_, - fuzzy_match_binomial_APC_known = NA_character_, + fuzzy_match_binomial_APC_synonym = NA_character_, fuzzy_match_trinomial = NA_character_, - fuzzy_match_trinomial_known = NA_character_, + fuzzy_match_trinomial_synonym = NA_character_, fuzzy_match_cleaned_APC = NA_character_, - fuzzy_match_cleaned_APC_known = NA_character_, + fuzzy_match_cleaned_APC_synonym = NA_character_, fuzzy_match_cleaned_APNI = NA_character_, fuzzy_match_cleaned_APC_imprecise = NA_character_, - fuzzy_match_cleaned_APC_known_imprecise = NA_character_, + fuzzy_match_cleaned_APC_synonym_imprecise = NA_character_, fuzzy_match_cleaned_APNI_imprecise = NA_character_, taxonomic_dataset = NA_character_, taxon_rank = NA_character_, diff --git a/R/create_taxonomic_update_lookup.R b/R/create_taxonomic_update_lookup.R index 1753781a..8fa2577b 100644 --- a/R/create_taxonomic_update_lookup.R +++ b/R/create_taxonomic_update_lookup.R @@ -31,7 +31,7 @@ #' - update_reason: the explanation of a specific taxon name update (from an aligned name to an accepted or suggested name). #' - subclass: the subclass of the accepted name. #' - taxon_distribution: the distribution of the accepted name; only filled in if an APC accepted_name is available. -#' - scientific_name_authorship: the authorship information for the accepted (or known) name; available for both APC and APNI names. +#' - scientific_name_authorship: the authorship information for the accepted (or synonymous) name; available for both APC and APNI names. #' - taxon_ID: the unique taxon concept identifier for the accepted_name; only filled in if an APC accepted_name is available. #' - taxon_ID_genus: an identifier for the genus; only filled in if an APC-accepted genus name is available. #' - scientific_name_ID: an identifier for the nomenclatural (not taxonomic) details of a scientific name; available for both APC and APNI names. diff --git a/R/load_taxonomic_resources.R b/R/load_taxonomic_resources.R index 90cc5e93..8fe5a6c9 100644 --- a/R/load_taxonomic_resources.R +++ b/R/load_taxonomic_resources.R @@ -195,9 +195,10 @@ load_taxonomic_resources <- genus ) %>% dplyr::filter(taxon_rank %in% c("genus"), taxonomic_status == "accepted") %>% + dplyr::filter(!stringr::str_detect(stringr::word(genus, 1), "aceae$")) %>% dplyr::mutate(taxonomic_dataset = "APC") - taxonomic_resources[["genera_known"]] <- + taxonomic_resources[["genera_synonym"]] <- taxonomic_resources$APC %>% dplyr::select( canonical_name, @@ -213,6 +214,7 @@ load_taxonomic_resources <- ) %>% dplyr::filter(taxon_rank %in% c("genus")) %>% dplyr::filter(!canonical_name %in% taxonomic_resources$genera_accepted$canonical_name) %>% + dplyr::filter(!stringr::str_detect(stringr::word(genus, 1), "aceae$")) %>% dplyr::mutate(taxonomic_dataset = "APC") %>% dplyr::distinct(canonical_name, .keep_all = TRUE) @@ -229,13 +231,14 @@ load_taxonomic_resources <- ) %>% dplyr::filter(taxon_rank %in% c("genus")) %>% dplyr::filter(!canonical_name %in% taxonomic_resources$APC$canonical_name) %>% + dplyr::filter(!stringr::str_detect(stringr::word(genus, 1), "aceae$")) %>% dplyr::mutate(taxonomic_dataset = "APNI") %>% dplyr::distinct(canonical_name, .keep_all = TRUE) taxonomic_resources[["genera_all"]] <- dplyr::bind_rows( taxonomic_resources$genera_accepted, - taxonomic_resources$genera_known, + taxonomic_resources$genera_synonym, taxonomic_resources$genera_APNI ) %>% dplyr::mutate( diff --git a/R/match_taxa.R b/R/match_taxa.R index e17321af..64f8c1c7 100644 --- a/R/match_taxa.R +++ b/R/match_taxa.R @@ -86,11 +86,11 @@ match_taxa <- function( binomial = stringr::word(stripped_name2, start = 1, end = 2), genus = extract_genus(original_name), fuzzy_match_genus = - fuzzy_match_genera(genus, resources$genera_accepted$canonical_name), - fuzzy_match_genus_known = - fuzzy_match_genera(genus, resources$genera_known$canonical_name), + fuzzy_match_genera(genus, resources$genera_accepted$genus), + fuzzy_match_genus_synonym = + fuzzy_match_genera(genus, resources$genera_synonym$genus), fuzzy_match_genus_APNI = - fuzzy_match_genera(genus, resources$genera_APNI$canonical_name) + fuzzy_match_genera(genus, resources$genera_APNI$genus) ) ## Taxa that have been checked are moved from `taxa$tocheck` to `taxa$checked` @@ -101,7 +101,7 @@ match_taxa <- function( return(taxa) # START MATCHES - # match_05a: Scientific name matches + # match_01a: Scientific name matches # Taxon names that are an accepted scientific name, with authorship. i <- @@ -125,14 +125,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_05a_accepted_scientific_name_with_authorship" + alignment_code = "match_01a_accepted_scientific_name_with_authorship" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_05b: Scientific name matches + # match_01b: Scientific name matches # Taxon names that are an APC-known scientific name, with authorship. i <- @@ -156,14 +156,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_05b_known_scientific_name_with_authorship" + alignment_code = "match_01b_synonym_scientific_name_with_authorship" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_06a: APC-accepted canonical name + # match_01c: APC-accepted canonical name # Taxon names that are exact matches to APC-accepted canonical names, once filler words and punctuation are removed. i <- taxa$tocheck$cleaned_name %in% resources$`APC list (accepted)`$canonical_name @@ -186,14 +186,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_06a_accepted_canonical_name" + alignment_code = "match_01c_accepted_canonical_name" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_06b: APC-known canonical name + # match_01d: APC-known canonical name # Taxon names that are exact matches to APC-known canonical names, once filler words and punctuation are removed. i <- taxa$tocheck$cleaned_name %in% resources$`APC list (known names)`$canonical_name @@ -216,33 +216,33 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_06b_known_canonical_name" + alignment_code = "match_01d_synonym_canonical_name" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_01a: Genus-level resolution + # match_02a: Genus-level resolution # Exact matches of APC-accepted or APC-known genus for names where the final "word" is `sp` or `spp` # Aligned name includes identifier to indicate `genus sp.` refers to a specific species (or infra-specific taxon), associated with a specific dataset/location. i <- stringr::str_detect(taxa$tocheck$cleaned_name, "[:space:]sp\\.$") & - taxa$tocheck$genus %in% resources$genera_all2$canonical_name & + taxa$tocheck$genus %in% resources$genera_all2$genus & stringr::word(taxa$tocheck$cleaned_name, 2) %in% c("sp.") ii <- match( taxa$tocheck[i,]$genus, - resources$genera_all2$canonical_name + resources$genera_all2$genus ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = resources$genera_all2$taxonomic_dataset[ii], taxon_rank = "genus", - aligned_name_tmp = paste0(resources$genera_all2$canonical_name[ii], " sp."), + aligned_name_tmp = paste0(resources$genera_all2$genus[ii], " sp."), aligned_name = ifelse(is.na(identifier_string), aligned_name_tmp, paste0(aligned_name_tmp, identifier_string) @@ -256,27 +256,27 @@ match_taxa <- function( ), checked = TRUE, known = TRUE, - alignment_code = "match_01a_exact_genus_accepted_or_known" + alignment_code = "match_02a_exact_genus_accepted_or_synonym" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_01b: Genus-level resolution + # match_02b: Genus-level resolution # Fuzzy matches of APC accepted genera for names where the final "word" is `sp` or `spp` and # there isn't an exact match to an APC accepted genus name # Aligned name includes identifier to indicate `genus sp.` refers to a specific species (or infra-specific taxon), associated with a specific dataset/location. i <- stringr::str_detect(taxa$tocheck$cleaned_name, "[:space:]sp\\.$") & - taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$canonical_name & + taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus & stringr::word(taxa$tocheck$cleaned_name, 2) %in% c("sp.") ii <- match( taxa$tocheck[i,]$fuzzy_match_genus, - resources$genera_accepted$canonical_name + resources$genera_accepted$genus ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% @@ -284,7 +284,7 @@ match_taxa <- function( taxonomic_dataset = resources$genera_accepted$taxonomic_dataset[ii], taxon_rank = "genus", aligned_name_tmp = - paste0(resources$genera_accepted$canonical_name[ii], " sp."), + paste0(resources$genera_accepted$genus[ii], " sp."), aligned_name = ifelse(is.na(identifier_string), aligned_name_tmp, paste0(aligned_name_tmp, identifier_string) @@ -296,33 +296,33 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_01b_fuzzy_genus_accepted" + alignment_code = "match_02b_fuzzy_genus_accepted" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_01c: Genus-level resolution - # Fuzzy matches of APC known genera for names where the final "word" is `sp` or `spp` and - # there isn't an exact match to an APC known genus name. + # match_02c: Genus-level resolution + # Fuzzy matches of APC synonymous genera for names where the final "word" is `sp` or `spp` and + # there isn't an exact match to an APC synonymous genus name. # Aligned name includes identifier to indicate `genus sp.` refers to a specific species (or infra-specific taxon), associated with a specific dataset/location. i <- stringr::str_detect(taxa$tocheck$cleaned_name, "[:space:]sp\\.$") & - taxa$tocheck$fuzzy_match_genus_known %in% resources$genera_known$canonical_name & + taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus & stringr::word(taxa$tocheck$cleaned_name, 2) %in% c("sp.") ii <- match( - taxa$tocheck[i,]$fuzzy_match_genus_known, - resources$genera_known$canonical_name + taxa$tocheck[i,]$fuzzy_match_genus_synonym, + resources$genera_synonym$genus ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( - taxonomic_dataset = resources$genera_known$taxonomic_dataset[ii], + taxonomic_dataset = resources$genera_synonym$taxonomic_dataset[ii], taxon_rank = "genus", - aligned_name_tmp = paste0(resources$genera_known$canonical_name[ii], " sp."), + aligned_name_tmp = paste0(resources$genera_synonym$genus[ii], " sp."), aligned_name = ifelse(is.na(identifier_string), aligned_name_tmp, paste0(aligned_name_tmp, identifier_string) @@ -334,14 +334,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_01c_fuzzy_genus_known" + alignment_code = "match_02c_fuzzy_genus_synonym" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_02: Family-level resolution + # match_02d: Family-level resolution # Exact matches of APC-accepted family for names where the final "word" is `sp` or `spp`. # Aligned name includes identifier to indicate `family sp.` refers to a specific species (or infra-specific taxon), associated with a specific dataset/location. i <- @@ -363,7 +363,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_02a_exact_family_accepted" + alignment_code = "match_02d_exact_family_accepted" ) taxa <- redistribute(taxa) @@ -376,19 +376,19 @@ match_taxa <- function( # since this is the highest taxon rank that can be attached to the plant name i <- stringr::str_detect(taxa$tocheck$cleaned_name, "\\ -- |\\--") & - taxa$tocheck$genus %in% resources$genera_all2$canonical_name + taxa$tocheck$genus %in% resources$genera_all2$genus ii <- match( taxa$tocheck[i,]$genus, - resources$genera_all2$canonical_name + resources$genera_all2$genus ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = resources$genera_all2$taxonomic_dataset[ii], taxon_rank = "genus", - aligned_name_tmp = paste0(resources$genera_all2$canonical_name[ii], " sp. [", cleaned_name), + aligned_name_tmp = paste0(resources$genera_all2$genus[ii], " sp. [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -402,7 +402,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_03a_intergrade_accepted_or_known_genus" + alignment_code = "match_03a_intergrade_accepted_or_synonym_genus" ) taxa <- redistribute(taxa) @@ -416,7 +416,7 @@ match_taxa <- function( i <- stringr::str_detect(taxa$tocheck$cleaned_name, "\\ -- |\\--") & - taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$canonical_name + taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -448,13 +448,13 @@ match_taxa <- function( i <- stringr::str_detect(taxa$tocheck$cleaned_name, "\\ -- |\\--") & - taxa$tocheck$fuzzy_match_genus_known %in% resources$genera_known$canonical_name + taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = "APC", taxon_rank = "genus", - aligned_name_tmp = paste0(fuzzy_match_genus_known, " sp. [", cleaned_name), + aligned_name_tmp = paste0(fuzzy_match_genus_synonym, " sp. [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -466,7 +466,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_03c_intergrade_fuzzy_known_genus" + alignment_code = "match_03c_intergrade_fuzzy_synonym_genus" ) taxa <- redistribute(taxa) @@ -480,7 +480,7 @@ match_taxa <- function( if (APNI_matches == TRUE) { i <- stringr::str_detect(taxa$tocheck$cleaned_name, "\\ -- |\\--") & - taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$canonical_name + taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -512,7 +512,7 @@ match_taxa <- function( # Neither perfect nor fuzzy matches identify the genus. i <- stringr::str_detect(taxa$tocheck$cleaned_name, "\\ -- |\\--") & - !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$canonical_name + !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -548,19 +548,19 @@ match_taxa <- function( !stringr::str_detect(taxa$tocheck$cleaned_name, "[:digit:]") & !stringr::str_detect(taxa$tocheck$cleaned_name, "\\(") & !stringr::str_detect(taxa$tocheck$cleaned_name, "\\'") & - taxa$tocheck$genus %in% resources$genera_all2$canonical_name + taxa$tocheck$genus %in% resources$genera_all2$genus ii <- match( taxa$tocheck[i,]$genus, - resources$genera_all2$canonical_name + resources$genera_all2$genus ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = resources$genera_all2$taxonomic_dataset[ii], taxon_rank = "genus", - aligned_name_tmp = paste0(resources$genera_all2$canonical_name[ii], " sp. [", cleaned_name), + aligned_name_tmp = paste0(resources$genera_all2$genus[ii], " sp. [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -574,7 +574,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_04a_indecision_accepted_or_known_genus" + alignment_code = "match_04a_indecision_accepted_or_synonym_genus" ) taxa <- redistribute(taxa) @@ -595,7 +595,7 @@ match_taxa <- function( !stringr::str_detect(taxa$tocheck$cleaned_name, "[:digit:]") & !stringr::str_detect(taxa$tocheck$cleaned_name, "\\(") & !stringr::str_detect(taxa$tocheck$cleaned_name, "\\'") & - taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$canonical_name + taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -634,13 +634,13 @@ match_taxa <- function( !stringr::str_detect(taxa$tocheck$cleaned_name, "[:digit:]") & !stringr::str_detect(taxa$tocheck$cleaned_name, "\\(") & !stringr::str_detect(taxa$tocheck$cleaned_name, "\\'") & - taxa$tocheck$fuzzy_match_genus_known %in% resources$genera_known$canonical_name + taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = "APC", taxon_rank = "genus", - aligned_name_tmp = paste0(fuzzy_match_genus_known, " sp. [", cleaned_name), + aligned_name_tmp = paste0(fuzzy_match_genus_synonym, " sp. [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -652,7 +652,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_04c_indecision_fuzzy_known_genus" + alignment_code = "match_04c_indecision_fuzzy_synonym_genus" ) taxa <- redistribute(taxa) @@ -673,7 +673,7 @@ match_taxa <- function( !stringr::str_detect(taxa$tocheck$cleaned_name, "[:digit:]") & !stringr::str_detect(taxa$tocheck$cleaned_name, "\\(") & !stringr::str_detect(taxa$tocheck$cleaned_name, "\\'") & - taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$canonical_name + taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -714,7 +714,7 @@ match_taxa <- function( !stringr::str_detect(taxa$tocheck$cleaned_name, "[:digit:]") & !stringr::str_detect(taxa$tocheck$cleaned_name, "\\(") & !stringr::str_detect(taxa$tocheck$cleaned_name, "\\'") & - !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$canonical_name + !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -738,7 +738,7 @@ match_taxa <- function( if (nrow(taxa$tocheck) == 0) return(taxa) - # match_07a: fuzzy match to APC-accepted canonical name + # match_05a: fuzzy match to APC-accepted canonical name # Fuzzy match of taxon name to an APC-accepted canonical name, once filler words and punctuation are removed. for (i in 1:nrow(taxa$tocheck)) { taxa$tocheck$fuzzy_match_cleaned_APC[i] <- @@ -772,17 +772,17 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_07a_fuzzy_accepted_canonical_name" + alignment_code = "match_05a_fuzzy_accepted_canonical_name" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_07b: fuzzy match to APC-known canonical name + # match_05b: fuzzy match to APC-known canonical name # Fuzzy match of taxon name to an APC-known canonical name, once filler words and punctuation are removed. for (i in 1:nrow(taxa$tocheck)) { - taxa$tocheck$fuzzy_match_cleaned_APC_known[i] <- + taxa$tocheck$fuzzy_match_cleaned_APC_synonym[i] <- fuzzy_match( txt = taxa$tocheck$stripped_name[i], accepted_list = resources$`APC list (known names)`$stripped_canonical, @@ -793,11 +793,11 @@ match_taxa <- function( } i <- - taxa$tocheck$fuzzy_match_cleaned_APC_known %in% resources$`APC list (known names)`$stripped_canonical + taxa$tocheck$fuzzy_match_cleaned_APC_synonym %in% resources$`APC list (known names)`$stripped_canonical ii <- match( - taxa$tocheck[i,]$fuzzy_match_cleaned_APC_known, + taxa$tocheck[i,]$fuzzy_match_cleaned_APC_synonym, resources$`APC list (known names)`$stripped_canonical ) @@ -813,14 +813,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_07b_fuzzy_known_canonical_name" + alignment_code = "match_05b_fuzzy_synonym_canonical_name" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_08a: APNI-listed canonical name + # match_05c: APNI-listed canonical name # Taxon names that are exact matches to APNI-listed canonical names, once filler words and punctuation are removed. if (APNI_matches == TRUE) { i <- @@ -844,7 +844,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_08a_APNI_canonical_name" + alignment_code = "match_05c_APNI_canonical_name" ) taxa <- redistribute(taxa) @@ -852,7 +852,7 @@ match_taxa <- function( return(taxa) } - # match_09a: `genus aff. species` and `genus cf. species`taxa + # match_06a: `genus aff. species` and `genus cf. species`taxa # Exact match to APC-accepted or APC-known genus for names where "aff" indicates the taxon has an affinity to another taxon, but isn't the other taxon. # Similarly, "cf" indicates that a comparison should be made between the specific taxon and another taxon, but again, isn't the other taxon. # Taxon names fitting this pattern that are not APC-accepted, APC-known, or APNI-listed species are automatically aligned to genus, @@ -866,19 +866,19 @@ match_taxa <- function( stringr::str_detect(taxa$tocheck$cleaned_name, " affinis ") | stringr::str_detect(taxa$tocheck$cleaned_name, " cf[\\.\\s]") ) & - taxa$tocheck$genus %in% resources$genera_all2$canonical_name + taxa$tocheck$genus %in% resources$genera_all2$genus ii <- match( taxa$tocheck[i,]$genus, - resources$genera_all2$canonical_name + resources$genera_all2$genus ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = resources$genera_all2$taxonomic_dataset[ii], taxon_rank = "genus", - aligned_name_tmp = paste0(resources$genera_all2$canonical_name[ii], " sp. [", cleaned_name), + aligned_name_tmp = paste0(resources$genera_all2$genus[ii], " sp. [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -892,14 +892,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_09a_species_affinis_APC_exact" + alignment_code = "match_06a_species_affinis_APC_exact" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_09b: `genus aff. species` taxa + # match_06b: `genus aff. species` taxa # Fuzzy match to APC-accepted genus for names where "aff" indicates the taxon has an affinity to another taxon, but isn't the other taxon. # Taxon names fitting this pattern that are not APC-accepted, APC-known, or APNI-listed species are automatically aligned to genus, # since this is the highest taxon rank that can be attached to the plant name. @@ -910,7 +910,7 @@ match_taxa <- function( stringr::str_detect(taxa$tocheck$cleaned_name, "[Aa]ff[\\.\\s]") | stringr::str_detect(taxa$tocheck$cleaned_name, " affinis ") ) & - taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$canonical_name + taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -928,14 +928,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_09b_species_affinis_APC_accepted_fuzzy" + alignment_code = "match_06b_species_affinis_APC_accepted_fuzzy" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_09c: `genus aff. species` taxa + # match_06c: `genus aff. species` taxa # Fuzzy match to APC-known genus for names where "aff" indicates the taxon has an affinity to another taxon, but isn't the other taxon. # Taxon names fitting this pattern that are not APC-accepted, APC-known, or APNI-listed species are automatically aligned to genus, # since this is the highest taxon rank that can be attached to the plant name. @@ -946,13 +946,13 @@ match_taxa <- function( stringr::str_detect(taxa$tocheck$cleaned_name, "[Aa]ff[\\.\\s]") | stringr::str_detect(taxa$tocheck$cleaned_name, " affinis ") ) & - taxa$tocheck$fuzzy_match_genus_known %in% resources$genera_known$canonical_name + taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = "APC", taxon_rank = "genus", - aligned_name_tmp = paste0(fuzzy_match_genus_known, " sp. [", cleaned_name), + aligned_name_tmp = paste0(fuzzy_match_genus_synonym, " sp. [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -964,14 +964,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_09c_species_affinis_APC_known_fuzzy" + alignment_code = "match_06c_species_affinis_APC_synonym_fuzzy" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_09d: `genus aff. species` taxa + # match_06d: `genus aff. species` taxa # Fuzzy match to APNI_listed genus for names where "aff" indicates the taxon has an affinity to another taxon, but isn't the other taxon. # Taxon names fitting this pattern that are not APC-accepted, APC-known, or APNI-listed species are automatically aligned to genus, # since this is the highest taxon rank that can be attached to the plant name. @@ -983,7 +983,7 @@ match_taxa <- function( stringr::str_detect(taxa$tocheck$cleaned_name, "[Aa]ff[\\.\\s]") | stringr::str_detect(taxa$tocheck$cleaned_name, " affinis ") ) & - taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$canonical_name + taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -1001,7 +1001,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_09d_species_affinis_APNI_fuzzy" + alignment_code = "match_06d_species_affinis_APNI_fuzzy" ) taxa <- redistribute(taxa) @@ -1009,7 +1009,7 @@ match_taxa <- function( return(taxa) } - # match_09e: `genus aff. species` taxa + # match_06e: `genus aff. species` taxa # Taxon names where "aff" indicates the taxon has an affinity to another taxon, but isn't the other taxon, # when an exact or fuzzy genus-level match to APC & APNI genera cannot be made. # Taxon names fitting this pattern that are not APC-accepted, APC-known, or APNI-listed species are automatically aligned to genus, @@ -1021,7 +1021,7 @@ match_taxa <- function( stringr::str_detect(taxa$tocheck$cleaned_name, "[Aa]ff[\\.\\s]") | stringr::str_detect(taxa$tocheck$cleaned_name, " affinis ") ) & - !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$canonical_name + !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -1036,14 +1036,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_09e_species_affinis_unknown_genus" + alignment_code = "match_06e_species_affinis_unknown_genus" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_10a: imprecise fuzzy match + # match_07a: imprecise fuzzy match # Imprecise fuzzy match of taxon name to an APC-accepted canonical name, once filler words and punctuation are removed. # For imprecise fuzzy matches, the taxon name can differ from the `APC-accepted` names by 5 characters & up to 25% of the string length. # These matches require individual review and are turned off as a default. @@ -1081,7 +1081,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_10a_imprecise_fuzzy_accepted_canonical_name" + alignment_code = "match_07a_imprecise_fuzzy_accepted_canonical_name" ) taxa <- redistribute(taxa) @@ -1089,13 +1089,13 @@ match_taxa <- function( return(taxa) } - # match_10b: imprecise fuzzy match + # match_07b: imprecise fuzzy match # Imprecise fuzzy match of taxon name to an APC-known canonical name, once filler words and punctuation are removed. # For imprecise fuzzy matches, the taxon name can differ from the `APC -known` names by 5 characters & up to 25% of the string length. # These matches require individual review and are turned off as a default. if (imprecise_fuzzy_matches == TRUE) { for (i in 1:nrow(taxa$tocheck)) { - taxa$tocheck$fuzzy_match_cleaned_APC_known_imprecise[i] <- + taxa$tocheck$fuzzy_match_cleaned_APC_synonym_imprecise[i] <- fuzzy_match( txt = taxa$tocheck$stripped_name[i], accepted_list = resources$`APC list (known names)`$stripped_canonical, @@ -1107,11 +1107,11 @@ match_taxa <- function( } i <- - taxa$tocheck$fuzzy_match_cleaned_APC_known_imprecise %in% resources$`APC list (known names)`$stripped_canonical + taxa$tocheck$fuzzy_match_cleaned_APC_synonym_imprecise %in% resources$`APC list (known names)`$stripped_canonical ii <- match( - taxa$tocheck[i,]$fuzzy_match_cleaned_APC_known_imprecise, + taxa$tocheck[i,]$fuzzy_match_cleaned_APC_synonym_imprecise, resources$`APC list (known names)`$stripped_canonical ) @@ -1127,7 +1127,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_10b_imprecise_fuzzy_known_canonical_name" + alignment_code = "match_07b_imprecise_fuzzy_synonym_canonical_name" ) taxa <- redistribute(taxa) @@ -1135,7 +1135,7 @@ match_taxa <- function( return(taxa) } - # match_11a: hybrid taxa + # match_08a: hybrid taxa # Exact match to APC-accepted, APC-known, or APNI-listed genus for names where " x " indicates taxon is a hybrid. # Taxon names fitting this pattern that are not APC-accepted, APC-known, or APNI-listed species are automatically aligned to genus, # since this is the highest taxon rank that can be attached to the plant name. @@ -1143,19 +1143,19 @@ match_taxa <- function( # because there are hybrid taxa listed in both APC & APNI. i <- stringr::str_detect(taxa$tocheck$cleaned_name, " [xX] ") & - taxa$tocheck$genus %in% resources$genera_all2$canonical_name + taxa$tocheck$genus %in% resources$genera_all2$genus ii <- match( taxa$tocheck[i,]$genus, - resources$genera_all2$canonical_name + resources$genera_all2$genus ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = resources$genera_all2$taxonomic_dataset[ii], taxon_rank = "genus", - aligned_name_tmp = paste0(resources$genera_all2$canonical_name[ii], " x [", cleaned_name), + aligned_name_tmp = paste0(resources$genera_all2$genus[ii], " x [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -1169,14 +1169,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_11a_hybrid_taxon_exact" + alignment_code = "match_08a_hybrid_taxon_exact" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_11b: hybrid taxa + # match_08b: hybrid taxa # Fuzzy match to APC-accepted genus for names where " x " indicates taxon is a hybrid. # Taxon names fitting this pattern that are not APC-accepted, APC-known, or APNI-listed species are automatically aligned to genus, # since this is the highest taxon rank that can be attached to the plant name. @@ -1184,7 +1184,7 @@ match_taxa <- function( # because there are hybrid taxa listed in both APC & APNI. i <- stringr::str_detect(taxa$tocheck$cleaned_name, " [xX] ") & - taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$canonical_name + taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -1202,14 +1202,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_11b_hybrid_taxon_accepted_fuzzy" + alignment_code = "match_08b_hybrid_taxon_accepted_fuzzy" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_11c: hybrid taxa + # match_08c: hybrid taxa # Fuzzy match to APC-known genus for names where " x " indicates taxon is a hybrid. # Taxon names fitting this pattern that are not APC-accepted, APC-known, or APNI-listed species are automatically aligned to genus, # since this is the highest taxon rank that can be attached to the plant name. @@ -1217,13 +1217,13 @@ match_taxa <- function( # because there are hybrid taxa listed in both APC & APNI. i <- stringr::str_detect(taxa$tocheck$cleaned_name, " [xX] ") & - taxa$tocheck$fuzzy_match_genus_known %in% resources$genera_known$canonical_name + taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = "APC", taxon_rank = "genus", - aligned_name_tmp = paste0(fuzzy_match_genus_known, " x [", cleaned_name), + aligned_name_tmp = paste0(fuzzy_match_genus_synonym, " x [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -1235,14 +1235,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_11c_hybrid_taxon_known_fuzzy" + alignment_code = "match_08c_hybrid_taxon_synonym_fuzzy" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_11d: hybrid taxa + # match_08d: hybrid taxa # Fuzzy match to APNI-listed genus for names where " x " indicates taxon is a hybrid. # Taxon names fitting this pattern that are not APC-accepted, APC-known, or APNI-listed species are automatically aligned to genus, # since this is the highest taxon rank that can be attached to the plant name. @@ -1251,7 +1251,7 @@ match_taxa <- function( if (APNI_matches == TRUE) { i <- stringr::str_detect(taxa$tocheck$cleaned_name, " [xX] ") & - taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$canonical_name + taxa$tocheck$fuzzy_match_genus_APNI %in% resources$genera_APNI$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -1269,7 +1269,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_11d_hybrid_taxon_APNI_fuzzy" + alignment_code = "match_08d_hybrid_taxon_APNI_fuzzy" ) taxa <- redistribute(taxa) @@ -1277,7 +1277,7 @@ match_taxa <- function( return(taxa) } - # match_11e: hybrid taxa + # match_08e: hybrid taxa # Taxon names where " x " indicates taxon is a hybrid, but an exact or fuzzy genus-level match to APC & APNI genera cannot be made. # Taxon names fitting this pattern that are not APC-accepted, APC-known, or APNI-listed species are automatically aligned to genus, # since this is the highest taxon rank that can be attached to the plant name. @@ -1285,7 +1285,7 @@ match_taxa <- function( # because there are hybrid taxa listed in both APC & APNI. i <- stringr::str_detect(taxa$tocheck$cleaned_name, " [xX] ") & - !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$canonical_name + !taxa$tocheck$fuzzy_match_genus %in% resources$genera_all2$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -1300,14 +1300,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_11e_hybrid_taxon_unknown" + alignment_code = "match_08e_hybrid_taxon_unknown" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_12a: exact trinomial matches, APC + # match_09a: exact trinomial matches, APC # Exact match of first three words of taxon name ("trinomial") to APC-accepted canonical name. # The purpose of matching only the first three words only to APC-accepted names is that # sometimes the submitted taxon name is a valid trinomial + notes and @@ -1334,14 +1334,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_12a_trinomial_exact_accepted" + alignment_code = "match_09a_trinomial_exact_accepted" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_12b: exact trinomial matches, APC + # match_09b: exact trinomial matches, APC # Exact match of first three words of taxon name ("trinomial") to APC-known canonical name. # The purpose of matching only the first three words only to APC-known names is that # sometimes the submitted taxon name is a valid trinomial + notes and @@ -1368,14 +1368,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_12b_trinomial_exact_known" + alignment_code = "match_09b_trinomial_exact_synonym" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_13a: fuzzy trinomial matches, APC + # match_09c: fuzzy trinomial matches, APC # Fuzzy match of first three words of taxon name ("trinomial") to APC-accepted canonical name. # The purpose of matching only the first three words only to APC-accepted names is that # sometimes the submitted taxon name is a valid trinomial + notes and @@ -1415,14 +1415,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_13a_trinomial_fuzzy_accepted" + alignment_code = "match_09c_trinomial_fuzzy_accepted" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_13b: fuzzy trinomial matches, APC + # match_09d: fuzzy trinomial matches, APC # Fuzzy match of first three words of taxon name ("trinomial") to APC-known canonical name. # The purpose of matching only the first three words only to APC-known names is that # sometimes the submitted taxon name is a valid trinomial + notes and @@ -1430,7 +1430,7 @@ match_taxa <- function( # This match also does a good job aligning and correcting syntax of phrase names for (i in 1:nrow(taxa$tocheck)) { if (!is.na(taxa$tocheck$trinomial[i])) { - taxa$tocheck$fuzzy_match_trinomial_known[i] <- + taxa$tocheck$fuzzy_match_trinomial_synonym[i] <- fuzzy_match( txt = taxa$tocheck$trinomial[i], accepted_list = resources$`APC list (known names)`$trinomial, @@ -1442,11 +1442,11 @@ match_taxa <- function( } i <- - taxa$tocheck$fuzzy_match_trinomial_known %in% resources$`APC list (known names)`$trinomial + taxa$tocheck$fuzzy_match_trinomial_synonym %in% resources$`APC list (known names)`$trinomial ii <- match( - taxa$tocheck[i,]$fuzzy_match_trinomial_known, + taxa$tocheck[i,]$fuzzy_match_trinomial_synonym, resources$`APC list (known names)`$trinomial ) @@ -1462,14 +1462,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_13b_trinomial_fuzzy_known" + alignment_code = "match_09d_trinomial_fuzzy_synonym" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_14a: exact binomial matches, APC + # match_10a: exact binomial matches, APC # Exact match of first two words of taxon name ("binomial") to APC-accepted canonical name. # The purpose of matching only the first two words only to APC-accepted names is that # sometimes the submitted taxon name is a valid binomial + notes @@ -1498,14 +1498,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_14a_binomial_exact_accepted" + alignment_code = "match_10a_binomial_exact_accepted" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_14b: exact binomial matches, APC + # match_10b: exact binomial matches, APC # Exact match of first two words of taxon name ("binomial") to APC-known canonical name. # The purpose of matching only the first two words only to APC-known names is that # sometimes the submitted taxon name is a valid binomial + notes @@ -1533,14 +1533,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_14b_binomial_exact_known" + alignment_code = "match_10b_binomial_exact_synonym" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_15a: fuzzy binomial matches, APC + # match_10c: fuzzy binomial matches, APC # Fuzzy match of first two words of taxon name ("binomial") to APC-accepted canonical name. # The purpose of matching only the first two words only to APC-accepted names is that # sometimes the submitted taxon name is a valid binomial + notes @@ -1583,14 +1583,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_15a_binomial_fuzzy_accepted" + alignment_code = "match_10c_binomial_fuzzy_accepted" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_15b: fuzzy binomial matches, APC + # match_10d: fuzzy binomial matches, APC # Fuzzy match of first two words of taxon name ("binomial") to APC-known canonical name. # The purpose of matching only the first two words only to APC-known names is that # sometimes the submitted taxon name is a valid binomial + notes @@ -1599,8 +1599,8 @@ match_taxa <- function( # This match also does a good job aligning and correcting syntax of phrase names. for (i in 1:nrow(taxa$tocheck)) { if (!is.na(taxa$tocheck$binomial[i]) & - is.na(taxa$tocheck$fuzzy_match_binomial_APC_known[i])) { - taxa$tocheck$fuzzy_match_binomial_APC_known[i] <- + is.na(taxa$tocheck$fuzzy_match_binomial_APC_synonym[i])) { + taxa$tocheck$fuzzy_match_binomial_APC_synonym[i] <- fuzzy_match( txt = taxa$tocheck$binomial[i], accepted_list = resources$`APC list (known names)`$binomial, @@ -1613,11 +1613,11 @@ match_taxa <- function( } i <- - taxa$tocheck$fuzzy_match_binomial_APC_known %in% resources$`APC list (known names)`$binomial + taxa$tocheck$fuzzy_match_binomial_APC_synonym %in% resources$`APC list (known names)`$binomial ii <- match( - taxa$tocheck[i,]$fuzzy_match_binomial_APC_known, + taxa$tocheck[i,]$fuzzy_match_binomial_APC_synonym, resources$`APC list (known names)`$binomial ) @@ -1633,14 +1633,14 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_15b_binomial_fuzzy_known" + alignment_code = "match_10d_binomial_fuzzy_synonym" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_16a: fuzzy match to APNI-listed canonical name + # match_11a: fuzzy match to APNI-listed canonical name # Fuzzy match of taxon name to an APNI-listed canonical name, once filler words and punctuation are removed. # Fuzzy matches to APNI names occur toward the end of the alignment function, # because names exclusively in the APNI are often misspellings of APC accepted/known taxa and @@ -1681,7 +1681,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_16a_fuzzy_APNI_canonical" + alignment_code = "match_11a_fuzzy_APNI_canonical" ) taxa <- redistribute(taxa) @@ -1689,7 +1689,7 @@ match_taxa <- function( return(taxa) } - # match_17a: imprecise fuzzy APNI match + # match_11b: imprecise fuzzy APNI match # Imprecise fuzzy match of taxon name to an APNI-listed canonical name, once filler words and punctuation are removed. # For imprecise fuzzy matches, the taxon name can differ from the `APNI-listed` names by 5 characters & up to 25% of the string length. # These matches require individual review and are turned off as a default. @@ -1728,7 +1728,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_17a_imprecise_fuzzy_APNI_canonical_name" + alignment_code = "match_11b_imprecise_fuzzy_APNI_canonical_name" ) taxa <- redistribute(taxa) @@ -1736,7 +1736,7 @@ match_taxa <- function( return(taxa) } - # match_18a: exact trinomial matches, APNI + # match_11c: exact trinomial matches, APNI # Exact match of first three words of taxon name ("trinomial") to APNI-listed canonical name. # The purpose of matching only the first three words only to APNI-listed names is that # sometimes the submitted taxon name is a valid trinomial + notes and @@ -1764,7 +1764,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_18a_trinomial_exact_APNI" + alignment_code = "match_11c_trinomial_exact_APNI" ) taxa <- redistribute(taxa) @@ -1772,7 +1772,7 @@ match_taxa <- function( return(taxa) } - # match_19a: exact binomial matches, APNI + # match_11d: exact binomial matches, APNI # Exact match of first two words of taxon name ("binomial") to APNI-listed canonical name. # The purpose of matching only the first two words only to APNI-listed names is that # sometimes the submitted taxon name is a valid binomial + notes @@ -1801,7 +1801,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_19a_binomial_exact_APNI" + alignment_code = "match_11d_binomial_exact_APNI" ) taxa <- redistribute(taxa) @@ -1809,23 +1809,23 @@ match_taxa <- function( return(taxa) } - # match_20a: genus-level alignment + # match_12a: genus-level alignment # Toward the end of the alignment function, see if first word of unmatched taxa is an APC-accepted genus. # The 'taxon name' is then reformatted as `genus sp.` with the original name in square brackets. i <- - taxa$tocheck$genus %in% resources$genera_accepted$canonical_name + taxa$tocheck$genus %in% resources$genera_accepted$genus ii <- match( taxa$tocheck[i,]$genus, - resources$genera_accepted$canonical_name + resources$genera_accepted$genus ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = "APC", taxon_rank = "genus", - aligned_name_tmp = paste0(resources$genera_accepted$canonical_name[ii], " sp. [", cleaned_name), + aligned_name_tmp = paste0(resources$genera_accepted$genus[ii], " sp. [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -1837,30 +1837,30 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_20a_genus_exact_accepted" + alignment_code = "match_12a_genus_exact_accepted" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_20b: genus-level alignment + # match_12b: genus-level alignment # Toward the end of the alignment function, see if first word of unmatched taxa is an APC-known genus. # The 'taxon name' is then reformatted as `genus sp.` with the original name in square brackets. i <- - taxa$tocheck$genus %in% resources$genera_known$canonical_name + taxa$tocheck$genus %in% resources$genera_synonym$genus ii <- match( taxa$tocheck[i,]$genus, - resources$genera_known$canonical_name + resources$genera_synonym$genus ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = "APC", taxon_rank = "genus", - aligned_name_tmp = paste0(resources$genera_known$canonical_name[ii], " sp. [", cleaned_name), + aligned_name_tmp = paste0(resources$genera_synonym$genus[ii], " sp. [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -1872,31 +1872,31 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_20b_genus_exact_known" + alignment_code = "match_12b_genus_exact_synonym" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_20c: genus-level alignment + # match_12c: genus-level alignment # Toward the end of the alignment function, see if first word of unmatched taxa is an APNI-listed genus. # The 'taxon name' is then reformatted as `genus sp.` with the original name in square brackets. if (APNI_matches == TRUE) { i <- - (taxa$tocheck$genus %in% resources$genera_APNI$canonical_name) + (taxa$tocheck$genus %in% resources$genera_APNI$genus) ii <- match( taxa$tocheck[i,]$genus, - resources$genera_APNI$canonical_name + resources$genera_APNI$genus ) taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = "APNI", taxon_rank = "genus", - aligned_name_tmp = paste0(resources$genera_APNI$canonical_name[ii], " sp. [", cleaned_name), + aligned_name_tmp = paste0(resources$genera_APNI$genus[ii], " sp. [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -1908,7 +1908,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_20c_genus_exact_APNI" + alignment_code = "match_12c_genus_exact_APNI" ) taxa <- redistribute(taxa) @@ -1916,7 +1916,7 @@ match_taxa <- function( return(taxa) } - # match_21a: family-level alignment + # match_12d: family-level alignment # Toward the end of the alignment function, see if first word of unmatched taxa is an APC-accepted family. # The 'taxon name' is then reformatted as `family sp.` with the original name in square brackets. @@ -1940,19 +1940,19 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_21a_family_exact_accepted" + alignment_code = "match_12d_family_exact_accepted" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_22a: genus-level fuzzy alignment + # match_12e: genus-level fuzzy alignment # The final alignment step is to see if a fuzzy match can be made for the first word of unmatched taxa to an APC-accepted genus . # The 'taxon name' is then reformatted as `genus sp.` with the original name in square brackets. i <- - taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$canonical_name + taxa$tocheck$fuzzy_match_genus %in% resources$genera_accepted$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( @@ -1970,25 +1970,25 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_22a_genus_fuzzy_accepted" + alignment_code = "match_12e_genus_fuzzy_accepted" ) taxa <- redistribute(taxa) if (nrow(taxa$tocheck) == 0) return(taxa) - # match_22b: genus-level fuzzy alignment + # match_12f: genus-level fuzzy alignment # The final alignment step is to see if a fuzzy match can be made for the first word of unmatched taxa to an APC-known genus . # The 'taxon name' is then reformatted as `genus sp.` with the original name in square brackets. i <- - taxa$tocheck$fuzzy_match_genus_known %in% resources$genera_known$canonical_name + taxa$tocheck$fuzzy_match_genus_synonym %in% resources$genera_synonym$genus taxa$tocheck[i,] <- taxa$tocheck[i,] %>% mutate( taxonomic_dataset = "APC", taxon_rank = "genus", - aligned_name_tmp = paste0(fuzzy_match_genus_known, " sp. [", cleaned_name), + aligned_name_tmp = paste0(fuzzy_match_genus_synonym, " sp. [", cleaned_name), aligned_name = ifelse(is.na(identifier_string2), paste0(aligned_name_tmp, "]"), paste0(aligned_name_tmp, identifier_string2, "]") @@ -2000,7 +2000,7 @@ match_taxa <- function( ), known = TRUE, checked = TRUE, - alignment_code = "match_22b_genus_fuzzy_known" + alignment_code = "match_12f_genus_fuzzy_synonym" ) taxa <- redistribute(taxa) diff --git a/R/standardise_names.R b/R/standardise_names.R index e1bfb4e8..94fd25ec 100644 --- a/R/standardise_names.R +++ b/R/standardise_names.R @@ -115,9 +115,9 @@ standardise_names <- function(taxon_names) { extract_genus <- function(taxon_name) { genus <- ifelse( - stringr::word(taxon_name, 1) == "x", - stringr::word(taxon_name, start = 1, end = 2), - stringr::word(taxon_name, 1) + stringr::word(taxon_name, 1) %>% stringr::str_to_lower() == "x", + paste(stringr::word(taxon_name, 1) %>% stringr::str_to_lower(), stringr::word(taxon_name, 2) %>% stringr::str_to_sentence()), + stringr::word(taxon_name, 1) %>% stringr::str_to_sentence() ) genus } diff --git a/R/update_taxonomy.R b/R/update_taxonomy.R index f49c0f25..8c232e97 100644 --- a/R/update_taxonomy.R +++ b/R/update_taxonomy.R @@ -39,7 +39,7 @@ #' - update_reason: the explanation of a specific taxon name update (from an aligned name to an accepted or suggested name). #' - subclass: the subclass of the accepted name. #' - taxon_distribution: the distribution of the accepted name; only filled in if an APC accepted_name is available. -#' - scientific_name_authorship: the authorship information for the accepted (or known) name; available for both APC and APNI names. +#' - scientific_name_authorship: the authorship information for the accepted (or synonymous) name; available for both APC and APNI names. #' - taxon_ID: the unique taxon concept identifier for the accepted_name; only filled in if an APC accepted_name is available. #' - taxon_ID_genus: an identifier for the genus; only filled in if an APC-accepted genus name is available. #' - scientific_name_ID: an identifier for the nomenclatural (not taxonomic) details of a scientific name; available for both APC and APNI names. diff --git a/inst/extdata/APCalign_outputs_documentation.csv b/inst/extdata/APCalign_outputs_documentation.csv index 12a48d13..3f98489d 100644 --- a/inst/extdata/APCalign_outputs_documentation.csv +++ b/inst/extdata/APCalign_outputs_documentation.csv @@ -12,7 +12,7 @@ aligned_reason,default,The explanation of a specific taxon name alignment (from update_reason,default,The explanation of a specific taxon name update (from an aligned name to an accepted or suggested name). subclass,full,The subclass of the accepted name. taxon_distribution,full,The distribution of the accepted name; only filled in if an APC accepted_name is available. -scientific_name_authorship,default,The authorship information for the accepted (or known) name; available for both APC and APNI names. +scientific_name_authorship,default,The authorship information for the accepted (or synonymous) name; available for both APC and APNI names. taxon_ID,full,The unique taxon concept identifier for the accepted_name; only filled in if an APC accepted_name is available. taxon_ID_genus,full,An identifier for the genus; only filled in if an APC-accepted genus name is available. scientific_name_ID,full,An identifier for the nomenclatural (not taxonomic) details of a scientific name; available for both APC and APNI names. diff --git a/inst/extdata/match_taxa_documentation.csv b/inst/extdata/match_taxa_documentation.csv index 0da47f8e..582811b5 100644 --- a/inst/extdata/match_taxa_documentation.csv +++ b/inst/extdata/match_taxa_documentation.csv @@ -1,8 +1,12 @@ alignment_code,search algorithm,original name variant matched to,match type,taxonomic dataset aligned to,taxon_rank of alignment,notes about sequence -match_01a,"Detect `genus sp. `, `genus ssp.` and `genus spp.`","first word (""genus"")",exact,"APC accepted taxon concepts, other APC taxon concepts, APNI",genus,First goal is to align 2-word strings that indicate an unknown species within a genus (or family) -match_01b,"Detect `genus sp. `, `genus ssp.` and `genus spp.`","first word (""genus"")",fuzzy,APC accepted taxon concepts,genus, -match_01c,"Detect `genus sp. `, `genus ssp.` and `genus spp.`","first word (""genus"")",fuzzy,other APC taxon concepts,genus, -match_02a,"Detect `family sp. `, `family ssp.` and `family spp.`","first word (""genus"")",exact,APC accepted taxon concepts,family, +match_01a,"Detect scientific names, including authorship",original_name,exact,APC accepted taxon concepts,species/infraspecific,"Check if strings are full scientific names, including authorship." +match_01b,"Detect scientific names, including authorship",original_name,exact,other APC taxon concepts,species/infraspecific, +match_01c,"Detect canonical names, lacking authorship",cleaned_name,exact,APC accepted taxon concepts,species/infraspecific,"Check if strings are taxon names, lacking authorship." +match_01d,"Detect canonical names, lacking authorship",cleaned_name,exact,other APC taxon concepts,species/infraspecific, +match_02a,"Detect `genus sp. `, `genus ssp.` and `genus spp.`","first word (""genus"")",exact,"APC accepted taxon concepts, other APC taxon concepts, APNI",genus,First goal is to align 2-word strings that indicate an unknown species within a genus (or family) +match_02b,"Detect `genus sp. `, `genus ssp.` and `genus spp.`","first word (""genus"")",fuzzy,APC accepted taxon concepts,genus, +match_02c,"Detect `genus sp. `, `genus ssp.` and `genus spp.`","first word (""genus"")",fuzzy,other APC taxon concepts,genus, +match_02d,"Detect `family sp. `, `family ssp.` and `family spp.`","first word (""genus"")",exact,APC accepted taxon concepts,family, match_03a,"Detect ` -- `, `--` (intergrade taxa) and align to genus","first word (""genus"")",exact,"APC accepted taxon concepts, other APC taxon concepts, APNI",genus,Next find strings that indicate a name reflects an intergrade between two taxa. These names can only be aligned to a genus. match_03b,"Detect ` -- `, `--` (intergrade taxa) and align to genus","first word (""genus"")",fuzzy,APC accepted taxon concepts,genus, match_03c,"Detect ` -- `, `--` (intergrade taxa) and align to genus","first word (""genus"")",fuzzy,other APC taxon concepts,genus, @@ -13,40 +17,36 @@ match_04b,Detect ` \` (indecision between taxa) and align to genus.,"first word match_04c,Detect ` \` (indecision between taxa) and align to genus.,"first word (""genus"")",fuzzy,other APC taxon concepts,genus, match_04d,Detect ` \` (indecision between taxa) and align to genus.,"first word (""genus"")",fuzzy,APNI,genus, match_04e,"Detect ` \` (indecision between taxa), but fail to align to genus",NA,no match,NA,NA, -match_05a,"Detect scientific names, including authorship",original_name,exact,APC accepted taxon concepts,species/infraspecific,"Check if strings are full scientific names, including authorship." -match_05b,"Detect scientific names, including authorship",original_name,exact,other APC taxon concepts,species/infraspecific, -match_06a,"Detect canonical names, lacking authorship",cleaned_name,exact,APC accepted taxon concepts,species/infraspecific,"Check if strings are taxon names, lacking authorship." -match_06b,"Detect canonical names, lacking authorship",cleaned_name,exact,other APC taxon concepts,species/infraspecific, -match_07a,"Detect canonical names, lacking authorship",stripped_name,fuzzy,APC accepted taxon concepts,species/infraspecific, -match_07b,"Detect canonical names, lacking authorship",stripped_name,fuzzy,other APC taxon concepts,species/infraspecific, -match_08a,"Detect canonical names, lacking authorship",cleaned_name,exact,APNI,species/infraspecific, -match_09a,"Detect `aff`, `affinis` (affinity to) and align to genus","first word (""genus"")",exact,"APC accepted taxon concepts, other APC taxon concepts, APNI",genus,"Find strings that indicate a name that indicates an affinity to a specific taxon, but the name itself is not that taxon. Such names, unless documented in APC (i.e. matches 6, 7 above) can only be aligned to genus." -match_09b,"Detect `aff`, `affinis` (affinity to) and align to genus","first word (""genus"")",fuzzy,APC accepted taxon concepts,genus, -match_09c,"Detect `aff`, `affinis` (affinity to) and align to genus","first word (""genus"")",fuzzy,other APC taxon concepts,genus, -match_09d,"Detect `aff`, `affinis` (affinity to) and align to genus","first word (""genus"")",fuzzy,APNI,genus, -match_09e,"Detect `aff`, `affinis` (affinity to), but fail to align to genus",NA,no match,NA,NA, -match_10a,"Detect canonical names, lacking authorship",stripped_name,imprecise fuzzy,APC accepted taxon concepts,species/infraspecific,"Further checks if strings are taxon names, lacking authorship, now with imprecise fuzzy matching" -match_10b,"Detect canonical names, lacking authorship",stripped_name,imprecise fuzzy,other APC taxon concepts,species/infraspecific, -match_11a,Detect ` x ` (hybrid taxon) and align to genus,"first word (""genus"")",exact,"APC accepted taxon concepts, other APC taxon concepts, APNI",genus,"Find strings that indicate a name that is a hybrid between two taxa. Such names, unless documented in APC (i.e. matches 6, 7 above) can only be aligned to genus." -match_11b,Detect ` x ` (hybrid taxon) and align to genus,"first word (""genus"")",fuzzy,APC accepted taxon concepts,genus, -match_11c,Detect ` x ` (hybrid taxon) and align to genus,"first word (""genus"")",fuzzy,other APC taxon concepts,genus, -match_11d,Detect ` x ` (hybrid taxon) and align to genus,"first word (""genus"")",fuzzy,APNI,genus, -match_11e,"Detect ` x ` (hybrid taxon), but fail to align to genus",NA,no match,NA,NA, -match_12a,"Detect canonical names, by checking first three words in string",trinomial (from stripped_name_2),exact,APC accepted taxon concepts,species/infraspecific,"Check if the first three words in the name string match with a taxon name, allowing notes to be discarded. Also useful for aligning phrase names." -match_12b,"Detect canonical names, by checking first three words in string",trinomial (from stripped_name_2),exact,other APC taxon concepts,species/infraspecific, -match_13a,"Detect canonical names, by checking first three words in string",trinomial (from stripped_name_2),fuzzy,APC accepted taxon concepts,species/infraspecific, -match_13b,"Detect canonical names, by checking first three words in string",trinomial (from stripped_name_2),fuzzy,other APC taxon concepts,species/infraspecific, -match_14a,"Detect canonical names, by checking first two words in string",binomial (from stripped_name_2),exact,APC accepted taxon concepts,species/infraspecific,"Check if the first two words in the name string match with a taxon name, allowing notes and invalid infraspecific names to be discarded. Also useful for aligning phrase names." -match_14b,"Detect canonical names, by checking first two words in string",binomial (from stripped_name_2),exact,other APC taxon concepts,species/infraspecific, -match_15a,"Detect canonical names, by checking first two words in string",binomial (from stripped_name_2),fuzzy,APC accepted taxon concepts,species/infraspecific, -match_15b,"Detect canonical names, by checking first two words in string",binomial (from stripped_name_2),fuzzy,other APC taxon concepts,species/infraspecific, -match_16a,"Detect canonical names, lacking authorship",stripped_name,fuzzy,APNI,species/infraspecific,"Further checks if strings are APNI taxon names, lacking authorship, now with fuzzy matching or considering just the first three or two words in the string." -match_17a,"Detect canonical names, lacking authorship",stripped_name,imprecise fuzzy,APNI,species/infraspecific, -match_18a,"Detect canonical names, by checking first three words in string",trinomial (from stripped_name_2),exact,APNI,species/infraspecific, -match_19a,"Detect canonical names, by checking first two words in string",binomial (from stripped_name_2),exact,APNI,species/infraspecific, -match_20a,"Detect an APC-accepted genus, by checking the first word in the string","first word (""genus"")",exact,APC accepted taxon concepts,genus,"Check if the first two word in the name string match with a taxon name, allowing an alignment to the genus-level or family-level" -match_20b,"Detect an APC-known genus, by checking the first word in the string","first word (""genus"")",exact,other APC taxon concepts,genus, -match_20c,"Detect an APC-known genus, by checking the first word in the string","first word (""genus"")",exact,APNI,genus, -match_21a,"Detect an APC-known family, by checking the first word in the string","first word (""genus"")",exact,APC accepted taxon concepts,family, -match_22a,"Detect an APC-accepted genus, by checking the first word in the string","first word (""genus"")",fuzzy,APC accepted taxon concepts,genus, -match_22b,"Detect an APC-known genus, by checking the first word in the string","first word (""genus"")",fuzzy,other APC taxon concepts,genus, +match_05a,"Detect canonical names, lacking authorship",stripped_name,fuzzy,APC accepted taxon concepts,species/infraspecific, +match_05b,"Detect canonical names, lacking authorship",stripped_name,fuzzy,other APC taxon concepts,species/infraspecific, +match_05c,"Detect canonical names, lacking authorship",cleaned_name,exact,APNI,species/infraspecific, +match_06a,"Detect `aff`, `affinis` (affinity to) and align to genus","first word (""genus"")",exact,"APC accepted taxon concepts, other APC taxon concepts, APNI",genus,"Find strings that indicate a name that indicates an affinity to a specific taxon, but the name itself is not that taxon. Such names, unless documented in APC (i.e. matches 6, 7 above) can only be aligned to genus." +match_06b,"Detect `aff`, `affinis` (affinity to) and align to genus","first word (""genus"")",fuzzy,APC accepted taxon concepts,genus, +match_06c,"Detect `aff`, `affinis` (affinity to) and align to genus","first word (""genus"")",fuzzy,other APC taxon concepts,genus, +match_06d,"Detect `aff`, `affinis` (affinity to) and align to genus","first word (""genus"")",fuzzy,APNI,genus, +match_06e,"Detect `aff`, `affinis` (affinity to), but fail to align to genus",NA,no match,NA,NA, +match_07a,"Detect canonical names, lacking authorship",stripped_name,imprecise fuzzy,APC accepted taxon concepts,species/infraspecific,"Further checks if strings are taxon names, lacking authorship, now with imprecise fuzzy matching" +match_07b,"Detect canonical names, lacking authorship",stripped_name,imprecise fuzzy,other APC taxon concepts,species/infraspecific, +match_08a,Detect ` x ` (hybrid taxon) and align to genus,"first word (""genus"")",exact,"APC accepted taxon concepts, other APC taxon concepts, APNI",genus,"Find strings that indicate a name that is a hybrid between two taxa. Such names, unless documented in APC (i.e. matches 6, 7 above) can only be aligned to genus." +match_08b,Detect ` x ` (hybrid taxon) and align to genus,"first word (""genus"")",fuzzy,APC accepted taxon concepts,genus, +match_08c,Detect ` x ` (hybrid taxon) and align to genus,"first word (""genus"")",fuzzy,other APC taxon concepts,genus, +match_08d,Detect ` x ` (hybrid taxon) and align to genus,"first word (""genus"")",fuzzy,APNI,genus, +match_08e,"Detect ` x ` (hybrid taxon), but fail to align to genus",NA,no match,NA,NA, +match_09a,"Detect canonical names, by checking first three words in string",three words (from stripped_name_2),exact,APC accepted taxon concepts,species/infraspecific,"Check if the first three words in the name string match with a taxon name, allowing notes to be discarded. Also useful for aligning phrase names." +match_09b,"Detect canonical names, by checking first three words in string",three words (from stripped_name_2),exact,other APC taxon concepts,species/infraspecific, +match_09c,"Detect canonical names, by checking first three words in string",three words (from stripped_name_2),fuzzy,APC accepted taxon concepts,species/infraspecific, +match_09d,"Detect canonical names, by checking first three words in string",three words (from stripped_name_2),fuzzy,other APC taxon concepts,species/infraspecific, +match_10a,"Detect canonical names, by checking first two words in string",two words (from stripped_name_2),exact,APC accepted taxon concepts,species/infraspecific,"Check if the first two words in the name string match with a taxon name, allowing notes and invalid infraspecific names to be discarded. Also useful for aligning phrase names." +match_10b,"Detect canonical names, by checking first two words in string",two words (from stripped_name_2),exact,other APC taxon concepts,species/infraspecific, +match_10c,"Detect canonical names, by checking first two words in string",two words (from stripped_name_2),fuzzy,APC accepted taxon concepts,species/infraspecific, +match_10d,"Detect canonical names, by checking first two words in string",two words (from stripped_name_2),fuzzy,other APC taxon concepts,species/infraspecific, +match_11a,"Detect canonical names, lacking authorship",stripped_name,fuzzy,APNI,species/infraspecific,"Further checks if strings are APNI taxon names, lacking authorship, now with fuzzy matching or considering just the first three or two words in the string." +match_11b,"Detect canonical names, lacking authorship",stripped_name,imprecise fuzzy,APNI,species/infraspecific, +match_11c,"Detect canonical names, by checking first three words in string",three words (from stripped_name_2),exact,APNI,species/infraspecific, +match_11d,"Detect canonical names, by checking first two words in string",two words (from stripped_name_2),exact,APNI,species/infraspecific, +match_12a,"Detect genus, by checking the first word in the string","first word (""genus"")",exact,APC accepted taxon concepts,genus,"Check if the first two word in the name string match with a taxon name, allowing an alignment to the genus-level or family-level" +match_12b,"Detect genus, by checking the first word in the string","first word (""genus"")",exact,other APC taxon concepts,genus, +match_12c,"Detect genus, by checking the first word in the string","first word (""genus"")",exact,APNI,genus, +match_12d,"Detect family, by checking the first word in the string","first word (""genus"")",exact,APC accepted taxon concepts,family, +match_12e,"Detect genus, by checking the first word in the string","first word (""genus"")",fuzzy,APC accepted taxon concepts,genus, +match_12f,"Detect genus, by checking the first word in the string","first word (""genus"")",fuzzy,other APC taxon concepts,genus, diff --git a/man/align_taxa.Rd b/man/align_taxa.Rd index 2598d66c..2d165adb 100644 --- a/man/align_taxa.Rd +++ b/man/align_taxa.Rd @@ -55,16 +55,16 @@ A tibble with columns that include original_name, aligned_name, taxonomic_datase \item binomial: the first two words in \code{stripped_name2}, required for matches that ignore all other text in the original_name; improves phrase name matches. \item genus: the first two words in \code{cleaned_name}; required for genus-rank matches and reprocessing of genus-rank names. \item fuzzy_match_genus: fuzzy match of genus column to best match among APC-accepted names; required for fuzzy matches of genus-rank names. -\item fuzzy_match_genus_known: fuzzy match of genus column to best match among APC-known names, only considering different matches to those documented under APC-accepted genera; required for fuzzy matches of genus-rank names. +\item fuzzy_match_genus_synonym: fuzzy match of genus column to best match among APC-known names, only considering different matches to those documented under APC-accepted genera; required for fuzzy matches of genus-rank names. \item fuzzy_match_genus_APNI: fuzzy match of genus column to best match among APNI names, only considering different matches to those documented under APC-accepted and APC-known genera; required for fuzzy matches of genus-rank names. \item fuzzy_match_cleaned_APC: fuzzy match of stripped_name to APC-accepted names; created for yet-to-be-aligned names at the match step 07a in the function \code{match_taxa}. -\item fuzzy_match_cleaned_APC_known: fuzzy match of stripped_name to APC-known names; created for yet-to-be-aligned names at the match step 07b in the function \code{match_taxa}. +\item fuzzy_match_cleaned_APC_synonym: fuzzy match of stripped_name to APC-known names; created for yet-to-be-aligned names at the match step 07b in the function \code{match_taxa}. \item fuzzy_match_cleaned_APC_imprecise: imprecise fuzzy match of stripped_name to APC-accepted names; created for yet-to-be-aligned names at the match step 10a in the function \code{match_taxa}. -\item fuzzy_match_cleaned_APC_known_imprecise: imprecise fuzzy match of stripped_name to APC-accepted names; created for yet-to-be-aligned names at the match step 10b in the function \code{match_taxa}. +\item fuzzy_match_cleaned_APC_synonym_imprecise: imprecise fuzzy match of stripped_name to APC-accepted names; created for yet-to-be-aligned names at the match step 10b in the function \code{match_taxa}. \item fuzzy_match_binomial: fuzzy match of binomial column to best match among APC-accepted names; created for yet-to-be-aligned names at match step 15a in the function \code{match_taxa}. -\item fuzzy_match_binomial_APC_known: fuzzy match of binomial column to best match among APC-known names; created for yet-to-be-aligned names at match step 15a in the function \code{match_taxa}. +\item fuzzy_match_binomial_APC_synonym: fuzzy match of binomial column to best match among APC-known names; created for yet-to-be-aligned names at match step 15a in the function \code{match_taxa}. \item fuzzy_match_trinomial: fuzzy match of trinomial column to best match among APC-accepted names; created for yet-to-be-aligned names at match step 16a in the function \code{match_taxa}. -\item fuzzy_match_trinomial_known: fuzzy match of trinomial column to best match among APC-known names; created for yet-to-be-aligned names at match step 16b in the function \code{match_taxa}. +\item fuzzy_match_trinomial_synonym: fuzzy match of trinomial column to best match among APC-known names; created for yet-to-be-aligned names at match step 16b in the function \code{match_taxa}. \item fuzzy_match_cleaned_APNI: fuzzy match of stripped_name to APNI names; created for yet-to-be-aligned names at the match step 16a in the function \code{match_taxa}. \item fuzzy_match_cleaned_APNI_imprecise: imprecise fuzzy match of stripped_name to APNI names; created for yet-to-be-aligned names at the match step 17a in the function \code{match_taxa}. } diff --git a/man/create_taxonomic_update_lookup.Rd b/man/create_taxonomic_update_lookup.Rd index b72cd64e..0ece0bd6 100644 --- a/man/create_taxonomic_update_lookup.Rd +++ b/man/create_taxonomic_update_lookup.Rd @@ -55,7 +55,7 @@ A lookup table containing the accepted and suggested names for each original nam \item update_reason: the explanation of a specific taxon name update (from an aligned name to an accepted or suggested name). \item subclass: the subclass of the accepted name. \item taxon_distribution: the distribution of the accepted name; only filled in if an APC accepted_name is available. -\item scientific_name_authorship: the authorship information for the accepted (or known) name; available for both APC and APNI names. +\item scientific_name_authorship: the authorship information for the accepted (or synonymous) name; available for both APC and APNI names. \item taxon_ID: the unique taxon concept identifier for the accepted_name; only filled in if an APC accepted_name is available. \item taxon_ID_genus: an identifier for the genus; only filled in if an APC-accepted genus name is available. \item scientific_name_ID: an identifier for the nomenclatural (not taxonomic) details of a scientific name; available for both APC and APNI names. diff --git a/man/update_taxonomy.Rd b/man/update_taxonomy.Rd index 487d23a4..4a5a84ad 100644 --- a/man/update_taxonomy.Rd +++ b/man/update_taxonomy.Rd @@ -45,7 +45,7 @@ A tibble with updated taxonomy for the specified plant names. The tibble contain \item update_reason: the explanation of a specific taxon name update (from an aligned name to an accepted or suggested name). \item subclass: the subclass of the accepted name. \item taxon_distribution: the distribution of the accepted name; only filled in if an APC accepted_name is available. -\item scientific_name_authorship: the authorship information for the accepted (or known) name; available for both APC and APNI names. +\item scientific_name_authorship: the authorship information for the accepted (or synonymous) name; available for both APC and APNI names. \item taxon_ID: the unique taxon concept identifier for the accepted_name; only filled in if an APC accepted_name is available. \item taxon_ID_genus: an identifier for the genus; only filled in if an APC-accepted genus name is available. \item scientific_name_ID: an identifier for the nomenclatural (not taxonomic) details of a scientific name; available for both APC and APNI names. diff --git a/tests/testthat/benchmarks/test_matches_alignments_updates.csv b/tests/testthat/benchmarks/test_matches_alignments_updates.csv index 5029abf0..bf158aaa 100644 --- a/tests/testthat/benchmarks/test_matches_alignments_updates.csv +++ b/tests/testthat/benchmarks/test_matches_alignments_updates.csv @@ -1,224 +1,224 @@ -original_name,alignment_code_all_matches_TRUE,aligned_name_all_matches_TRUE,taxonomic_dataset_all_matches_TRUE,taxon_rank_all_matches_TRUE,updated_name,updated_name_passes,taxon_ID,scientific_name_ID,scientific_name -Actinotus sp.,match_01a,Actinotus sp. [test_all_matches_TRUE],APC,genus,Actinotus,FALSE,https://id.biodiversity.org.au/node/apni/6903559,https://id.biodiversity.org.au/name/apni/75003,Actinotus Labill. -Actinotus spp,match_01a,Actinotus sp. [test_all_matches_TRUE],APC,genus,Actinotus,FALSE,https://id.biodiversity.org.au/node/apni/6903559,https://id.biodiversity.org.au/name/apni/75003,Actinotus Labill. -Actinocarpus sp,match_01a,Actinocarpus sp. [test_all_matches_TRUE],APC,genus,Damasonium,FALSE,https://id.biodiversity.org.au/instance/apni/884226,https://id.biodiversity.org.au/name/apni/74816,Actinocarpus R.Br. -Actinocarpus spp.,match_01a,Actinocarpus sp. [test_all_matches_TRUE],APC,genus,Damasonium,FALSE,https://id.biodiversity.org.au/instance/apni/884226,https://id.biodiversity.org.au/name/apni/74816,Actinocarpus R.Br. -Actinocladum sp.,match_01a,Actinocladum sp. [test_all_matches_TRUE],APNI,genus,Actinocladum,FALSE,NA,https://id.biodiversity.org.au/name/apni/181935,Actinocladum McClure ex Soderstr. -Actinocladum spp,match_01a,Actinocladum sp. [test_all_matches_TRUE],APNI,genus,Actinocladum,FALSE,NA,https://id.biodiversity.org.au/name/apni/181935,Actinocladum McClure ex Soderstr. -Xystidium sp,match_01a,Xystidium sp. [test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. -Zygia spp.,match_01a,Zygia sp. [test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne -Actinatus sp.,match_01b,Actinotus sp. [test_all_matches_TRUE],APC,genus,Actinotus,FALSE,https://id.biodiversity.org.au/node/apni/6903559,https://id.biodiversity.org.au/name/apni/75003,Actinotus Labill. -Banksiaa sp.,match_01b,Banksia sp. [test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Actinocarros sp,match_01c,Actinocarpus sp. [test_all_matches_TRUE],APC,genus,Damasonium,FALSE,https://id.biodiversity.org.au/instance/apni/884226,https://id.biodiversity.org.au/name/apni/74816,Actinocarpus R.Br. -Dryandraa spp.,match_01c,Dryandra sp. [test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Asteraceae sp.,match_02a,Asteraceae sp. [test_all_matches_TRUE],APC,family,Asteraceae,FALSE,https://id.biodiversity.org.au/taxon/apni/51695393,https://id.biodiversity.org.au/name/apni/54580,Asteraceae Bercht. & J.Presl -Rutaceae spp,match_02a,Rutaceae sp. [test_all_matches_TRUE],APC,family,Rutaceae,FALSE,https://id.biodiversity.org.au/taxon/apni/51461748,https://id.biodiversity.org.au/name/apni/54479,Rutaceae Juss. -Abildgaardia odontocarpa -- Abildgaardia oxystachya,match_03a,Abildgaardia sp. [Abildgaardia odontocarpa -- Abildgaardia oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl -Acanthocarpus fimbriatus -- Acanthocarpus mucronatus,match_03a,Acanthocarpus sp. [Acanthocarpus fimbriatus -- Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Acanthocarpus fimbriatus -- mucronatus,match_03a,Acanthocarpus sp. [Acanthocarpus fimbriatus -- mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Banksia serrata -- Banksia ericifolia,match_03a,Banksia sp. [Banksia serrata -- Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Banksia serrata -- ericifolia,match_03a,Banksia sp. [Banksia serrata -- ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Banksia serrata--Banksia ericifolia,match_03a,Banksia sp. [Banksia serrata--Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Aporuellia abc--def,match_03a,Aporuellia sp. [Aporuellia abc--def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke -Dryandra abc--def,match_03a,Dryandra sp. [Dryandra abc--def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Xystidium abc--def,match_03a,Xystidium sp. [Xystidium abc--def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. -Zygia abc--def,match_03a,Zygia sp. [Zygia abc--def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne -Abildgardiia odontocarpa -- oxystachya,match_03b,Abildgaardia sp. [Abildgardiia odontocarpa -- oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl -Accanthocarpis fimbriatus -- Acanthocarpus mucronatus,match_03b,Acanthocarpus sp. [Accanthocarpis fimbriatus -- Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Bankseea serrata -- ericifolia,match_03b,Banksia sp. [Bankseea serrata -- ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Bannksia serrata -- Banksia ericifolia,match_03b,Banksia sp. [Bannksia serrata -- Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Aporuelliaa abc--def,match_03c,Aporuellia sp. [Aporuelliaa abc--def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke -Driandra abc--def,match_03c,Dryandra sp. [Driandra abc--def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Xyystidium abc--def,match_03d,Xystidium sp. [Xyystidium abc--def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. -Zygiaa abc--def,match_03d,Zygia sp. [Zygiaa abc--def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne -Abcde fgh -- ijk,match_03e,NA,NA,genus,NA,TRUE,NA,NA,NA -Ryandra abc--def,match_03e,NA,NA,genus,NA,TRUE,NA,NA,NA -Abildgaardia odontocarpa / Abildgaardia oxystachya,match_04a,Abildgaardia sp. [Abildgaardia odontocarpa / Abildgaardia oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl -Acanthocarpus fimbriatus / Acanthocarpus mucronatus,match_04a,Acanthocarpus sp. [Acanthocarpus fimbriatus / Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Acanthocarpus fimbriatus / mucronatus,match_04a,Acanthocarpus sp. [Acanthocarpus fimbriatus / mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Banksia serrata / Banksia ericifolia,match_04a,Banksia sp. [Banksia serrata / Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Banksia serrata / ericifolia,match_04a,Banksia sp. [Banksia serrata / ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Banksia serrata/Banksia ericifolia,match_04a,Banksia sp. [Banksia serrata/Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Aporuellia abc / def,match_04a,Aporuellia sp. [Aporuellia abc / def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke -Dryandra abc / def,match_04a,Dryandra sp. [Dryandra abc / def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Xystidium abc/def,match_04a,Xystidium sp. [Xystidium abc/def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. -Zygia abc/def,match_04a,Zygia sp. [Zygia abc/def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne -Abildgardiia odontocarpa / oxystachya,match_04b,Abildgaardia sp. [Abildgardiia odontocarpa / oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl -Accanthocarpis fimbriatus / Acanthocarpus mucronatus,match_04b,Acanthocarpus sp. [Accanthocarpis fimbriatus / Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Bankseea serrata / ericifolia,match_04b,Banksia sp. [Bankseea serrata / ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Bannksia serrata / Banksia ericifolia,match_04b,Banksia sp. [Bannksia serrata / Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Aporuelliaa abc / def,match_04c,Aporuellia sp. [Aporuelliaa abc / def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke -Drrandra abc / def,match_04c,Dryandra sp. [Drrandra abc / def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Xyystidium abc/def,match_04d,Xystidium sp. [Xyystidium abc/def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. -Zygiaa abc / def,match_04d,Zygia sp. [Zygiaa abc / def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne -Abcde fgh / ijk,match_04e,NA,NA,genus,NA,TRUE,NA,NA,NA -Ryandra abc / def,match_04e,NA,NA,genus,NA,TRUE,NA,NA,NA -Cycas candida K.D.Hill,match_05a,Cycas candida,APC,species,Cycas candida,TRUE,https://id.biodiversity.org.au/node/apni/2893335,https://id.biodiversity.org.au/name/apni/188177,Cycas candida K.D.Hill -Eremophila papillata Chinnock,match_05a,Eremophila papillata,APC,species,Eremophila papillata,TRUE,https://id.biodiversity.org.au/node/apni/2910890,https://id.biodiversity.org.au/name/apni/207453,Eremophila papillata Chinnock -Acalypha indica var. australis F.M.Bailey,match_05b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey -Acanthocarpus serra F.Muell.,match_05b,Acanthocarpus serra,APC,species,Chamaexeros serra,TRUE,https://id.biodiversity.org.au/instance/apni/851959,https://id.biodiversity.org.au/name/apni/203327,Acanthocarpus serra F.Muell. -Dillwynia sp. C (Budawang Range),match_05b,Dillwynia sp. C (Budawang Range),APC,species,Dillwynia crispii,TRUE,https://id.biodiversity.org.au/instance/apni/933273,https://id.biodiversity.org.au/name/apni/137780,Dillwynia sp. C (Budawang Range) -Acaena x ovina,match_06a,Acaena x ovina,APC,species,Acaena x ovina,FALSE,https://id.biodiversity.org.au/taxon/apni/51446291,https://id.biodiversity.org.au/name/apni/72209,Acaena x ovina A.Cunn. -Acanthocarpus sp. Cooloomia (S.D.Hopper 3301),match_06a,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301),APC,species,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301),TRUE,https://id.biodiversity.org.au/node/apni/2903920,https://id.biodiversity.org.au/name/apni/203323,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301) WA Herbarium -Banksia serrata,match_06a,Banksia serrata,APC,species,Banksia serrata,TRUE,https://id.biodiversity.org.au/taxon/apni/51293610,https://id.biodiversity.org.au/name/apni/109014,Banksia serrata L.f. -Eremophila oppositifolia ssp. rubra,match_06a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock -Eremophila oppositifolia subsp. rubra,match_06a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock -Leucanthemum x superbum,match_06a,Leucanthemum x superbum,APC,species,Leucanthemum x superbum,TRUE,https://id.biodiversity.org.au/node/apni/2912531,https://id.biodiversity.org.au/name/apni/172142,Leucanthemum x superbum (Bergmans ex J.W.Ingram) D.H.Kent -Notelaea longifolia,match_06a,Notelaea longifolia,APC,species,Notelaea longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2919068,https://id.biodiversity.org.au/name/apni/95265,Notelaea longifolia Vent. -Notelaea longifolia f longifolia,match_06a,Notelaea longifolia f. longifolia,APC,form,Notelaea longifolia f. longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2915469,https://id.biodiversity.org.au/name/apni/95381,Notelaea longifolia Vent. f. longifolia -Notelaea longifolia f. intermedia,match_06a,Notelaea longifolia f. intermedia,APC,form,Notelaea longifolia f. intermedia,TRUE,https://id.biodiversity.org.au/node/apni/2914551,https://id.biodiversity.org.au/name/apni/95355,Notelaea longifolia f. intermedia P.S.Green -Notelaea longifolia f. longifolia,match_06a,Notelaea longifolia f. longifolia,APC,form,Notelaea longifolia f. longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2915469,https://id.biodiversity.org.au/name/apni/95381,Notelaea longifolia Vent. f. longifolia -Notelaea longifolia form. longifolia,match_06a,Notelaea longifolia f. longifolia,APC,form,Notelaea longifolia f. longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2915469,https://id.biodiversity.org.au/name/apni/95381,Notelaea longifolia Vent. f. longifolia -Notelaea longifolia forma longifolia,match_06a,Notelaea longifolia f. longifolia,APC,form,Notelaea longifolia f. longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2915469,https://id.biodiversity.org.au/name/apni/95381,Notelaea longifolia Vent. f. longifolia -Onopordum acanthium x Onopordum illyricum,match_06a,Onopordum acanthium x Onopordum illyricum,APC,species,Onopordum acanthium x Onopordum illyricum,TRUE,https://id.biodiversity.org.au/node/apni/7017361,https://id.biodiversity.org.au/name/apni/164808,Onopordum acanthium L. x Onopordum illyricum L. -Ranunculus pentandrus,match_06a,Ranunculus pentandrus,APC,species,Ranunculus pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2887738,https://id.biodiversity.org.au/name/apni/113007,Ranunculus pentandrus J.M.Black -Ranunculus pentandrus v pentandrus,match_06a,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus -Ranunculus pentandrus var pentandrus,match_06a,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus -Ranunculus pentandrus var. pentandrus,match_06a,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus -Thynninorchis huntiana,match_06a,Thynninorchis huntiana,APC,species,Thynninorchis huntiana,TRUE,https://id.biodiversity.org.au/taxon/apni/51414495,https://id.biodiversity.org.au/name/apni/178809,Thynninorchis huntiana (F.Muell.) D.L.Jones & M.A.Clem. -Acalypha indica var. australis,match_06b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey -Aceratium megalospermum var. coriaceum,match_06b,Aceratium megalospermum var. coriaceum,APC,variety,Aceratium megalospermum,TRUE,https://id.biodiversity.org.au/instance/apni/896479,https://id.biodiversity.org.au/name/apni/72795,Aceratium megalospermum var. coriaceum Balgooy -Achneria brevifolia,match_06b,Achneria brevifolia,APC,species,Eriachne brevifolia,TRUE,https://id.biodiversity.org.au/instance/apni/51443025,https://id.biodiversity.org.au/name/apni/72928,Achneria brevifolia (R.Br.) P.Beauv. -Dillwynia sp. C ( Budawang Range ),match_06b,Dillwynia sp. C (Budawang Range),APC,species,Dillwynia crispii,TRUE,https://id.biodiversity.org.au/instance/apni/933273,https://id.biodiversity.org.au/name/apni/137780,Dillwynia sp. C (Budawang Range) -Aceeena x ovinaa,match_07a,Acaena x ovina,APC,species,Acaena x ovina,FALSE,https://id.biodiversity.org.au/taxon/apni/51446291,https://id.biodiversity.org.au/name/apni/72209,Acaena x ovina A.Cunn. -Aceena x ovina,match_07a,Acaena x ovina,APC,species,Acaena x ovina,FALSE,https://id.biodiversity.org.au/taxon/apni/51446291,https://id.biodiversity.org.au/name/apni/72209,Acaena x ovina A.Cunn. -Banksia serrate,match_07a,Banksia serrata,APC,species,Banksia serrata,TRUE,https://id.biodiversity.org.au/taxon/apni/51293610,https://id.biodiversity.org.au/name/apni/109014,Banksia serrata L.f. -Eremophila opositifolia ssp. rubra,match_07a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock -Eremophila opositifoliia subsp. rubra,match_07a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock -Hemigenia sp. Tallering (H. Pringle 3323),match_07a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium -Hemigenia sp. Tallering (H.Pringle 33223),match_07a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium -Hemigeniia sp. Tallering (H.Pringle 3323),match_07a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium -Notelaea longifoliaa forma longifoliaa,match_07a,Notelaea longifolia f. longifolia,APC,form,Notelaea longifolia f. longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2915469,https://id.biodiversity.org.au/name/apni/95381,Notelaea longifolia Vent. f. longifolia -Onopordum acanthium x Onnopordum illyricum,match_07a,Onopordum acanthium x Onopordum illyricum,APC,species,Onopordum acanthium x Onopordum illyricum,TRUE,https://id.biodiversity.org.au/node/apni/7017361,https://id.biodiversity.org.au/name/apni/164808,Onopordum acanthium L. x Onopordum illyricum L. -Ranunculus pentandra var pentandru,match_07a,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus -Thynninorchis huntianaa,match_07a,Thynninorchis huntiana,APC,species,Thynninorchis huntiana,TRUE,https://id.biodiversity.org.au/taxon/apni/51414495,https://id.biodiversity.org.au/name/apni/178809,Thynninorchis huntiana (F.Muell.) D.L.Jones & M.A.Clem. -Acalyffa indice australis,match_07b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey -Acalypha indica australis,match_07b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey -Acalypha indice australis,match_07b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey -Acalypha inndica var. australis,match_07b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey -Achneriia brevifoliaa,match_07b,Achneria brevifolia,APC,species,Eriachne brevifolia,TRUE,https://id.biodiversity.org.au/instance/apni/51443025,https://id.biodiversity.org.au/name/apni/72928,Achneria brevifolia (R.Br.) P.Beauv. -Dillwinnia sp. C ( Budawang Range ),match_07b,Dillwynia sp. C (Budawang Range),APC,species,Dillwynia crispii,TRUE,https://id.biodiversity.org.au/instance/apni/933273,https://id.biodiversity.org.au/name/apni/137780,Dillwynia sp. C (Budawang Range) -Acanthus ebracteatus subsp. ebracteatus,match_08a,Acanthus ebracteatus subsp. ebracteatus,APNI,subspecies,Acanthus ebracteatus subsp. ebracteatus,TRUE,NA,https://id.biodiversity.org.au/name/apni/72713,Acanthus ebracteatus Vahl subsp. ebracteatus -Acanthus ilicifolius var. typica,match_08a,Acanthus ilicifolius var. typica,APNI,variety,Acanthus ilicifolius var. typica,TRUE,NA,https://id.biodiversity.org.au/name/apni/72730,Acanthus ilicifolius var. typica Domin -Asystasia sp. (Newcastle Bay),match_08a,Asystasia sp. (Newcastle Bay),APNI,species,Asystasia sp. (Newcastle Bay),TRUE,NA,https://id.biodiversity.org.au/name/apni/3493285,Asystasia sp. (Newcastle Bay) -Blechum pyramidatum,match_08a,Blechum pyramidatum,APNI,species,Blechum pyramidatum,TRUE,NA,https://id.biodiversity.org.au/name/apni/189742,Blechum pyramidatum (Lam.) Urb. -Daviesia sp. ( Wadbilliga NP - Deua NP ),match_08a,Daviesia sp. (Wadbilliga NP - Deua NP),APNI,species,Daviesia sp. (Wadbilliga NP - Deua NP),TRUE,NA,https://id.biodiversity.org.au/name/apni/51681812,Daviesia sp. (Wadbilliga NP - Deua NP) -Dillwynia sp. ( Gibralter Range ),match_08a,Dillwynia sp. (Gibralter Range),APNI,species,Dillwynia sp. (Gibralter Range),TRUE,NA,https://id.biodiversity.org.au/name/apni/51681862,Dillwynia sp. (Gibralter Range) -Dillwynia sp. (Gibralter Range),match_08a,Dillwynia sp. (Gibralter Range),APNI,species,Dillwynia sp. (Gibralter Range),TRUE,NA,https://id.biodiversity.org.au/name/apni/51681862,Dillwynia sp. (Gibralter Range) -Jasminum sp (Beechmont G.Holmes AQ633577),match_08a,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) -Thunbergia alata var. arnhemica,match_08a,Thunbergia alata var. arnhemica,APNI,variety,Thunbergia alata var. arnhemica,TRUE,NA,https://id.biodiversity.org.au/name/apni/89722,Thunbergia alata var. arnhemica (F.Muell.) Domin -Abildgaardia aff odontocarpa,match_09a,Abildgaardia sp. [Abildgaardia aff. odontocarpa; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl -Acanthocarpus aff. fimbriatus,match_09a,Acanthocarpus sp. [Acanthocarpus aff. fimbriatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Acanthocarpus affinis fimbriatus,match_09a,Acanthocarpus sp. [Acanthocarpus aff. fimbriatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Banksia aff serrata,match_09a,Banksia sp. [Banksia aff. serrata; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Banksia aff. serrata,match_09a,Banksia sp. [Banksia aff. serrata; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Banksia affinis serrata,match_09a,Banksia sp. [Banksia aff. serrata; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Aporuellia aff abc,match_09a,Aporuellia sp. [Aporuellia aff. abc; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke -Dryandra aff def,match_09a,Dryandra sp. [Dryandra aff. def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Xystidium aff. def,match_09a,Xystidium sp. [Xystidium aff. def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. -Zygia affinis def,match_09a,Zygia sp. [Zygia aff. def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne -Abildgardiia aff odontocarpa,match_09b,Abildgaardia sp. [Abildgardiia aff. odontocarpa; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl -Accanthocarpis aff fimbriatus,match_09b,Acanthocarpus sp. [Accanthocarpis aff. fimbriatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Bankseea aff. serrata,match_09b,Banksia sp. [Bankseea aff. serrata; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Bannksia affinis serrata,match_09b,Banksia sp. [Bannksia aff. serrata; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Aporuelliaa aff def,match_09c,Aporuellia sp. [Aporuelliaa aff. def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke -Drrandra affinis def,match_09c,Dryandra sp. [Drrandra aff. def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Xyystidium aff. abc,match_09d,Xystidium sp. [Xyystidium aff. abc; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. -Zygiaa aff. abc,match_09d,Zygia sp. [Zygiaa aff. abc; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne -Abcde affinis fgh,match_09e,NA,NA,genus,NA,TRUE,NA,NA,NA -Rryandra aff def,match_09e,NA,NA,genus,NA,TRUE,NA,NA,NA -Aceeena x ovinaaa,match_10a,Acaena x ovina,APC,species,Acaena x ovina,FALSE,https://id.biodiversity.org.au/taxon/apni/51446291,https://id.biodiversity.org.au/name/apni/72209,Acaena x ovina A.Cunn. -Banksiia serrratte,match_10a,Banksia serrata,APC,species,Banksia serrata,TRUE,https://id.biodiversity.org.au/taxon/apni/51293610,https://id.biodiversity.org.au/name/apni/109014,Banksia serrata L.f. -Eremoophila opppositifolia ssp. rubraaa,match_10a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock -Eremophillaa oppositifoliia subsp. rrubra,match_10a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock -Hemigenia sp. Tallering (H.Pringle),match_10a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium -Thynninorchisss huntianaaaa,match_10a,Thynninorchis huntiana,APC,species,Thynninorchis huntiana,TRUE,https://id.biodiversity.org.au/taxon/apni/51414495,https://id.biodiversity.org.au/name/apni/178809,Thynninorchis huntiana (F.Muell.) D.L.Jones & M.A.Clem. -Acalyffa indice australiss,match_10b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey -Accalypha inndicaa var. australiss,match_10b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey -Aceratiumm meggalospermumm var. coriaceumm,match_10b,Aceratium megalospermum var. coriaceum,APC,variety,Aceratium megalospermum,TRUE,https://id.biodiversity.org.au/instance/apni/896479,https://id.biodiversity.org.au/name/apni/72795,Aceratium megalospermum var. coriaceum Balgooy -Abildgaardia odontocarpa x Abildgaardia oxystachya,match_11a,Abildgaardia x [Abildgaardia odontocarpa x Abildgaardia oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl -Acanthocarpus fimbriatus x Acanthocarpus mucronatus,match_11a,Acanthocarpus x [Acanthocarpus fimbriatus x Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Acanthocarpus fimbriatus x mucronatus,match_11a,Acanthocarpus x [Acanthocarpus fimbriatus x mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Banksia serrata x Banksia ericifolia,match_11a,Banksia x [Banksia serrata x Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Banksia serrata x ericifolia,match_11a,Banksia x [Banksia serrata x ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Thynninorchis x huntiana,match_11a,Thynninorchis x [Thynninorchis x huntiana; test_all_matches_TRUE],APC,genus,Thynninorchis,FALSE,https://id.biodiversity.org.au/taxon/apni/51414493,https://id.biodiversity.org.au/name/apni/178808,Thynninorchis D.L.Jones & M.A.Clem. -Aporuellia abc x def,match_11a,Aporuellia x [Aporuellia abc x def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke -Dryandra abc x def,match_11a,Dryandra x [Dryandra abc x def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Xystidium abc x Xystidium def,match_11a,Xystidium x [Xystidium abc x Xystidium def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. -Zygia abc x def,match_11a,Zygia x [Zygia abc x def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne -Abildgardiia odontocarpa x oxystachya,match_11b,Abildgaardia x [Abildgardiia odontocarpa x oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl -Accanthocarpis fimbriatus x Acanthocarpus mucronatus,match_11b,Acanthocarpus x [Accanthocarpis fimbriatus x Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. -Bankseea serrata x ericifolia,match_11b,Banksia x [Bankseea serrata x ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Bannksia serrata x Banksia ericifolia,match_11b,Banksia x [Bannksia serrata x Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Aporuelliaa abc x def,match_11c,Aporuellia x [Aporuelliaa abc x def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke -Drrandra x def,match_11c,Dryandra x [Drrandra x def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Xyystidium x def,match_11d,Xystidium x [Xyystidium x def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. -Zygiaa abc x Zygia def,match_11d,Zygia x [Zygiaa abc x Zygia def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne -Abcde fgh x ijk,match_11e,NA,NA,genus,NA,TRUE,NA,NA,NA -Ryandra abc x def,match_11e,NA,NA,genus,NA,TRUE,NA,NA,NA -Baeckea sp. murchison river,match_12a,Baeckea sp. Murchison River (M.E.Trudgen 12009),APC,species,Baeckea sp. Murchison River (M.E.Trudgen 12009),TRUE,https://id.biodiversity.org.au/node/apni/2888052,https://id.biodiversity.org.au/name/apni/191267,Baeckea sp. Murchison River (M.E.Trudgen 12009) WA Herbarium -Eremophila oppositifolia rubra (needle leaves),match_12a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock -Eremophila oppositifolia rubra early collection,match_12a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock -Eremophila oppositifolia ssp. rubra needle leaves,match_12a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock -Ranunculus pentandrus var. pentandrus (flooded area),match_12a,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus -Acalypha indica var. australis (double check),match_12b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey -Aceratium megalospermum var. coriaceum (top of hill),match_12b,Aceratium megalospermum var. coriaceum,APC,variety,Aceratium megalospermum,TRUE,https://id.biodiversity.org.au/instance/apni/896479,https://id.biodiversity.org.au/name/apni/72795,Aceratium megalospermum var. coriaceum Balgooy -Eremophila opositifolia rubra early collection,match_13a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock -Ranunculus pentandrus var. pentand (flooded area),match_13a,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus -Acalypha indica var. austral. (double check),match_13b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey -Aceratiuum megalospermum var. coriaceuum (top of hill),match_13b,Aceratium megalospermum var. coriaceum,APC,variety,Aceratium megalospermum,TRUE,https://id.biodiversity.org.au/instance/apni/896479,https://id.biodiversity.org.au/name/apni/72795,Aceratium megalospermum var. coriaceum Balgooy -Acalypha indica var. aus,match_10a,Acalypha indica,APC,species,Acalypha indica,TRUE,https://id.biodiversity.org.au/node/apni/2908627,https://id.biodiversity.org.au/name/apni/72584,Acalypha indica L. -Acanthocarpus sp. cooloomia,match_14a,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301),APC,species,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301),TRUE,https://id.biodiversity.org.au/node/apni/2903920,https://id.biodiversity.org.au/name/apni/203323,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301) WA Herbarium -Acanthus ebracteatus subsp. ebracteatussss,match_14a,Acanthus ebracteatus,APC,species,Acanthus ebracteatus,TRUE,https://id.biodiversity.org.au/node/apni/2906336,https://id.biodiversity.org.au/name/apni/72706,Acanthus ebracteatus Vahl -Aceratium megalospermum var. might be coriaceum,match_14a,Aceratium megalospermum,APC,species,Aceratium megalospermum,TRUE,https://id.biodiversity.org.au/node/apni/2915767,https://id.biodiversity.org.au/name/apni/72789,Aceratium megalospermum (F.Muell.) Balgooy -Banksia paludosa (key to subspecies),match_14a,Banksia paludosa,APC,species,Banksia paludosa,TRUE,https://id.biodiversity.org.au/node/apni/2891165,https://id.biodiversity.org.au/name/apni/108449,Banksia paludosa R.Br. -Banksia plagiocarpa (giant plants),match_14a,Banksia plagiocarpa,APC,species,Banksia plagiocarpa,TRUE,https://id.biodiversity.org.au/node/apni/2900302,https://id.biodiversity.org.au/name/apni/108639,Banksia plagiocarpa A.S.George -Hemigenia sp. Tallering (H. Pringle),match_14a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium -Hemigenia sp. Tallering Pringle,match_14a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium -Leucopogon sp. murchison,match_14a,Leucopogon sp. Murchison (R.J.Cranfield 9224),APC,species,Leucopogon sp. Murchison (R.J.Cranfield 9224),TRUE,https://id.biodiversity.org.au/node/apni/2886129,https://id.biodiversity.org.au/name/apni/239999,Leucopogon sp. Murchison (R.J.Cranfield 9224) WA Herbarium -Notelaea longifolia f. iongifolia,match_14a,Notelaea longifolia,APC,species,Notelaea longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2919068,https://id.biodiversity.org.au/name/apni/95265,Notelaea longifolia Vent. -Schoenus sp. murchison,match_14a,Schoenus sp. Murchison (K.L.Wilson 2647),APC,species,Schoenus sp. Murchison (K.L.Wilson 2647),TRUE,https://id.biodiversity.org.au/node/apni/2915697,https://id.biodiversity.org.au/name/apni/243799,Schoenus sp. Murchison (K.L.Wilson 2647) WA Herbarium -Senna sp. austin,match_14a,Senna sp. Austin (A.Strid 20210),APC,species,Senna sp. Austin (A.Strid 20210),TRUE,https://id.biodiversity.org.au/node/apni/2891919,https://id.biodiversity.org.au/name/apni/198508,Senna sp. Austin (A.Strid 20210) WA Herbarium -Thunbergia alata (probably var. arnhemica),match_14a,Thunbergia alata,APC,species,Thunbergia alata,TRUE,https://id.biodiversity.org.au/node/apni/2896895,https://id.biodiversity.org.au/name/apni/89707,Thunbergia alata Bojer ex Sims -Thunbergia alata var. arnhemica (uncertain),match_14a,Thunbergia alata,APC,species,Thunbergia alata,TRUE,https://id.biodiversity.org.au/node/apni/2896895,https://id.biodiversity.org.au/name/apni/89707,Thunbergia alata Bojer ex Sims -Achneria brevifolia (collected in May),match_14b,Achneria brevifolia,APC,species,Eriachne brevifolia,TRUE,https://id.biodiversity.org.au/instance/apni/51443025,https://id.biodiversity.org.au/name/apni/72928,Achneria brevifolia (R.Br.) P.Beauv. -Dryandra octotriginta (update name),match_14b,Dryandra octotriginta,APC,species,Banksia octotriginta,TRUE,https://id.biodiversity.org.au/instance/apni/955349,https://id.biodiversity.org.au/name/apni/138097,Dryandra octotriginta A.S.George -Acanthus illlicifoliuss var. typicaa,match_15a,Acanthus ilicifolius,APC,species,Acanthus ilicifolius,TRUE,https://id.biodiversity.org.au/node/apni/2913784,https://id.biodiversity.org.au/name/apni/72714,Acanthus ilicifolius L. -Banksia paludose (key to subspecies),match_15a,Banksia paludosa,APC,species,Banksia paludosa,TRUE,https://id.biodiversity.org.au/node/apni/2891165,https://id.biodiversity.org.au/name/apni/108449,Banksia paludosa R.Br. -Bannksia plagiocarpa (giant plants),match_15a,Banksia plagiocarpa,APC,species,Banksia plagiocarpa,TRUE,https://id.biodiversity.org.au/node/apni/2900302,https://id.biodiversity.org.au/name/apni/108639,Banksia plagiocarpa A.S.George -Achneriia brevifoliia (collected in May),match_15b,Achneria brevifolia,APC,species,Eriachne brevifolia,TRUE,https://id.biodiversity.org.au/instance/apni/51443025,https://id.biodiversity.org.au/name/apni/72928,Achneria brevifolia (R.Br.) P.Beauv. -Dryandra octotrigginta (update name),match_15b,Dryandra octotriginta,APC,species,Banksia octotriginta,TRUE,https://id.biodiversity.org.au/instance/apni/955349,https://id.biodiversity.org.au/name/apni/138097,Dryandra octotriginta A.S.George -Blechumm pyramidatum,match_16a,Blechum pyramidatum,APNI,species,Blechum pyramidatum,TRUE,NA,https://id.biodiversity.org.au/name/apni/189742,Blechum pyramidatum (Lam.) Urb. -Jasminum sp (Beechmont G. Holmes AQ633577),match_16a,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) -Jasminum sp (Beechmont G.Holms AQ633577),match_16a,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) -Jasminum sp (Beechmontte G.Holmes AQ633577),match_16a,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) -Blechummm pyramidatummm,match_17a,Blechum pyramidatum,APNI,species,Blechum pyramidatum,TRUE,NA,https://id.biodiversity.org.au/name/apni/189742,Blechum pyramidatum (Lam.) Urb. -Jasminummm sp (Beeechmontte G.Holmes AQ633577),match_17a,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) -Dillwynia sp. (Gibralter Range) (phrase name),match_18a,Dillwynia sp. (Gibralter Range),APNI,species,Dillwynia sp. (Gibralter Range),TRUE,NA,https://id.biodiversity.org.au/name/apni/51681862,Dillwynia sp. (Gibralter Range) -Jasminum sp (Beechmont G.Holmes),match_18a,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) -Dillwynia sp. (Gibralter) (phrase name),match_19a,Dillwynia sp. (Gibralter Range),APNI,species,Dillwynia sp. (Gibralter Range),TRUE,NA,https://id.biodiversity.org.au/name/apni/51681862,Dillwynia sp. (Gibralter Range) -Jasminum sp (Beechmont),match_19a,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) -Actinotus,match_20a,Actinotus sp. [Actinotus; test_all_matches_TRUE],APC,genus,Actinotus,FALSE,https://id.biodiversity.org.au/node/apni/6903559,https://id.biodiversity.org.au/name/apni/75003,Actinotus Labill. -Asystasia,match_20a,Asystasia sp. [Asystasia; test_all_matches_TRUE],APC,genus,Asystasia,FALSE,https://id.biodiversity.org.au/taxon/apni/51430302,https://id.biodiversity.org.au/name/apni/109497,Asystasia Blume -Asystasia - pink flower,match_20a,Asystasia sp. [Asystasia - pink flower; test_all_matches_TRUE],APC,genus,Asystasia,FALSE,https://id.biodiversity.org.au/taxon/apni/51430302,https://id.biodiversity.org.au/name/apni/109497,Asystasia Blume -Asystasia (voucher),match_20a,Asystasia sp. [Asystasia (voucher); test_all_matches_TRUE],APC,genus,Asystasia,FALSE,https://id.biodiversity.org.au/taxon/apni/51430302,https://id.biodiversity.org.au/name/apni/109497,Asystasia Blume -Banksia serrataxBanksia ericifolia,match_20a,Banksia sp. [Banksia serrataxBanksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Barleria maybe alba,match_20a,Barleria sp. [Barleria maybe alba; test_all_matches_TRUE],APC,genus,Barleria,FALSE,https://id.biodiversity.org.au/node/apni/2894241,https://id.biodiversity.org.au/name/apni/109526,Barleria L. -Dillwynia sp. 3 ( Budawang Range ),match_20a,Dillwynia sp. [Dillwynia sp. 3 (Budawang Range); test_all_matches_TRUE],APC,genus,Dillwynia,FALSE,https://id.biodiversity.org.au/taxon/apni/51285570,https://id.biodiversity.org.au/name/apni/105354,Dillwynia Sm. -Actinocarpus,match_20b,Actinocarpus sp. [Actinocarpus; test_all_matches_TRUE],APC,genus,Damasonium,FALSE,https://id.biodiversity.org.au/instance/apni/884226,https://id.biodiversity.org.au/name/apni/74816,Actinocarpus R.Br. -Dilwynia sp. 3 ( Budawang Range ),match_20b,Dilwynia sp. [Dilwynia sp. 3 (Budawang Range); test_all_matches_TRUE],APC,genus,Dillwynia,FALSE,https://id.biodiversity.org.au/instance/apni/933270,https://id.biodiversity.org.au/name/apni/106624,Dilwynia Pers. -Dryandra,match_20b,Dryandra sp. [Dryandra; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Actinocladum,match_20c,Actinocladum sp. [Actinocladum; test_all_matches_TRUE],APNI,genus,Actinocladum,FALSE,NA,https://id.biodiversity.org.au/name/apni/181935,Actinocladum McClure ex Soderstr. -Xystidium is very interesting,match_20c,Xystidium sp. [Xystidium is very interesting; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. -Zygia outlier genus,match_20c,Zygia sp. [Zygia outlier genus; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne -Poaceae (purple stems),match_21a,Poaceae sp. [Poaceae (purple stems); test_all_matches_TRUE],APC,family,Poaceae,FALSE,https://id.biodiversity.org.au/taxon/apni/51644646,https://id.biodiversity.org.au/name/apni/54563,Poaceae Barnhart -Rutaceae (an unknown species),match_21a,Rutaceae sp. [Rutaceae (an unknown species); test_all_matches_TRUE],APC,family,Rutaceae,FALSE,https://id.biodiversity.org.au/taxon/apni/51461748,https://id.biodiversity.org.au/name/apni/54479,Rutaceae Juss. -Assystasia - pink flower,match_22a,Asystasia sp. [Assystasia - pink flower; test_all_matches_TRUE],APC,genus,Asystasia,FALSE,https://id.biodiversity.org.au/taxon/apni/51430302,https://id.biodiversity.org.au/name/apni/109497,Asystasia Blume -Baarleria maybe alba,match_22a,Barleria sp. [Baarleria maybe alba; test_all_matches_TRUE],APC,genus,Barleria,FALSE,https://id.biodiversity.org.au/node/apni/2894241,https://id.biodiversity.org.au/name/apni/109526,Barleria L. -Bankssia serrataxBanksia ericifolia,match_22a,Banksia sp. [Bankssia serrataxBanksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. -Achneriia crevifoliaa,match_22b,Achneria sp. [Achneriia crevifoliaa; test_all_matches_TRUE],APC,genus,Eriachne,FALSE,https://id.biodiversity.org.au/instance/apni/876102,https://id.biodiversity.org.au/name/apni/72923,Achneria P.Beauv. -Actinocarpos,match_22b,Actinocarpus sp. [Actinocarpos; test_all_matches_TRUE],APC,genus,Damasonium,FALSE,https://id.biodiversity.org.au/instance/apni/884226,https://id.biodiversity.org.au/name/apni/74816,Actinocarpus R.Br. -Drryandra,match_22b,Dryandra sp. [Drryandra; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Dryandraa,match_22b,Dryandra sp. [Dryandraa; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. -Actiniladum sp.,NA,NA,NA,NA,NA,TRUE,NA,NA,NA -Ecalypha indica australis,NA,NA,NA,NA,NA,TRUE,NA,NA,NA +original_name,alignment_code-OLD,alignment_code_all_matches_TRUE,aligned_name_all_matches_TRUE,taxonomic_dataset_all_matches_TRUE,taxon_rank_all_matches_TRUE,updated_name,updated_name_passes,taxon_ID,scientific_name_ID,scientific_name +Actinotus sp.,match_01a,match_02a,Actinotus sp. [test_all_matches_TRUE],APC,genus,Actinotus,FALSE,https://id.biodiversity.org.au/node/apni/6903559,https://id.biodiversity.org.au/name/apni/75003,Actinotus Labill. +Actinotus spp,match_01a,match_02a,Actinotus sp. [test_all_matches_TRUE],APC,genus,Actinotus,FALSE,https://id.biodiversity.org.au/node/apni/6903559,https://id.biodiversity.org.au/name/apni/75003,Actinotus Labill. +Actinocarpus sp,match_01a,match_02a,Actinocarpus sp. [test_all_matches_TRUE],APC,genus,Damasonium,FALSE,https://id.biodiversity.org.au/instance/apni/884226,https://id.biodiversity.org.au/name/apni/74816,Actinocarpus R.Br. +Actinocarpus spp.,match_01a,match_02a,Actinocarpus sp. [test_all_matches_TRUE],APC,genus,Damasonium,FALSE,https://id.biodiversity.org.au/instance/apni/884226,https://id.biodiversity.org.au/name/apni/74816,Actinocarpus R.Br. +Actinocladum sp.,match_01a,match_02a,Actinocladum sp. [test_all_matches_TRUE],APNI,genus,Actinocladum,FALSE,NA,https://id.biodiversity.org.au/name/apni/181935,Actinocladum McClure ex Soderstr. +Actinocladum spp,match_01a,match_02a,Actinocladum sp. [test_all_matches_TRUE],APNI,genus,Actinocladum,FALSE,NA,https://id.biodiversity.org.au/name/apni/181935,Actinocladum McClure ex Soderstr. +Xystidium sp,match_01a,match_02a,Xystidium sp. [test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. +Zygia spp.,match_01a,match_02a,Zygia sp. [test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne +Actinatus sp.,match_01b,match_02b,Actinotus sp. [test_all_matches_TRUE],APC,genus,Actinotus,FALSE,https://id.biodiversity.org.au/node/apni/6903559,https://id.biodiversity.org.au/name/apni/75003,Actinotus Labill. +Banksiaa sp.,match_01b,match_02b,Banksia sp. [test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Actinocarros sp,match_01c,match_02c,Actinocarpus sp. [test_all_matches_TRUE],APC,genus,Damasonium,FALSE,https://id.biodiversity.org.au/instance/apni/884226,https://id.biodiversity.org.au/name/apni/74816,Actinocarpus R.Br. +Dryandraa spp.,match_01c,match_02c,Dryandra sp. [test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Asteraceae sp.,match_02a,match_02d,Asteraceae sp. [test_all_matches_TRUE],APC,family,Asteraceae,FALSE,https://id.biodiversity.org.au/taxon/apni/51695393,https://id.biodiversity.org.au/name/apni/54580,Asteraceae Bercht. & J.Presl +Rutaceae spp,match_02a,match_02d,Rutaceae sp. [test_all_matches_TRUE],APC,family,Rutaceae,FALSE,https://id.biodiversity.org.au/taxon/apni/51461748,https://id.biodiversity.org.au/name/apni/54479,Rutaceae Juss. +Abildgaardia odontocarpa -- Abildgaardia oxystachya,match_03a,match_03a,Abildgaardia sp. [Abildgaardia odontocarpa -- Abildgaardia oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl +Acanthocarpus fimbriatus -- Acanthocarpus mucronatus,match_03a,match_03a,Acanthocarpus sp. [Acanthocarpus fimbriatus -- Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Acanthocarpus fimbriatus -- mucronatus,match_03a,match_03a,Acanthocarpus sp. [Acanthocarpus fimbriatus -- mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Banksia serrata -- Banksia ericifolia,match_03a,match_03a,Banksia sp. [Banksia serrata -- Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Banksia serrata -- ericifolia,match_03a,match_03a,Banksia sp. [Banksia serrata -- ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Banksia serrata--Banksia ericifolia,match_03a,match_03a,Banksia sp. [Banksia serrata--Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Aporuellia abc--def,match_03a,match_03a,Aporuellia sp. [Aporuellia abc--def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke +Dryandra abc--def,match_03a,match_03a,Dryandra sp. [Dryandra abc--def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Xystidium abc--def,match_03a,match_03a,Xystidium sp. [Xystidium abc--def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. +Zygia abc--def,match_03a,match_03a,Zygia sp. [Zygia abc--def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne +Abildgardiia odontocarpa -- oxystachya,match_03b,match_03b,Abildgaardia sp. [Abildgardiia odontocarpa -- oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl +Accanthocarpis fimbriatus -- Acanthocarpus mucronatus,match_03b,match_03b,Acanthocarpus sp. [Accanthocarpis fimbriatus -- Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Bankseea serrata -- ericifolia,match_03b,match_03b,Banksia sp. [Bankseea serrata -- ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Bannksia serrata -- Banksia ericifolia,match_03b,match_03b,Banksia sp. [Bannksia serrata -- Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Aporuelliaa abc--def,match_03c,match_03c,Aporuellia sp. [Aporuelliaa abc--def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke +Driandra abc--def,match_03c,match_03c,Dryandra sp. [Driandra abc--def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Xyystidium abc--def,match_03d,match_03d,Xystidium sp. [Xyystidium abc--def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. +Zygiaa abc--def,match_03d,match_03d,Zygia sp. [Zygiaa abc--def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne +Abcde fgh -- ijk,match_03e,match_03e,NA,NA,genus,NA,TRUE,NA,NA,NA +Ryandra abc--def,match_03e,match_03e,NA,NA,genus,NA,TRUE,NA,NA,NA +Abildgaardia odontocarpa / Abildgaardia oxystachya,match_04a,match_04a,Abildgaardia sp. [Abildgaardia odontocarpa / Abildgaardia oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl +Acanthocarpus fimbriatus / Acanthocarpus mucronatus,match_04a,match_04a,Acanthocarpus sp. [Acanthocarpus fimbriatus / Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Acanthocarpus fimbriatus / mucronatus,match_04a,match_04a,Acanthocarpus sp. [Acanthocarpus fimbriatus / mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Banksia serrata / Banksia ericifolia,match_04a,match_04a,Banksia sp. [Banksia serrata / Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Banksia serrata / ericifolia,match_04a,match_04a,Banksia sp. [Banksia serrata / ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Banksia serrata/Banksia ericifolia,match_04a,match_04a,Banksia sp. [Banksia serrata/Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Aporuellia abc / def,match_04a,match_04a,Aporuellia sp. [Aporuellia abc / def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke +Dryandra abc / def,match_04a,match_04a,Dryandra sp. [Dryandra abc / def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Xystidium abc/def,match_04a,match_04a,Xystidium sp. [Xystidium abc/def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. +Zygia abc/def,match_04a,match_04a,Zygia sp. [Zygia abc/def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne +Abildgardiia odontocarpa / oxystachya,match_04b,match_04b,Abildgaardia sp. [Abildgardiia odontocarpa / oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl +Accanthocarpis fimbriatus / Acanthocarpus mucronatus,match_04b,match_04b,Acanthocarpus sp. [Accanthocarpis fimbriatus / Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Bankseea serrata / ericifolia,match_04b,match_04b,Banksia sp. [Bankseea serrata / ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Bannksia serrata / Banksia ericifolia,match_04b,match_04b,Banksia sp. [Bannksia serrata / Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Aporuelliaa abc / def,match_04c,match_04c,Aporuellia sp. [Aporuelliaa abc / def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke +Drrandra abc / def,match_04c,match_04c,Dryandra sp. [Drrandra abc / def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Xyystidium abc/def,match_04d,match_04d,Xystidium sp. [Xyystidium abc/def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. +Zygiaa abc / def,match_04d,match_04d,Zygia sp. [Zygiaa abc / def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne +Abcde fgh / ijk,match_04e,match_04e,NA,NA,genus,NA,TRUE,NA,NA,NA +Ryandra abc / def,match_04e,match_04e,NA,NA,genus,NA,TRUE,NA,NA,NA +Cycas candida K.D.Hill,match_05a,match_01a,Cycas candida,APC,species,Cycas candida,TRUE,https://id.biodiversity.org.au/node/apni/2893335,https://id.biodiversity.org.au/name/apni/188177,Cycas candida K.D.Hill +Eremophila papillata Chinnock,match_05a,match_01a,Eremophila papillata,APC,species,Eremophila papillata,TRUE,https://id.biodiversity.org.au/node/apni/2910890,https://id.biodiversity.org.au/name/apni/207453,Eremophila papillata Chinnock +Acalypha indica var. australis F.M.Bailey,match_05b,match_01b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey +Acanthocarpus serra F.Muell.,match_05b,match_01b,Acanthocarpus serra,APC,species,Chamaexeros serra,TRUE,https://id.biodiversity.org.au/instance/apni/851959,https://id.biodiversity.org.au/name/apni/203327,Acanthocarpus serra F.Muell. +Dillwynia sp. C (Budawang Range),match_05b,match_01b,Dillwynia sp. C (Budawang Range),APC,species,Dillwynia crispii,TRUE,https://id.biodiversity.org.au/instance/apni/933273,https://id.biodiversity.org.au/name/apni/137780,Dillwynia sp. C (Budawang Range) +Acaena x ovina,match_06a,match_01c,Acaena x ovina,APC,species,Acaena x ovina,FALSE,https://id.biodiversity.org.au/taxon/apni/51446291,https://id.biodiversity.org.au/name/apni/72209,Acaena x ovina A.Cunn. +Acanthocarpus sp. Cooloomia (S.D.Hopper 3301),match_06a,match_01c,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301),APC,species,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301),TRUE,https://id.biodiversity.org.au/node/apni/2903920,https://id.biodiversity.org.au/name/apni/203323,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301) WA Herbarium +Banksia serrata,match_06a,match_01c,Banksia serrata,APC,species,Banksia serrata,TRUE,https://id.biodiversity.org.au/taxon/apni/51293610,https://id.biodiversity.org.au/name/apni/109014,Banksia serrata L.f. +Eremophila oppositifolia ssp. rubra,match_06a,match_01c,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock +Eremophila oppositifolia subsp. rubra,match_06a,match_01c,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock +Leucanthemum x superbum,match_06a,match_01c,Leucanthemum x superbum,APC,species,Leucanthemum x superbum,TRUE,https://id.biodiversity.org.au/node/apni/2912531,https://id.biodiversity.org.au/name/apni/172142,Leucanthemum x superbum (Bergmans ex J.W.Ingram) D.H.Kent +Notelaea longifolia,match_06a,match_01c,Notelaea longifolia,APC,species,Notelaea longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2919068,https://id.biodiversity.org.au/name/apni/95265,Notelaea longifolia Vent. +Notelaea longifolia f longifolia,match_06a,match_01c,Notelaea longifolia f. longifolia,APC,form,Notelaea longifolia f. longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2915469,https://id.biodiversity.org.au/name/apni/95381,Notelaea longifolia Vent. f. longifolia +Notelaea longifolia f. intermedia,match_06a,match_01c,Notelaea longifolia f. intermedia,APC,form,Notelaea longifolia f. intermedia,TRUE,https://id.biodiversity.org.au/node/apni/2914551,https://id.biodiversity.org.au/name/apni/95355,Notelaea longifolia f. intermedia P.S.Green +Notelaea longifolia f. longifolia,match_06a,match_01c,Notelaea longifolia f. longifolia,APC,form,Notelaea longifolia f. longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2915469,https://id.biodiversity.org.au/name/apni/95381,Notelaea longifolia Vent. f. longifolia +Notelaea longifolia form. longifolia,match_06a,match_01c,Notelaea longifolia f. longifolia,APC,form,Notelaea longifolia f. longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2915469,https://id.biodiversity.org.au/name/apni/95381,Notelaea longifolia Vent. f. longifolia +Notelaea longifolia forma longifolia,match_06a,match_01c,Notelaea longifolia f. longifolia,APC,form,Notelaea longifolia f. longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2915469,https://id.biodiversity.org.au/name/apni/95381,Notelaea longifolia Vent. f. longifolia +Onopordum acanthium x Onopordum illyricum,match_06a,match_01c,Onopordum acanthium x Onopordum illyricum,APC,species,Onopordum acanthium x Onopordum illyricum,TRUE,https://id.biodiversity.org.au/node/apni/7017361,https://id.biodiversity.org.au/name/apni/164808,Onopordum acanthium L. x Onopordum illyricum L. +Ranunculus pentandrus,match_06a,match_01c,Ranunculus pentandrus,APC,species,Ranunculus pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2887738,https://id.biodiversity.org.au/name/apni/113007,Ranunculus pentandrus J.M.Black +Ranunculus pentandrus v pentandrus,match_06a,match_01c,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus +Ranunculus pentandrus var pentandrus,match_06a,match_01c,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus +Ranunculus pentandrus var. pentandrus,match_06a,match_01c,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus +Thynninorchis huntiana,match_06a,match_01c,Thynninorchis huntiana,APC,species,Thynninorchis huntiana,TRUE,https://id.biodiversity.org.au/taxon/apni/51414495,https://id.biodiversity.org.au/name/apni/178809,Thynninorchis huntiana (F.Muell.) D.L.Jones & M.A.Clem. +Acalypha indica var. australis,match_06b,match_01d,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey +Aceratium megalospermum var. coriaceum,match_06b,match_01d,Aceratium megalospermum var. coriaceum,APC,variety,Aceratium megalospermum,TRUE,https://id.biodiversity.org.au/instance/apni/896479,https://id.biodiversity.org.au/name/apni/72795,Aceratium megalospermum var. coriaceum Balgooy +Achneria brevifolia,match_06b,match_01d,Achneria brevifolia,APC,species,Eriachne brevifolia,TRUE,https://id.biodiversity.org.au/instance/apni/51443025,https://id.biodiversity.org.au/name/apni/72928,Achneria brevifolia (R.Br.) P.Beauv. +Dillwynia sp. C ( Budawang Range ),match_06b,match_01d,Dillwynia sp. C (Budawang Range),APC,species,Dillwynia crispii,TRUE,https://id.biodiversity.org.au/instance/apni/933273,https://id.biodiversity.org.au/name/apni/137780,Dillwynia sp. C (Budawang Range) +Aceeena x ovinaa,match_07a,match_05a,Acaena x ovina,APC,species,Acaena x ovina,FALSE,https://id.biodiversity.org.au/taxon/apni/51446291,https://id.biodiversity.org.au/name/apni/72209,Acaena x ovina A.Cunn. +Aceena x ovina,match_07a,match_05a,Acaena x ovina,APC,species,Acaena x ovina,FALSE,https://id.biodiversity.org.au/taxon/apni/51446291,https://id.biodiversity.org.au/name/apni/72209,Acaena x ovina A.Cunn. +Banksia serrate,match_07a,match_05a,Banksia serrata,APC,species,Banksia serrata,TRUE,https://id.biodiversity.org.au/taxon/apni/51293610,https://id.biodiversity.org.au/name/apni/109014,Banksia serrata L.f. +Eremophila opositifolia ssp. rubra,match_07a,match_05a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock +Eremophila opositifoliia subsp. rubra,match_07a,match_05a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock +Hemigenia sp. Tallering (H. Pringle 3323),match_07a,match_05a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium +Hemigenia sp. Tallering (H.Pringle 33223),match_07a,match_05a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium +Hemigeniia sp. Tallering (H.Pringle 3323),match_07a,match_05a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium +Notelaea longifoliaa forma longifoliaa,match_07a,match_05a,Notelaea longifolia f. longifolia,APC,form,Notelaea longifolia f. longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2915469,https://id.biodiversity.org.au/name/apni/95381,Notelaea longifolia Vent. f. longifolia +Onopordum acanthium x Onnopordum illyricum,match_07a,match_05a,Onopordum acanthium x Onopordum illyricum,APC,species,Onopordum acanthium x Onopordum illyricum,TRUE,https://id.biodiversity.org.au/node/apni/7017361,https://id.biodiversity.org.au/name/apni/164808,Onopordum acanthium L. x Onopordum illyricum L. +Ranunculus pentandra var pentandru,match_07a,match_05a,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus +Thynninorchis huntianaa,match_07a,match_05a,Thynninorchis huntiana,APC,species,Thynninorchis huntiana,TRUE,https://id.biodiversity.org.au/taxon/apni/51414495,https://id.biodiversity.org.au/name/apni/178809,Thynninorchis huntiana (F.Muell.) D.L.Jones & M.A.Clem. +Acalyffa indice australis,match_07b,match_05b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey +Acalypha indica australis,match_07b,match_05b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey +Acalypha indice australis,match_07b,match_05b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey +Acalypha inndica var. australis,match_07b,match_05b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey +Achneriia brevifoliaa,match_07b,match_05b,Achneria brevifolia,APC,species,Eriachne brevifolia,TRUE,https://id.biodiversity.org.au/instance/apni/51443025,https://id.biodiversity.org.au/name/apni/72928,Achneria brevifolia (R.Br.) P.Beauv. +Dillwinnia sp. C ( Budawang Range ),match_07b,match_05b,Dillwynia sp. C (Budawang Range),APC,species,Dillwynia crispii,TRUE,https://id.biodiversity.org.au/instance/apni/933273,https://id.biodiversity.org.au/name/apni/137780,Dillwynia sp. C (Budawang Range) +Acanthus ebracteatus subsp. ebracteatus,match_08a,match_05c,Acanthus ebracteatus subsp. ebracteatus,APNI,subspecies,Acanthus ebracteatus subsp. ebracteatus,TRUE,NA,https://id.biodiversity.org.au/name/apni/72713,Acanthus ebracteatus Vahl subsp. ebracteatus +Acanthus ilicifolius var. typica,match_08a,match_05c,Acanthus ilicifolius var. typica,APNI,variety,Acanthus ilicifolius var. typica,TRUE,NA,https://id.biodiversity.org.au/name/apni/72730,Acanthus ilicifolius var. typica Domin +Asystasia sp. (Newcastle Bay),match_08a,match_05c,Asystasia sp. (Newcastle Bay),APNI,species,Asystasia sp. (Newcastle Bay),TRUE,NA,https://id.biodiversity.org.au/name/apni/3493285,Asystasia sp. (Newcastle Bay) +Blechum pyramidatum,match_08a,match_05c,Blechum pyramidatum,APNI,species,Blechum pyramidatum,TRUE,NA,https://id.biodiversity.org.au/name/apni/189742,Blechum pyramidatum (Lam.) Urb. +Daviesia sp. ( Wadbilliga NP - Deua NP ),match_08a,match_05c,Daviesia sp. (Wadbilliga NP - Deua NP),APNI,species,Daviesia sp. (Wadbilliga NP - Deua NP),TRUE,NA,https://id.biodiversity.org.au/name/apni/51681812,Daviesia sp. (Wadbilliga NP - Deua NP) +Dillwynia sp. ( Gibralter Range ),match_08a,match_05c,Dillwynia sp. (Gibralter Range),APNI,species,Dillwynia sp. (Gibralter Range),TRUE,NA,https://id.biodiversity.org.au/name/apni/51681862,Dillwynia sp. (Gibralter Range) +Dillwynia sp. (Gibralter Range),match_08a,match_05c,Dillwynia sp. (Gibralter Range),APNI,species,Dillwynia sp. (Gibralter Range),TRUE,NA,https://id.biodiversity.org.au/name/apni/51681862,Dillwynia sp. (Gibralter Range) +Jasminum sp (Beechmont G.Holmes AQ633577),match_08a,match_05c,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) +Thunbergia alata var. arnhemica,match_08a,match_05c,Thunbergia alata var. arnhemica,APNI,variety,Thunbergia alata var. arnhemica,TRUE,NA,https://id.biodiversity.org.au/name/apni/89722,Thunbergia alata var. arnhemica (F.Muell.) Domin +Abildgaardia aff odontocarpa,match_09a,match_06a,Abildgaardia sp. [Abildgaardia aff. odontocarpa; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl +Acanthocarpus aff. fimbriatus,match_09a,match_06a,Acanthocarpus sp. [Acanthocarpus aff. fimbriatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Acanthocarpus affinis fimbriatus,match_09a,match_06a,Acanthocarpus sp. [Acanthocarpus aff. fimbriatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Banksia aff serrata,match_09a,match_06a,Banksia sp. [Banksia aff. serrata; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Banksia aff. serrata,match_09a,match_06a,Banksia sp. [Banksia aff. serrata; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Banksia affinis serrata,match_09a,match_06a,Banksia sp. [Banksia aff. serrata; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Aporuellia aff abc,match_09a,match_06a,Aporuellia sp. [Aporuellia aff. abc; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke +Dryandra aff def,match_09a,match_06a,Dryandra sp. [Dryandra aff. def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Xystidium aff. def,match_09a,match_06a,Xystidium sp. [Xystidium aff. def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. +Zygia affinis def,match_09a,match_06a,Zygia sp. [Zygia aff. def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne +Abildgardiia aff odontocarpa,match_09b,match_06b,Abildgaardia sp. [Abildgardiia aff. odontocarpa; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl +Accanthocarpis aff fimbriatus,match_09b,match_06b,Acanthocarpus sp. [Accanthocarpis aff. fimbriatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Bankseea aff. serrata,match_09b,match_06b,Banksia sp. [Bankseea aff. serrata; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Bannksia affinis serrata,match_09b,match_06b,Banksia sp. [Bannksia aff. serrata; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Aporuelliaa aff def,match_09c,match_06c,Aporuellia sp. [Aporuelliaa aff. def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke +Drrandra affinis def,match_09c,match_06c,Dryandra sp. [Drrandra aff. def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Xyystidium aff. abc,match_09d,match_06d,Xystidium sp. [Xyystidium aff. abc; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. +Zygiaa aff. abc,match_09d,match_06d,Zygia sp. [Zygiaa aff. abc; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne +Abcde affinis fgh,match_09e,match_06e,NA,NA,genus,NA,TRUE,NA,NA,NA +Rryandra aff def,match_09e,match_06e,NA,NA,genus,NA,TRUE,NA,NA,NA +Aceeena x ovinaaa,match_10a,match_07a,Acaena x ovina,APC,species,Acaena x ovina,FALSE,https://id.biodiversity.org.au/taxon/apni/51446291,https://id.biodiversity.org.au/name/apni/72209,Acaena x ovina A.Cunn. +Banksiia serrratte,match_10a,match_07a,Banksia serrata,APC,species,Banksia serrata,TRUE,https://id.biodiversity.org.au/taxon/apni/51293610,https://id.biodiversity.org.au/name/apni/109014,Banksia serrata L.f. +Eremoophila opppositifolia ssp. rubraaa,match_10a,match_07a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock +Eremophillaa oppositifoliia subsp. rrubra,match_10a,match_07a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock +Hemigenia sp. Tallering (H.Pringle),match_10a,match_07a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium +Thynninorchisss huntianaaaa,match_10a,match_07a,Thynninorchis huntiana,APC,species,Thynninorchis huntiana,TRUE,https://id.biodiversity.org.au/taxon/apni/51414495,https://id.biodiversity.org.au/name/apni/178809,Thynninorchis huntiana (F.Muell.) D.L.Jones & M.A.Clem. +Acalyffa indice australiss,match_10b,match_07b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey +Accalypha inndicaa var. australiss,match_10b,match_07b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey +Aceratiumm meggalospermumm var. coriaceumm,match_10b,match_07b,Aceratium megalospermum var. coriaceum,APC,variety,Aceratium megalospermum,TRUE,https://id.biodiversity.org.au/instance/apni/896479,https://id.biodiversity.org.au/name/apni/72795,Aceratium megalospermum var. coriaceum Balgooy +Abildgaardia odontocarpa x Abildgaardia oxystachya,match_11a,match_08a,Abildgaardia x [Abildgaardia odontocarpa x Abildgaardia oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl +Acanthocarpus fimbriatus x Acanthocarpus mucronatus,match_11a,match_08a,Acanthocarpus x [Acanthocarpus fimbriatus x Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Acanthocarpus fimbriatus x mucronatus,match_11a,match_08a,Acanthocarpus x [Acanthocarpus fimbriatus x mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Banksia serrata x Banksia ericifolia,match_11a,match_08a,Banksia x [Banksia serrata x Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Banksia serrata x ericifolia,match_11a,match_08a,Banksia x [Banksia serrata x ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Thynninorchis x huntiana,match_11a,match_08a,Thynninorchis x [Thynninorchis x huntiana; test_all_matches_TRUE],APC,genus,Thynninorchis,FALSE,https://id.biodiversity.org.au/taxon/apni/51414493,https://id.biodiversity.org.au/name/apni/178808,Thynninorchis D.L.Jones & M.A.Clem. +Aporuellia abc x def,match_11a,match_08a,Aporuellia x [Aporuellia abc x def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke +Dryandra abc x def,match_11a,match_08a,Dryandra x [Dryandra abc x def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Xystidium abc x Xystidium def,match_11a,match_08a,Xystidium x [Xystidium abc x Xystidium def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. +Zygia abc x def,match_11a,match_08a,Zygia x [Zygia abc x def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne +Abildgardiia odontocarpa x oxystachya,match_11b,match_08b,Abildgaardia x [Abildgardiia odontocarpa x oxystachya; test_all_matches_TRUE],APC,genus,Abildgaardia,FALSE,https://id.biodiversity.org.au/node/apni/2905759,https://id.biodiversity.org.au/name/apni/55984,Abildgaardia Vahl +Accanthocarpis fimbriatus x Acanthocarpus mucronatus,match_11b,match_08b,Acanthocarpus x [Accanthocarpis fimbriatus x Acanthocarpus mucronatus; test_all_matches_TRUE],APC,genus,Acanthocarpus,FALSE,https://id.biodiversity.org.au/node/apni/2899190,https://id.biodiversity.org.au/name/apni/72610,Acanthocarpus Lehm. +Bankseea serrata x ericifolia,match_11b,match_08b,Banksia x [Bankseea serrata x ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Bannksia serrata x Banksia ericifolia,match_11b,match_08b,Banksia x [Bannksia serrata x Banksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Aporuelliaa abc x def,match_11c,match_08c,Aporuellia x [Aporuelliaa abc x def; test_all_matches_TRUE],APC,genus,Brunoniella,FALSE,https://id.biodiversity.org.au/instance/apni/903944,https://id.biodiversity.org.au/name/apni/97735,Aporuellia C.B.Clarke +Drrandra x def,match_11c,match_08c,Dryandra x [Drrandra x def; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Xyystidium x def,match_11d,match_08d,Xystidium x [Xyystidium x def; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. +Zygiaa abc x Zygia def,match_11d,match_08d,Zygia x [Zygiaa abc x Zygia def; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne +Abcde fgh x ijk,match_11e,match_08e,NA,NA,genus,NA,TRUE,NA,NA,NA +Ryandra abc x def,match_11e,match_08e,NA,NA,genus,NA,TRUE,NA,NA,NA +Baeckea sp. murchison river,match_12a,match_09a,Baeckea sp. Murchison River (M.E.Trudgen 12009),APC,species,Baeckea sp. Murchison River (M.E.Trudgen 12009),TRUE,https://id.biodiversity.org.au/node/apni/2888052,https://id.biodiversity.org.au/name/apni/191267,Baeckea sp. Murchison River (M.E.Trudgen 12009) WA Herbarium +Eremophila oppositifolia rubra (needle leaves),match_12a,match_09a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock +Eremophila oppositifolia rubra early collection,match_12a,match_09a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock +Eremophila oppositifolia ssp. rubra needle leaves,match_12a,match_09a,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock +Ranunculus pentandrus var. pentandrus (flooded area),match_12a,match_09a,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus +Acalypha indica var. australis (double check),match_12b,match_09b,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey +Aceratium megalospermum var. coriaceum (top of hill),match_12b,match_09b,Aceratium megalospermum var. coriaceum,APC,variety,Aceratium megalospermum,TRUE,https://id.biodiversity.org.au/instance/apni/896479,https://id.biodiversity.org.au/name/apni/72795,Aceratium megalospermum var. coriaceum Balgooy +Eremophila opositifolia rubra early collection,match_13a,match_09c,Eremophila oppositifolia subsp. rubra,APC,subspecies,Eremophila oppositifolia subsp. rubra,TRUE,https://id.biodiversity.org.au/node/apni/7951458,https://id.biodiversity.org.au/name/apni/117903,Eremophila oppositifolia subsp. rubra (C.T.White & W.D.Francis) Chinnock +Ranunculus pentandrus var. pentand (flooded area),match_13a,match_09c,Ranunculus pentandrus var. pentandrus,APC,variety,Ranunculus pentandrus var. pentandrus,TRUE,https://id.biodiversity.org.au/node/apni/2904152,https://id.biodiversity.org.au/name/apni/113072,Ranunculus pentandrus J.M.Black var. pentandrus +Acalypha indica var. austral. (double check),match_13b,match_09d,Acalypha indica var. australis,APC,variety,Acalypha lanceolata,TRUE,https://id.biodiversity.org.au/instance/apni/889946,https://id.biodiversity.org.au/name/apni/72588,Acalypha indica var. australis F.M.Bailey +Aceratiuum megalospermum var. coriaceuum (top of hill),match_13b,match_09d,Aceratium megalospermum var. coriaceum,APC,variety,Aceratium megalospermum,TRUE,https://id.biodiversity.org.au/instance/apni/896479,https://id.biodiversity.org.au/name/apni/72795,Aceratium megalospermum var. coriaceum Balgooy +Acalypha indica var. aus,match_10a,match_07a,Acalypha indica,APC,species,Acalypha indica,TRUE,https://id.biodiversity.org.au/node/apni/2908627,https://id.biodiversity.org.au/name/apni/72584,Acalypha indica L. +Acanthocarpus sp. cooloomia,match_14a,match_10a,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301),APC,species,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301),TRUE,https://id.biodiversity.org.au/node/apni/2903920,https://id.biodiversity.org.au/name/apni/203323,Acanthocarpus sp. Cooloomia (S.D.Hopper 3301) WA Herbarium +Acanthus ebracteatus subsp. ebracteatussss,match_14a,match_10a,Acanthus ebracteatus,APC,species,Acanthus ebracteatus,TRUE,https://id.biodiversity.org.au/node/apni/2906336,https://id.biodiversity.org.au/name/apni/72706,Acanthus ebracteatus Vahl +Aceratium megalospermum var. might be coriaceum,match_14a,match_10a,Aceratium megalospermum,APC,species,Aceratium megalospermum,TRUE,https://id.biodiversity.org.au/node/apni/2915767,https://id.biodiversity.org.au/name/apni/72789,Aceratium megalospermum (F.Muell.) Balgooy +Banksia paludosa (key to subspecies),match_14a,match_10a,Banksia paludosa,APC,species,Banksia paludosa,TRUE,https://id.biodiversity.org.au/node/apni/2891165,https://id.biodiversity.org.au/name/apni/108449,Banksia paludosa R.Br. +Banksia plagiocarpa (giant plants),match_14a,match_10a,Banksia plagiocarpa,APC,species,Banksia plagiocarpa,TRUE,https://id.biodiversity.org.au/node/apni/2900302,https://id.biodiversity.org.au/name/apni/108639,Banksia plagiocarpa A.S.George +Hemigenia sp. Tallering (H. Pringle),match_14a,match_10a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium +Hemigenia sp. Tallering Pringle,match_14a,match_10a,Hemigenia sp. Tallering (H.Pringle 3323),APC,species,Hemigenia sp. Tallering (H.Pringle 3323),TRUE,https://id.biodiversity.org.au/node/apni/2909722,https://id.biodiversity.org.au/name/apni/231235,Hemigenia sp. Tallering (H.Pringle 3323) WA Herbarium +Leucopogon sp. murchison,match_14a,match_10a,Leucopogon sp. Murchison (R.J.Cranfield 9224),APC,species,Leucopogon sp. Murchison (R.J.Cranfield 9224),TRUE,https://id.biodiversity.org.au/node/apni/2886129,https://id.biodiversity.org.au/name/apni/239999,Leucopogon sp. Murchison (R.J.Cranfield 9224) WA Herbarium +Notelaea longifolia f. iongifolia,match_14a,match_10a,Notelaea longifolia,APC,species,Notelaea longifolia,TRUE,https://id.biodiversity.org.au/node/apni/2919068,https://id.biodiversity.org.au/name/apni/95265,Notelaea longifolia Vent. +Schoenus sp. murchison,match_14a,match_10a,Schoenus sp. Murchison (K.L.Wilson 2647),APC,species,Schoenus sp. Murchison (K.L.Wilson 2647),TRUE,https://id.biodiversity.org.au/node/apni/2915697,https://id.biodiversity.org.au/name/apni/243799,Schoenus sp. Murchison (K.L.Wilson 2647) WA Herbarium +Senna sp. austin,match_14a,match_10a,Senna sp. Austin (A.Strid 20210),APC,species,Senna sp. Austin (A.Strid 20210),TRUE,https://id.biodiversity.org.au/node/apni/2891919,https://id.biodiversity.org.au/name/apni/198508,Senna sp. Austin (A.Strid 20210) WA Herbarium +Thunbergia alata (probably var. arnhemica),match_14a,match_10a,Thunbergia alata,APC,species,Thunbergia alata,TRUE,https://id.biodiversity.org.au/node/apni/2896895,https://id.biodiversity.org.au/name/apni/89707,Thunbergia alata Bojer ex Sims +Thunbergia alata var. arnhemica (uncertain),match_14a,match_10a,Thunbergia alata,APC,species,Thunbergia alata,TRUE,https://id.biodiversity.org.au/node/apni/2896895,https://id.biodiversity.org.au/name/apni/89707,Thunbergia alata Bojer ex Sims +Achneria brevifolia (collected in May),match_14b,match_10b,Achneria brevifolia,APC,species,Eriachne brevifolia,TRUE,https://id.biodiversity.org.au/instance/apni/51443025,https://id.biodiversity.org.au/name/apni/72928,Achneria brevifolia (R.Br.) P.Beauv. +Dryandra octotriginta (update name),match_14b,match_10b,Dryandra octotriginta,APC,species,Banksia octotriginta,TRUE,https://id.biodiversity.org.au/instance/apni/955349,https://id.biodiversity.org.au/name/apni/138097,Dryandra octotriginta A.S.George +Acanthus illlicifoliuss var. typicaa,match_15a,match_10c,Acanthus ilicifolius,APC,species,Acanthus ilicifolius,TRUE,https://id.biodiversity.org.au/node/apni/2913784,https://id.biodiversity.org.au/name/apni/72714,Acanthus ilicifolius L. +Banksia paludose (key to subspecies),match_15a,match_10c,Banksia paludosa,APC,species,Banksia paludosa,TRUE,https://id.biodiversity.org.au/node/apni/2891165,https://id.biodiversity.org.au/name/apni/108449,Banksia paludosa R.Br. +Bannksia plagiocarpa (giant plants),match_15a,match_10c,Banksia plagiocarpa,APC,species,Banksia plagiocarpa,TRUE,https://id.biodiversity.org.au/node/apni/2900302,https://id.biodiversity.org.au/name/apni/108639,Banksia plagiocarpa A.S.George +Achneriia brevifoliia (collected in May),match_15b,match_10d,Achneria brevifolia,APC,species,Eriachne brevifolia,TRUE,https://id.biodiversity.org.au/instance/apni/51443025,https://id.biodiversity.org.au/name/apni/72928,Achneria brevifolia (R.Br.) P.Beauv. +Dryandra octotrigginta (update name),match_15b,match_10d,Dryandra octotriginta,APC,species,Banksia octotriginta,TRUE,https://id.biodiversity.org.au/instance/apni/955349,https://id.biodiversity.org.au/name/apni/138097,Dryandra octotriginta A.S.George +Blechumm pyramidatum,match_16a,match_11a,Blechum pyramidatum,APNI,species,Blechum pyramidatum,TRUE,NA,https://id.biodiversity.org.au/name/apni/189742,Blechum pyramidatum (Lam.) Urb. +Jasminum sp (Beechmont G. Holmes AQ633577),match_16a,match_11a,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) +Jasminum sp (Beechmont G.Holms AQ633577),match_16a,match_11a,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) +Jasminum sp (Beechmontte G.Holmes AQ633577),match_16a,match_11a,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) +Blechummm pyramidatummm,match_17a,match_11b,Blechum pyramidatum,APNI,species,Blechum pyramidatum,TRUE,NA,https://id.biodiversity.org.au/name/apni/189742,Blechum pyramidatum (Lam.) Urb. +Jasminummm sp (Beeechmontte G.Holmes AQ633577),match_17a,match_11b,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) +Dillwynia sp. (Gibralter Range) (phrase name),match_18a,match_11c,Dillwynia sp. (Gibralter Range),APNI,species,Dillwynia sp. (Gibralter Range),TRUE,NA,https://id.biodiversity.org.au/name/apni/51681862,Dillwynia sp. (Gibralter Range) +Jasminum sp (Beechmont G.Holmes),match_18a,match_11c,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) +Dillwynia sp. (Gibralter) (phrase name),match_19a,match_11d,Dillwynia sp. (Gibralter Range),APNI,species,Dillwynia sp. (Gibralter Range),TRUE,NA,https://id.biodiversity.org.au/name/apni/51681862,Dillwynia sp. (Gibralter Range) +Jasminum sp (Beechmont),match_19a,match_11d,Jasminum sp. (Beechmont G.Holmes AQ633577),APNI,species,Jasminum sp. (Beechmont G.Holmes AQ633577),TRUE,NA,https://id.biodiversity.org.au/name/apni/51367466,Jasminum sp. (Beechmont G.Holmes AQ633577) +Actinotus,match_20a,match_12a,Actinotus sp. [Actinotus; test_all_matches_TRUE],APC,genus,Actinotus,FALSE,https://id.biodiversity.org.au/node/apni/6903559,https://id.biodiversity.org.au/name/apni/75003,Actinotus Labill. +Asystasia,match_20a,match_12a,Asystasia sp. [Asystasia; test_all_matches_TRUE],APC,genus,Asystasia,FALSE,https://id.biodiversity.org.au/taxon/apni/51430302,https://id.biodiversity.org.au/name/apni/109497,Asystasia Blume +Asystasia - pink flower,match_20a,match_12a,Asystasia sp. [Asystasia - pink flower; test_all_matches_TRUE],APC,genus,Asystasia,FALSE,https://id.biodiversity.org.au/taxon/apni/51430302,https://id.biodiversity.org.au/name/apni/109497,Asystasia Blume +Asystasia (voucher),match_20a,match_12a,Asystasia sp. [Asystasia (voucher); test_all_matches_TRUE],APC,genus,Asystasia,FALSE,https://id.biodiversity.org.au/taxon/apni/51430302,https://id.biodiversity.org.au/name/apni/109497,Asystasia Blume +Banksia serrataxBanksia ericifolia,match_20a,match_12a,Banksia sp. [Banksia serrataxBanksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Barleria maybe alba,match_20a,match_12a,Barleria sp. [Barleria maybe alba; test_all_matches_TRUE],APC,genus,Barleria,FALSE,https://id.biodiversity.org.au/node/apni/2894241,https://id.biodiversity.org.au/name/apni/109526,Barleria L. +Dillwynia sp. 3 ( Budawang Range ),match_20a,match_12a,Dillwynia sp. [Dillwynia sp. 3 (Budawang Range); test_all_matches_TRUE],APC,genus,Dillwynia,FALSE,https://id.biodiversity.org.au/taxon/apni/51285570,https://id.biodiversity.org.au/name/apni/105354,Dillwynia Sm. +Actinocarpus,match_20b,match_12b,Actinocarpus sp. [Actinocarpus; test_all_matches_TRUE],APC,genus,Damasonium,FALSE,https://id.biodiversity.org.au/instance/apni/884226,https://id.biodiversity.org.au/name/apni/74816,Actinocarpus R.Br. +Dilwynia sp. 3 ( Budawang Range ),match_20b,match_12b,Dilwynia sp. [Dilwynia sp. 3 (Budawang Range); test_all_matches_TRUE],APC,genus,Dillwynia,FALSE,https://id.biodiversity.org.au/instance/apni/933270,https://id.biodiversity.org.au/name/apni/106624,Dilwynia Pers. +Dryandra,match_20b,match_12b,Dryandra sp. [Dryandra; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Actinocladum,match_20c,match_12c,Actinocladum sp. [Actinocladum; test_all_matches_TRUE],APNI,genus,Actinocladum,FALSE,NA,https://id.biodiversity.org.au/name/apni/181935,Actinocladum McClure ex Soderstr. +Xystidium is very interesting,match_20c,match_12c,Xystidium sp. [Xystidium is very interesting; test_all_matches_TRUE],APNI,genus,Xystidium,FALSE,NA,https://id.biodiversity.org.au/name/apni/244613,Xystidium Trin. +Zygia outlier genus,match_20c,match_12c,Zygia sp. [Zygia outlier genus; test_all_matches_TRUE],APNI,genus,Zygia,FALSE,NA,https://id.biodiversity.org.au/name/apni/65077,Zygia P.Browne +Poaceae (purple stems),match_21a,match_12d,Poaceae sp. [Poaceae (purple stems); test_all_matches_TRUE],APC,family,Poaceae,FALSE,https://id.biodiversity.org.au/taxon/apni/51644646,https://id.biodiversity.org.au/name/apni/54563,Poaceae Barnhart +Rutaceae (an unknown species),match_21a,match_12d,Rutaceae sp. [Rutaceae (an unknown species); test_all_matches_TRUE],APC,family,Rutaceae,FALSE,https://id.biodiversity.org.au/taxon/apni/51461748,https://id.biodiversity.org.au/name/apni/54479,Rutaceae Juss. +Assystasia - pink flower,match_22a,match_12e,Asystasia sp. [Assystasia - pink flower; test_all_matches_TRUE],APC,genus,Asystasia,FALSE,https://id.biodiversity.org.au/taxon/apni/51430302,https://id.biodiversity.org.au/name/apni/109497,Asystasia Blume +Baarleria maybe alba,match_22a,match_12e,Barleria sp. [Baarleria maybe alba; test_all_matches_TRUE],APC,genus,Barleria,FALSE,https://id.biodiversity.org.au/node/apni/2894241,https://id.biodiversity.org.au/name/apni/109526,Barleria L. +Bankssia serrataxBanksia ericifolia,match_22a,match_12e,Banksia sp. [Bankssia serrataxBanksia ericifolia; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/taxon/apni/51445230,https://id.biodiversity.org.au/name/apni/105919,Banksia L.f. +Achneriia crevifoliaa,match_22b,match_12f,Achneria sp. [Achneriia crevifoliaa; test_all_matches_TRUE],APC,genus,Eriachne,FALSE,https://id.biodiversity.org.au/instance/apni/876102,https://id.biodiversity.org.au/name/apni/72923,Achneria P.Beauv. +Actinocarpos,match_22b,match_12f,Actinocarpus sp. [Actinocarpos; test_all_matches_TRUE],APC,genus,Damasonium,FALSE,https://id.biodiversity.org.au/instance/apni/884226,https://id.biodiversity.org.au/name/apni/74816,Actinocarpus R.Br. +Drryandra,match_22b,match_12f,Dryandra sp. [Drryandra; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Dryandraa,match_22b,match_12f,Dryandra sp. [Dryandraa; test_all_matches_TRUE],APC,genus,Banksia,FALSE,https://id.biodiversity.org.au/instance/apni/865048,https://id.biodiversity.org.au/name/apni/77744,Dryandra R.Br. +Actiniladum sp.,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA +Ecalypha indica australis,NA,NA,NA,NA,NA,NA,TRUE,NA,NA,NA diff --git a/vignettes/articles/function_notes.Rmd b/vignettes/articles/function_notes.Rmd index 7c0c6003..a2f57ef5 100644 --- a/vignettes/articles/function_notes.Rmd +++ b/vignettes/articles/function_notes.Rmd @@ -94,7 +94,7 @@ APNI_matches = TRUE #include (TRUE) or exclude (FALSE) APNI identifier = NA_character #include a unique identifier as part of informal names ``` -**output**: A data frame with rows representing each taxon and with columns documenting the alignment made, the reason for this alignment, and a selection of taxon name mutations to which the original name was compared (*original_name, aligned_name, taxonomic_dataset, taxon_rank, aligned_reason, alignment_code, cleaned_name, stripped_name, stripped_name2, trinomial, binomial, genus, fuzzy_match_genus, fuzzy_match_genus_known, fuzzy_match_genus_APNI, fuzzy_match_cleaned_APC, fuzzy_match_cleaned_APC_known, fuzzy_match_cleaned_APC_imprecise, fuzzy_match_cleaned_APC_known_imprecise, fuzzy_match_binomial, fuzzy_match_binomial_APC_known, fuzzy_match_trinomial, fuzzy_match_trinomial_known, fuzzy_match_cleaned_APNI, fuzzy_match_cleaned_APNI_imprecise*). +**output**: A data frame with rows representing each taxon and with columns documenting the alignment made, the reason for this alignment, and a selection of taxon name mutations to which the original name was compared (*original_name, aligned_name, taxonomic_dataset, taxon_rank, aligned_reason, alignment_code, cleaned_name, stripped_name, stripped_name2, trinomial, binomial, genus, fuzzy_match_genus, fuzzy_match_genus_synonym, fuzzy_match_genus_APNI, fuzzy_match_cleaned_APC, fuzzy_match_cleaned_APC_synonym, fuzzy_match_cleaned_APC_imprecise, fuzzy_match_cleaned_APC_synonym_imprecise, fuzzy_match_binomial, fuzzy_match_binomial_APC_synonym, fuzzy_match_trinomial, fuzzy_match_trinomial_synonym, fuzzy_match_cleaned_APNI, fuzzy_match_cleaned_APNI_imprecise*). **example**: