diff --git a/404.html b/404.html index 0a103ae..aad230e 100644 --- a/404.html +++ b/404.html @@ -70,7 +70,7 @@

Page not found (404)

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/LICENSE-text.html b/LICENSE-text.html index f21cb58..d897a53 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -51,7 +51,7 @@

License

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/articles/APCalign.html b/articles/APCalign.html index 126ca48..36bb344 100644 --- a/articles/APCalign.html +++ b/articles/APCalign.html @@ -62,7 +62,7 @@

APCalign

- Source: vignettes/APCalign.Rmd + Source: vignettes/APCalign.Rmd
APCalign.Rmd
@@ -571,7 +571,7 @@

Taxonomic splits
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/articles/data-providers.html b/articles/data-providers.html index 9f8cc39..0aabd90 100644 --- a/articles/data-providers.html +++ b/articles/data-providers.html @@ -62,7 +62,7 @@

Data Providers

- Source: vignettes/articles/data-providers.Rmd + Source: vignettes/articles/data-providers.Rmd
data-providers.Rmd
@@ -119,7 +119,7 @@

Data standards and meta-data -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/articles/index.html b/articles/index.html index d42106f..02f3ffc 100644 --- a/articles/index.html +++ b/articles/index.html @@ -59,7 +59,7 @@

All vignettes

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/articles/reproducibility.html b/articles/reproducibility.html index 7b4309e..fad0105 100644 --- a/articles/reproducibility.html +++ b/articles/reproducibility.html @@ -62,7 +62,7 @@

How to be more reproducible with APCalign

- Source: vignettes/articles/reproducibility.Rmd + Source: vignettes/articles/reproducibility.Rmd
reproducibility.Rmd
@@ -118,7 +118,7 @@

Taxonomic Resources
 default_version()
-#> [1] "2024-07+31"
+#> [1] "2024-09-25"

Then copying and pasting the output into load_taxonomic_resources() directly. This way makes the version of taxonomic resources more explicit in your code.

@@ -180,7 +180,7 @@

Citing the R package -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/articles/updating-taxon-names.html b/articles/updating-taxon-names.html index 53f1809..e247c49 100644 --- a/articles/updating-taxon-names.html +++ b/articles/updating-taxon-names.html @@ -62,7 +62,7 @@

Methods for updating taxon names in APCalign

- Source: vignettes/updating-taxon-names.Rmd + Source: vignettes/updating-taxon-names.Rmd
updating-taxon-names.Rmd
@@ -1941,7 +1941,7 @@

Outputs of APCalign -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/authors.html b/authors.html index 533691d..0417983 100644 --- a/authors.html +++ b/authors.html @@ -65,7 +65,7 @@

Authors

Citation

-

Source: inst/CITATION

+

Source: inst/CITATION

Wenk E, Cornwell W, Fuchs A, Kar F, Monro A, Sauquet H, Stephens R, Falster D (2024). “APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census.” @@ -91,7 +91,7 @@

Citation

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/index.html b/index.html index 081495e..0009420 100644 --- a/index.html +++ b/index.html @@ -229,7 +229,7 @@

Dev status

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/news/index.html b/news/index.html index c5ace1d..d5ba885 100644 --- a/news/index.html +++ b/news/index.html @@ -36,7 +36,7 @@

Changelog

- Source: NEWS.md + Source: NEWS.md
@@ -92,7 +92,7 @@

APCalign 1.0.1
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/pkgdown.js b/pkgdown.js index 9757bf9..1a99c65 100644 --- a/pkgdown.js +++ b/pkgdown.js @@ -152,3 +152,11 @@ async function searchFuse(query, callback) { }); }); })(window.jQuery || window.$) + +document.addEventListener('keydown', function(event) { + // Check if the pressed key is '/' + if (event.key === '/') { + event.preventDefault(); // Prevent any default action associated with the '/' key + document.getElementById('search-input').focus(); // Set focus to the search input + } +}); diff --git a/pkgdown.yml b/pkgdown.yml index a17fabf..06b2b17 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,12 +1,12 @@ pandoc: 3.1.11 -pkgdown: 2.1.0 +pkgdown: 2.1.1 pkgdown_sha: ~ articles: APCalign: APCalign.html articles/data-providers: data-providers.html articles/reproducibility: reproducibility.html updating-taxon-names: updating-taxon-names.html -last_built: 2024-08-26T07:23Z +last_built: 2024-09-25T02:55Z urls: reference: https://traitecoevo.github.io/APCalign/reference article: https://traitecoevo.github.io/APCalign/articles diff --git a/reference/APCalign.html b/reference/APCalign.html index 11a0f0f..c66c09a 100644 --- a/reference/APCalign.html +++ b/reference/APCalign.html @@ -44,7 +44,7 @@

Standardising Taxonomic Names in Australian Plants

- Source: R/APCalign-package.R + Source: R/APCalign-package.R
APCalign.Rd
@@ -100,7 +100,7 @@

Author<
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/align_taxa.html b/reference/align_taxa.html index 6e05183..05dbd64 100644 --- a/reference/align_taxa.html +++ b/reference/align_taxa.html @@ -52,7 +52,7 @@

Align Australian plant scientific names to the APC or APNI

- Source: R/align_taxa.R + Source: R/align_taxa.R
align_taxa.Rd
@@ -322,7 +322,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/create_species_state_origin_matrix.html b/reference/create_species_state_origin_matrix.html index 08a277b..3200806 100644 --- a/reference/create_species_state_origin_matrix.html +++ b/reference/create_species_state_origin_matrix.html @@ -42,7 +42,7 @@

State level native and introduced origin status

- Source: R/create_species_state_origin_matrix.R + Source: R/create_species_state_origin_matrix.R
create_species_state_origin_matrix.Rd
@@ -88,7 +88,7 @@

Examples#> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done -#> # A tibble: 26,507 × 19 +#> # A tibble: 26,509 × 19 #> species WA NT Qld SA NSW Vic Tas ChI LHI CoI NI #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 Acanthus e… nati… nati… nati… not … not … not … not … not … not … not … not … @@ -101,7 +101,7 @@

Examples#> 8 Asystasia … not … not … not … not … not … not … not … natu… not … not … not … #> 9 Asystasia … not … not … nati… not … not … not … not … not … not … not … not … #> 10 Asystasia … not … not … not … not … not … not … not … natu… not … not … not … -#> # ℹ 26,497 more rows +#> # ℹ 26,499 more rows #> # ℹ 7 more variables: ACT <chr>, CSI <chr>, AR <chr>, MI <chr>, HI <chr>, #> # MDI <chr>, CaI <chr> @@ -118,7 +118,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/create_taxonomic_update_lookup.html b/reference/create_taxonomic_update_lookup.html index eb0167e..f1ffb7e 100644 --- a/reference/create_taxonomic_update_lookup.html +++ b/reference/create_taxonomic_update_lookup.html @@ -44,7 +44,7 @@

Create a table with the best-possible scientific name match for Australian plant names

- Source: R/create_taxonomic_update_lookup.R + Source: R/create_taxonomic_update_lookup.R
create_taxonomic_update_lookup.Rd
@@ -342,7 +342,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/default_version.html b/reference/default_version.html index c9744f1..3f79030 100644 --- a/reference/default_version.html +++ b/reference/default_version.html @@ -38,7 +38,7 @@

Get the default version for stable data

- Source: R/load_taxonomic_resources.R + Source: R/load_taxonomic_resources.R
default_version.Rd
@@ -60,7 +60,7 @@

Value

Examples

default_version()
-#> [1] "2024-07+31"
+#> [1] "2024-09-25"
@@ -73,7 +73,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/gbif_lite.html b/reference/gbif_lite.html index fb37c2f..8f376c2 100644 --- a/reference/gbif_lite.html +++ b/reference/gbif_lite.html @@ -36,7 +36,7 @@

GBIF Australian Plant Data

- Source: R/data.R + Source: R/data.R
gbif_lite.Rd
@@ -89,7 +89,7 @@

Source<
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/get_apc_genus_family_lookup.html b/reference/get_apc_genus_family_lookup.html index f54601e..4cb3c8a 100644 --- a/reference/get_apc_genus_family_lookup.html +++ b/reference/get_apc_genus_family_lookup.html @@ -38,7 +38,7 @@

Lookup Family by Genus from APC

- Source: R/state_diversity_counts.R + Source: R/state_diversity_counts.R
get_apc_genus_family_lookup.Rd
@@ -100,7 +100,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/index.html b/reference/index.html index 9974f33..12f6ce0 100644 --- a/reference/index.html +++ b/reference/index.html @@ -176,7 +176,7 @@

Data

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/load_taxonomic_resources.html b/reference/load_taxonomic_resources.html index aa3f3c7..5152356 100644 --- a/reference/load_taxonomic_resources.html +++ b/reference/load_taxonomic_resources.html @@ -40,7 +40,7 @@

Load taxonomic reference lists, APC & APNI

- Source: R/load_taxonomic_resources.R + Source: R/load_taxonomic_resources.R
load_taxonomic_resources.Rd
@@ -335,7 +335,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/native_anywhere_in_australia.html b/reference/native_anywhere_in_australia.html index d6b2d65..1fb56fb 100644 --- a/reference/native_anywhere_in_australia.html +++ b/reference/native_anywhere_in_australia.html @@ -38,7 +38,7 @@

Native anywhere in Australia

- Source: R/native_anywhere_in_australia.R + Source: R/native_anywhere_in_australia.R
native_anywhere_in_australia.Rd
@@ -115,7 +115,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/reexports.html b/reference/reexports.html index 8828b56..039308d 100644 --- a/reference/reexports.html +++ b/reference/reexports.html @@ -50,7 +50,7 @@

Objects exported from other packages

- Source: R/reexports.R + Source: R/reexports.R
reexports.Rd
@@ -73,7 +73,7 @@

Objects exported from other packages

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/standardise_names.html b/reference/standardise_names.html index c2948e1..f86649b 100644 --- a/reference/standardise_names.html +++ b/reference/standardise_names.html @@ -44,7 +44,7 @@

Standardise taxon names

- Source: R/standardise_names.R + Source: R/standardise_names.R
standardise_names.Rd
@@ -108,7 +108,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/standardise_taxon_rank.html b/reference/standardise_taxon_rank.html index e195304..7466b30 100644 --- a/reference/standardise_taxon_rank.html +++ b/reference/standardise_taxon_rank.html @@ -36,7 +36,7 @@

Standardise taxon ranks

- Source: R/standardise_names.R + Source: R/standardise_names.R
standardise_taxon_rank.Rd
@@ -82,7 +82,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/state_diversity_counts.html b/reference/state_diversity_counts.html index 677c24c..5298c45 100644 --- a/reference/state_diversity_counts.html +++ b/reference/state_diversity_counts.html @@ -40,7 +40,7 @@

State- and territory-level diversity

- Source: R/state_diversity_counts.R + Source: R/state_diversity_counts.R
state_diversity_counts.Rd
@@ -116,7 +116,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/strip_names.html b/reference/strip_names.html index 5cbc4e3..1535f60 100644 --- a/reference/strip_names.html +++ b/reference/strip_names.html @@ -38,7 +38,7 @@

Strip taxon names

- Source: R/strip_names.R + Source: R/strip_names.R
strip_names.Rd
@@ -93,7 +93,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/strip_names_extra.html b/reference/strip_names_extra.html index 4fcdd56..8eeeef2 100644 --- a/reference/strip_names_extra.html +++ b/reference/strip_names_extra.html @@ -38,7 +38,7 @@

Strip taxon names, extra

- Source: R/strip_names.R + Source: R/strip_names.R
strip_names_extra.Rd
@@ -96,7 +96,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/reference/update_taxonomy.html b/reference/update_taxonomy.html index ddb147e..9b88e67 100644 --- a/reference/update_taxonomy.html +++ b/reference/update_taxonomy.html @@ -40,7 +40,7 @@

Update to currently accepted APC name and add APC/APNI name metadata

- Source: R/update_taxonomy.R + Source: R/update_taxonomy.R
update_taxonomy.Rd
@@ -212,7 +212,7 @@

Examples -

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.1.1.

diff --git a/search.json b/search.json index f63d2c0..b021ca8 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"APCalign","text":"demonstrate use APCalign, use example dataset gbif_lite documented ?gbif_lite","code":"install.packages(\"remotes\") remotes::install_github(\"traitecoevo/APCalign\") library(APCalign) dim(gbif_lite) #> [1] 129 7 gbif_lite |> print(n = 6) #> # A tibble: 129 × 7 #> species infraspecificepithet taxonrank decimalLongitude decimalLatitude scientificname #> #> 1 Tetratheca… SPECIES 145. -37.4 Tetratheca ci… #> 2 Peganum ha… SPECIES 139. -33.3 Peganum harma… #> 3 Calotis mu… SPECIES 115. -24.3 Calotis multi… #> 4 Leptosperm… SPECIES 151. -34.0 Leptospermum … #> 5 Lepidosper… SPECIES 142. -37.3 Lepidosperma … #> 6 Enneapogon… SPECIES 129. -17.8 Enneapogon po… #> # ℹ 123 more rows #> # ℹ 1 more variable: verbatimscientificname "},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"retrieve-taxonomic-resources","dir":"Articles","previous_headings":"","what":"Retrieve taxonomic resources","title":"APCalign","text":"first step retrieve entire APC APNI name databases store locally taxonomic resources. achieve using load_taxonomic_resources(). resources compressed parquet files speed download local loading. two versions databases can retrieve stable_or_current_data argument. Calling: stable retrieve recent, archived version databases GitHub releases. set default option. current retrieve --date databases directly APC APNI website. Note databases reasonably large initial retrieval core data take minutes. taxonomic resources stored locally, subsequent retrievals take less time. Retrieving current resources always take longer since accessing latest information website uncompressed format. reproducible workflow, recommend specifying exact stable version want use.","code":"# Benchmarking the retrieval of `stable` or `current` resources stable_start_time <- Sys.time() stable_resources <- load_taxonomic_resources(stable_or_current_data = \"stable\") #> Loading resources......done stable_end_time <- Sys.time() current_start_time <- Sys.time() current_resources <- load_taxonomic_resources(stable_or_current_data = \"current\") #> Loading resources......done current_end_time <- Sys.time() # Compare times stable_end_time - stable_start_time #> Time difference of 16.48976 secs resources <- load_taxonomic_resources(stable_or_current_data = \"stable\", version = \"0.0.2.9000\") #> Loading resources......done"},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"align-and-update-plant-taxon-names","dir":"Articles","previous_headings":"","what":"Align and update plant taxon names","title":"APCalign","text":"Now can query taxonomic names taxonomic resources just retrieved using create_taxonomic_update_lookup(). --one function : Align taxonomic names APC APNI using matching algorithms Update names APC-accepted species infraspecific name whenever possible. Return suggested name names, defaulting accepted_name available, otherwise providing APNI name name genus-level alignment possible. like learn step, take look section Closer look name alignment updating ‘APCalign’ original_name taxon name used original data. aligned_name taxon name used link APC identify synonyms. accepted_name currently, accepted taxon name used Australian Plant Census. suggested_name best possible name option original_name.","code":"library(dplyr) updated_gbif_names <- gbif_lite |> pull(species) |> create_taxonomic_update_lookup(resources = resources) #> Checking alignments of 121 taxa #> -> 0 names already matched; 0 names checked but without a match; 121 taxa yet to be checked updated_gbif_names |> print(n = 6) #> # A tibble: 129 × 12 #> original_name aligned_name accepted_name suggested_name genus taxon_rank taxonomic_dataset #> #> 1 Tetratheca c… Tetratheca … Tetratheca c… Tetratheca ci… Tetr… species APC #> 2 Peganum harm… Peganum har… Peganum harm… Peganum harma… Pega… species APC #> 3 Calotis mult… Calotis mul… Calotis mult… Calotis multi… Calo… species APC #> 4 Leptospermum… Leptospermu… Leptospermum… Leptospermum … Lept… species APC #> 5 Lepidosperma… Lepidosperm… Lepidosperma… Lepidosperma … Lepi… species APC #> 6 Enneapogon p… Enneapogon … Enneapogon p… Enneapogon po… Enne… species APC #> # ℹ 123 more rows #> # ℹ 5 more variables: taxonomic_status , scientific_name_authorship , #> # aligned_reason , update_reason , number_of_collapsed_taxa "},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"plant-established-status-across-statesterritories","dir":"Articles","previous_headings":"","what":"Plant established status across states/territories","title":"APCalign","text":"‘APCalign’ can also provide state/territory distribution established status (native/introduced) APC. can access established status data state/territory using create_species_state_origin_matrix() breakdown possible values origin can also obtain breakdown species established status particular state/territory using state_diversity_counts() Using established status data state/territory information, can check plant taxa native using native_anywhere_in_australia()","code":"# Retrieve status data by state/territory status_matrix <- create_species_state_origin_matrix(resources = resources) library(purrr) library(janitor) # Obtain unique values status_matrix |> select(-species) |> flatten_chr() |> tabyl() #> flatten_chr(select(status_matrix, -species)) n percent #> doubtfully naturalised 1120 2.371003e-03 #> formerly naturalised 277 5.863998e-04 #> native 40336 8.538997e-02 #> native and doubtfully naturalised 9 1.905270e-05 #> native and naturalised 136 2.879075e-04 #> native and uncertain origin 2 4.233933e-06 #> naturalised 8765 1.855521e-02 #> not present 421606 8.925258e-01 #> presumed extinct 101 2.138136e-04 #> uncertain origin 22 4.657327e-05 state_diversity_counts(\"NSW\", resources = resources) #> # A tibble: 7 × 3 #> origin state num_species #> #> 1 doubtfully naturalised NSW 93 #> 2 formerly naturalised NSW 8 #> 3 native NSW 5958 #> 4 native and doubtfully naturalised NSW 2 #> 5 native and naturalised NSW 34 #> 6 naturalised NSW 1580 #> 7 presumed extinct NSW 8 library(dplyr) updated_gbif_names |> sample_n(1) |> # Choosing a random species pull(suggested_name) |> # Extracting this APC accepted name native_anywhere_in_australia(resources = resources) #> # A tibble: 1 × 2 #> species native_anywhere_in_aus #> #> 1 Solanum prinophyllum considered native to Australia by APC"},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"closer-look","dir":"Articles","previous_headings":"","what":"Closer look at name standardisation with ‘APCalign’","title":"APCalign","text":"create_taxonomic_update_lookup simple, wrapper, function novice users want quickly check standardise taxon names. experienced users, can take look sub functions match_taxa(), align_taxa() update_taxonomy() see taxon names processed, aligned updated.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"aligning-names-to-apc-and-apni","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’","what":"Aligning names to APC and APNI","title":"APCalign","text":"function align_taxa : functions standardise_names, strip_names strip_names_extra standardise infraspecific taxon designations clean punctuation whitespaces taxonomic name flows progression 50 match algorithms able aligned name either APC APNI list. include exact fuzzy matches. Fuzzy matches designed capture small spelling mistakes syntax errors phrase names. include matches entire name string matches just select words sequence. sequence matches carefully curated align names fewest mistakes. names can resolved genus, reformats name offer standardised genus sp. name, additional information/notes provided part original name square brackets, Acacia sp. [skinny leaves] Acacia sp. [Broken Hill] Determine taxonomic_reference (APC APNI) name-alignment. Note align_taxa seek update outdated taxonomy. process occurs update_taxonomy process. align_taxa instead aligns name input closest match amongst names documented APC APNI. every aligned_name, align_taxa() provide aligned_reason can review table counts:","code":"library(dplyr) aligned_gbif_taxa <- gbif_lite |> pull(species) |> align_taxa(resources = resources) #> Checking alignments of 121 taxa #> -> 0 names already matched; 0 names checked but without a match; 121 taxa yet to be checked aligned_gbif_taxa |> print(n = 6) #> # A tibble: 129 × 7 #> original_name cleaned_name aligned_name taxonomic_dataset taxon_rank aligned_reason #> #> 1 Tetratheca ciliata Tetratheca … Tetratheca … APC species Exact match o… #> 2 Peganum harmala Peganum har… Peganum har… APC species Exact match o… #> 3 Calotis multicaulis Calotis mul… Calotis mul… APC species Exact match o… #> 4 Leptospermum triner… Leptospermu… Leptospermu… APC species Exact match o… #> 5 Lepidosperma latera… Lepidosperm… Lepidosperm… APC species Exact match o… #> 6 Enneapogon polyphyl… Enneapogon … Enneapogon … APC species Exact match o… #> # ℹ 123 more rows #> # ℹ 1 more variable: alignment_code library(janitor) aligned_gbif_taxa |> pull(aligned_reason) |> tabyl() |> tibble() #> # A tibble: 6 × 4 #> `pull(aligned_gbif_taxa, aligned_reason)` n percent valid_percent #> #> 1 Exact match of taxon name to an APC-accepted canonical name o… 118 0.915 0.929 #> 2 Exact match of taxon name to an APC-known canonical name once… 6 0.0465 0.0472 #> 3 Exact match of taxon name to an APNI-listed canonical name on… 1 0.00775 0.00787 #> 4 Exact match of the first two words of the taxon name to an AP… 1 0.00775 0.00787 #> 5 Exact match of the first word of the taxon name to an APC-acc… 1 0.00775 0.00787 #> 6 2 0.0155 NA"},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"fuzzy-match","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’ > Aligning names to APC and APNI","what":"Configuring matching precision and aligned output","title":"APCalign","text":"arguments align_taxa allows select 50 matching algorithms activated/deactivated degree fuzziness fuzzy matching function fuzzy_matches turns fuzzy matching / (defaults TRUE). fuzzy_abs_dist fuzzy_rel_dist control degree fuzzy matching (default fuzzy_abs_dist = 3 & fuzzy_rel_dist = 0.2). imprecise_fuzzy_matches turns imprecise fuzzy matching / (defaults FALSE; true set fuzzy_abs_dist = 5 & fuzzy_rel_dist = 0.25). APNI_matches turns matches APNI list /(defaults TRUE). identifier allows specify text string added genus-level matches, indicating site, study, etc e.g. Acacia sp. [Blue Mountains]","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"update","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’","what":"Updating to APC-accepted names","title":"APCalign","text":"update_taxonomy() uses information generated align_taxa() , whenever possible, update names APC-accepted names.","code":"updated_gbif_taxa <- aligned_gbif_taxa |> update_taxonomy(resources = resources) updated_gbif_taxa |> print(n = 6) #> # A tibble: 129 × 21 #> original_name aligned_name accepted_name suggested_name genus family taxon_rank #> #> 1 Tetratheca ciliata Tetratheca c… Tetratheca c… Tetratheca ci… Tetr… Elaeo… species #> 2 Peganum harmala Peganum harm… Peganum harm… Peganum harma… Pega… Nitra… species #> 3 Calotis multicaulis Calotis mult… Calotis mult… Calotis multi… Calo… Aster… species #> 4 Leptospermum trinervium Leptospermum… Leptospermum… Leptospermum … Lept… Myrta… species #> 5 Lepidosperma laterale Lepidosperma… Lepidosperma… Lepidosperma … Lepi… Cyper… species #> 6 Enneapogon polyphyllus Enneapogon p… Enneapogon p… Enneapogon po… Enne… Poace… species #> # ℹ 123 more rows #> # ℹ 14 more variables: taxonomic_dataset , taxonomic_status , #> # taxonomic_status_aligned , aligned_reason , update_reason , #> # subclass , taxon_distribution , scientific_name_authorship , #> # taxon_ID , taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa "},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"taxonomic-resources-used-for-updating-names","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’ > Updating to APC-accepted names","what":"Taxonomic resources used for updating names","title":"APCalign","text":"APC includes previously recorded taxonomic names current taxon concept, designating currently-accepted name taxonomic_status: accepted, previously used inappropriately used names taxon concept alternative taxonomic statuses documented (e.g. taxonomic synonym, orthographic variant, misapplied). APC includes column acceptedNameUsageID links taxon name alternative taxonomic status current taxon name, allowing outdated/inappropriately used names synced current name. Note: Names listed APNI absent APC designated taxonomic_dataset: APNI APCalign. names currently unknown APC. time, list shrinks, taxonomists link ever occasionally used name variants APC-accepted taxon. However, now, names listed APNI updated","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"name-updates-at-different-taxonomic-levels","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’ > Updating to APC-accepted names","what":"Name updates at different taxonomic levels","title":"APCalign","text":"update_taxonomy() divides names lists based taxon_rank taxonomic_dataset assigned align_taxa, list requires different updating algorithms. taxonomic names designated taxon_rank = species/infraspecific taxonomic_dataset = APC can updated APC-accepted name. taxa, may possible align genus-name APC-accepted genus. taxa, suggested_name provided, selecting accepted_name available, otherwise aligned_name, , possible, updated, APC-accepted genus name.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"taxonomic-splits","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’ > Updating to APC-accepted names","what":"Taxonomic splits","title":"APCalign","text":"Taxonomic splits refers instances single taxon concept subsequently split multiple taxon concepts. taxa, aligned_name “old” taxon concept name, impossible know currently accepted taxon concepts name represents. function update_taxonomy includes argument taxonomic_splits, offering three alternative outputs taxon concepts split. most_likely_species default value, returns accepted_name original taxon_concept; alternative names documented square brackets part suggested name (Acacia aneura [alternative possible names: Acacia minyura (pro parte misapplied) | Acacia paraneura (pro parte misapplied) | Acacia quadrimarginea (misapplied)). return_all returns currently accepted names split original taxon_concept; leads increase number rows output table. (Acacia aneura, Acacia minyura Acacia paraneura output separate row, unique taxon_ID) collapse_to_higher_taxon declares split names, way certain accepted name appropriate therefore best possible match genus level; accepted_name returned, taxon_rank demoted genus suggested name documents possible species-level names square brackets (Acacia sp. [collapsed names: Acacia aneura (accepted) | Acacia minyura (pro parte misapplied) | Acacia paraneura (pro parte misapplied)])","code":"library(dplyr) aligned_gbif_taxa |> update_taxonomy(taxonomic_splits = \"most_likely_species\", resources = resources) |> filter(original_name == \"Acacia aneura\") # Subsetting Acacia aneura as an example #> # A tibble: 1 × 21 #> original_name aligned_name accepted_name suggested_name genus family taxon_rank #> #> 1 Acacia aneura Acacia aneura Acacia aneura Acacia aneura [alternat… Acac… Fabac… species #> # ℹ 14 more variables: taxonomic_dataset , taxonomic_status , #> # taxonomic_status_aligned , aligned_reason , update_reason , #> # subclass , taxon_distribution , scientific_name_authorship , #> # taxon_ID , taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa aligned_gbif_taxa |> update_taxonomy(taxonomic_splits = \"return_all\", resources = resources) |> filter(original_name == \"Acacia aneura\") # Subsetting Acacia aneura as an example #> # A tibble: 3 × 21 #> original_name aligned_name accepted_name suggested_name genus family taxon_rank #> #> 1 Acacia aneura Acacia aneura Acacia aneura Acacia aneura Acacia Fabaceae species #> 2 Acacia aneura Acacia aneura Acacia minyura Acacia minyura Acacia Fabaceae species #> 3 Acacia aneura Acacia aneura Acacia paraneura Acacia paraneura Acacia Fabaceae species #> # ℹ 14 more variables: taxonomic_dataset , taxonomic_status , #> # taxonomic_status_aligned , aligned_reason , update_reason , #> # subclass , taxon_distribution , scientific_name_authorship , #> # taxon_ID , taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa aligned_gbif_taxa |> update_taxonomy(taxonomic_splits = \"collapse_to_higher_taxon\", resources = resources) |> filter(original_name == \"Acacia aneura\") # Subsetting Acacia aneura as an example #> # A tibble: 1 × 21 #> original_name aligned_name accepted_name suggested_name genus family taxon_rank #> #> 1 Acacia aneura Acacia aneura Acacia sp. Acacia sp. [collapsed n… Acac… Fabac… species #> # ℹ 14 more variables: taxonomic_dataset , taxonomic_status , #> # taxonomic_status_aligned , aligned_reason , update_reason , #> # subclass , taxon_distribution , scientific_name_authorship , #> # taxon_ID , taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa "},{"path":"https://traitecoevo.github.io/APCalign/articles/data-providers.html","id":"australian-plant-census-apc","dir":"Articles","previous_headings":"","what":"Australian Plant Census (APC)","title":"Data Providers","text":"Australian Plant Census (APC) national taxonomic database accepted names Australian vascular plants. APC includes information synonyms, misapplications , well established status (native/introduced) distribution across states territories. ‘APCalign’ first attempt align plant names scientific names exist APC.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/data-providers.html","id":"australian-plant-names-index-apni","dir":"Articles","previous_headings":"","what":"Australian Plant Names Index (APNI)","title":"Data Providers","text":"Australian Plant Names Index (APNI) database containing names used Australian plants scientific literature. primarily used botanical community standardising synonyms. Importantly, APNI provide recommendations taxonomy nomenclature; APC indicates taxonomy considered accepted. ‘APCalign’ uses APNI alignment found APC.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/data-providers.html","id":"data-standards-and-meta-data","dir":"Articles","previous_headings":"","what":"Data standards and meta-data","title":"Data Providers","text":"Data APNI APC formatted according Darwin Core standard, widely used data standard biodiversity data. can find meta-data APC APNI : Meta-data APC output Meta-data APNI output details APNI APC, recommend taking read extensive documentation.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/reproducibility.html","id":"apcalign-r-package-version","dir":"Articles","previous_headings":"","what":"APCalign R package version","title":"How to be more reproducible with APCalign","text":"determine version APCalign package :","code":"packageVersion(\"APCalign\")"},{"path":"https://traitecoevo.github.io/APCalign/articles/reproducibility.html","id":"taxonomic-resources","dir":"Articles","previous_headings":"","what":"Taxonomic Resources","title":"How to be more reproducible with APCalign","text":"APCalign allows users load static downloads taxonomic resources APC APNI latest version National Species List website. functionality specified using stable_or_current_data argument load_taxonomic_resources(). want taxonomic alignment update reproducible, recommend always use stable_or_current_data = \"stable\". default value stable_or_current_data = \"stable\". static downloads version controlled stored repository releases. default, load_taxonomic_resources() load latest version static downloads. order transparent, recommend check latest default_version alignment copying pasting output load_taxonomic_resources() directly. way makes version taxonomic resources explicit code. ensure specific version taxonomic resources available subsequent functions make sure assign object: alignment update, make sure supply version taxonomic resources using resources argument:","code":"load_taxonomic_resources(stable_or_current_data = \"stable\") load_taxonomic_resources( stable_or_current_data = \"stable\", version = default_version() ) default_version() #> [1] \"2024-07+31\" resources_0.0.4.9000 <- load_taxonomic_resources( stable_or_current_data = \"stable\", version = \"0.0.4.9000\" ) # Align taxa aligned_taxa <- align_taxa(gbif_lite$species, resources = resources_0.0.4.9000) # Update taxonomy updated_taxa <- update_taxonomy(aligned_taxa, resources = resources_0.0.4.9000) # Align and update all-in-one aligned_updated_taxa <- create_taxonomic_update_lookup(gbif_lite$species, resources = resources_0.0.4.9000)"},{"path":"https://traitecoevo.github.io/APCalign/articles/reproducibility.html","id":"citing-the-r-package","dir":"Articles","previous_headings":"","what":"Citing the R package","title":"How to be more reproducible with APCalign","text":"completion, can also cite R package calling citation(). also research article introducing APCalign, share details citation press.","code":"citation(\"APCalign\") #> To cite package 'APCalign' in publications use: #> #> Wenk E, Cornwell W, Fuchs A, Kar F, Monro A, Sauquet H, Stephens R, #> Falster D (2024). \"APCalign: an R package workflow and app for #> aligning and updating flora names to the Australian Plant Census.\" #> _Australian Journal of Botany_. R package version: 1.0.1, #> . #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census}, #> journal = {Australian Journal of Botany}, #> author = {Elizabeth Wenk and Will Cornwell and Ann Fuchs and Fonti Kar and Anna Monro and Herve Sauquet and Ruby Stephens and Daniel Falster}, #> year = {2024}, #> note = {R package version: 1.0.1}, #> url = {https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1}, #> }"},{"path":"https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html","id":"aligning-taxon-names-with-taxon-conceptsnames-in-apc-and-apni","dir":"Articles","previous_headings":"","what":"Aligning taxon names with taxon concepts/names in APC and APNI","title":"Methods for updating taxon names in APCalign","text":"following table indicates rules 51 separate algorithms sequentially applied attempt align submitted name taxon concept APC scientific names APNI. Note, table truncated screen, use horizontal scroll view entire table.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html","id":"updating-taxonomy","dir":"Articles","previous_headings":"","what":"Updating taxonomy","title":"Methods for updating taxon names in APCalign","text":"following table indicates separate functions used : update aligned names accepted names APC add best-practice suggested names submitted names add identifiers taxon concepts (APC) scientific names (APC APNI) Different functions used depending taxon rank aligned name taxonomic dataset name aligned (APC vs APNI). -* genus updated APC accepted genus possible; ** species infraspecific taxon name","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html","id":"outputs-of-apcalign","dir":"Articles","previous_headings":"","what":"Outputs of APCalign","title":"Methods for updating taxon names in APCalign","text":"following columns output core function create_taxonomic_update_lookup two component functions align_taxa update_taxonomy.","code":""},{"path":"https://traitecoevo.github.io/APCalign/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Daniel Falster. Author, maintainer, copyright holder. Elizabeth Wenk. Author, contributor. Cornwell. Author, contributor. Fonti Kar. Author, contributor. Carl Boettiger. Contributor.","code":""},{"path":"https://traitecoevo.github.io/APCalign/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Wenk E, Cornwell W, Fuchs , Kar F, Monro , Sauquet H, Stephens R, Falster D (2024). “APCalign: R package workflow app aligning updating flora names Australian Plant Census.” Australian Journal Botany. R package version: 1.0.1, https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1.","code":"@Article{, title = {APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census}, journal = {Australian Journal of Botany}, author = {Elizabeth Wenk and Will Cornwell and Ann Fuchs and Fonti Kar and Anna Monro and Herve Sauquet and Ruby Stephens and Daniel Falster}, year = {2024}, note = {R package version: 1.0.1}, url = {https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1}, }"},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"apcalign-","dir":"","previous_headings":"","what":"Resolving Plant Taxon Names Using the Australian Plant Census","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"APCalign uses Australian Plant Census (APC) Australian Plant Name Index align update Australian plant taxon name strings. ‘APCalign’ also supplies information established status (native/introduced) plant taxa across different states/territories. ’s useful updating species list intersecting APC consensus understanding established status (native/introduced).","code":""},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"CRAN: github version:","code":"install.packages(\"APCalign\") install.packages(\"remotes\") remotes::install_github(\"traitecoevo/APCalign\")"},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"a-quick-demo","dir":"","previous_headings":"","what":"A quick demo","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"Generating look-table can done just one function: ’re going use APCalign , save time load taxonomic resources memory first: Checking list species see classified Australian natives: Getting family lookup table genera specified taxonomy:","code":"library(APCalign) create_taxonomic_update_lookup( taxa = c( \"Banksia integrifolia\", \"Acacia longifolia\", \"Commersonia rosea\" ) ) #> ================================================================================================================================================================ #> # A tibble: 3 × 12 #> original_name aligned_name accepted_name suggested_name genus taxon_rank #> #> 1 Banksia integrifol… Banksia int… Banksia inte… Banksia integ… Bank… species #> 2 Acacia longifolia Acacia long… Acacia longi… Acacia longif… Acac… species #> 3 Commersonia rosea Commersonia… Androcalva r… Androcalva ro… Andr… species #> # ℹ 6 more variables: taxonomic_dataset , taxonomic_status , #> # scientific_name , aligned_reason , update_reason , #> # number_of_collapsed_taxa tax_resources <- load_taxonomic_resources() #> ================================================================================================================================================================ create_taxonomic_update_lookup( taxa = c( \"Banksia integrifolia\", \"Acacia longifolia\", \"Commersonia rosea\", \"not a species\" ), resources = tax_resources ) #> # A tibble: 4 × 12 #> original_name aligned_name accepted_name suggested_name genus taxon_rank #> #> 1 Banksia integrifol… Banksia int… Banksia inte… Banksia integ… Bank… species #> 2 Acacia longifolia Acacia long… Acacia longi… Acacia longif… Acac… species #> 3 Commersonia rosea Commersonia… Androcalva r… Androcalva ro… Andr… species #> 4 not a species #> # ℹ 6 more variables: taxonomic_dataset , taxonomic_status , #> # scientific_name , aligned_reason , update_reason , #> # number_of_collapsed_taxa native_anywhere_in_australia(c(\"Eucalyptus globulus\",\"Pinus radiata\"), resources = tax_resources) #> # A tibble: 2 × 2 #> species native_anywhere_in_aus #> #> 1 Eucalyptus globulus native #> 2 Pinus radiata introduced get_apc_genus_family_lookup(c(\"Eucalyptus\", \"Pinus\", \"Actinotus\", \"Banksia\", \"Acacia\", \"Triodia\"), resources = tax_resources) #> # A tibble: 6 × 2 #> genus family #> #> 1 Eucalyptus Myrtaceae #> 2 Pinus Pinaceae #> 3 Actinotus Apiaceae #> 4 Banksia Proteaceae #> 5 Acacia Fabaceae #> 6 Triodia Poaceae"},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"shiny-application","dir":"","previous_headings":"","what":"Shiny application","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"also developed shiny application non-R users update align taxonomic names. can find application : https://unsw.shinyapps.io/APCalign-app","code":""},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"learn-more","dir":"","previous_headings":"","what":"Learn more","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"Highly recommend looking Getting Started vignette learn use APCalign. can also learn taxa matching algorithm.","code":""},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"found-a-bug","dir":"","previous_headings":"","what":"Found a bug?","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"come across unexpected taxon name change? Elusive error can’t debug - submit issue try best help.","code":""},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"comments-and-contributions","dir":"","previous_headings":"","what":"Comments and contributions","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"welcome comments contributions package, start submit issue can take !","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/APCalign.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardising Taxonomic Names in Australian Plants — APCalign","title":"Standardising Taxonomic Names in Australian Plants — APCalign","text":"process standardising taxon names necessary working biodiversity data. 'APCalign' uses Australian Plant Name Index (APNI) Australian Plant Census (APC) align update plant taxon names current, accepted standards. 'APCalign' can also supply information established status plant taxa across different states/territories.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/APCalign.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Standardising Taxonomic Names in Australian Plants — APCalign","text":"Standarise taxon names load_taxonomic_resources create_taxonomic_update_lookup align_taxa update_taxonomy Established status region state_diversity_counts create_species_state_origin_matrix native_anywhere_in_australia","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/APCalign.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Standardising Taxonomic Names in Australian Plants — APCalign","text":"questions, comments suggestions, please submit issue GitHub repository","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/APCalign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Standardising Taxonomic Names in Australian Plants — APCalign","text":"Maintainer: Daniel Falster daniel.falster@unsw.edu.au (ORCID) [copyright holder] Authors: Elizabeth Wenk e.wenk@unsw.edu.au (ORCID) [contributor] Cornwell w.cornwell@unsw.edu.au (ORCID) [contributor] Fonti Kar f.kar@unsw.edu.au (ORCID) [contributor] contributors: Carl Boettiger cboettig@gmail.com (ORCID) [contributor]","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":null,"dir":"Reference","previous_headings":"","what":"Align Australian plant scientific names to the APC or APNI — align_taxa","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"list Australian plant names, find taxonomic scientific name alignments APC APNI standardizing formatting fixing spelling errors. Usage case: Users run function wish see details matching algorithms, many output columns matching function compares seeks best alignment. may also select function want adjust “fuzziness” level fuzzy matches, options allowed create_taxonomic_update_lookup. function first half create_taxonomic_update_lookup.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"","code":"align_taxa( original_name, output = NULL, full = FALSE, resources = load_taxonomic_resources(), quiet = FALSE, fuzzy_abs_dist = 3, fuzzy_rel_dist = 0.2, fuzzy_matches = TRUE, imprecise_fuzzy_matches = FALSE, APNI_matches = TRUE, identifier = NA_character_ )"},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"original_name list names query taxonomic alignments. output (optional) name file save results . full Parameter determine many columns output resources taxonomic resources used align taxa names. Loading can slow, call load_taxonomic_resources separately greatly speed function pass resources . quiet Logical indicate whether display messages aligning taxa. fuzzy_abs_dist number characters allowed different fuzzy match. fuzzy_rel_dist proportion characters allowed different fuzzy match. fuzzy_matches Fuzzy matches turned default. relative absolute distances allowed fuzzy matches species infraspecific taxon names defined parameters fuzzy_abs_dist fuzzy_rel_dist imprecise_fuzzy_matches Imprecise fuzzy matches uses fuzzy matching function lenient levels set (absolute distance 5 characters; relative distance = 0.25). offers way get wider range possible names, possibly corresponding distant spelling mistakes. FALSE default outputs checked often makes erroneous matches. APNI_matches Name matches APNI (Australian Plant Names Index) turned default. identifier dataset, location identifier, defaults NA.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"tibble columns include original_name, aligned_name, taxonomic_dataset, taxon_rank, aligned_reason, alignment_code. original_name: original plant name input. aligned_name: original plant name function standardise_names standardised syntax infraspecific taxon designations. taxonomic_dataset: source aligned names (APC APNI). taxon_rank: taxonomic rank aligned name. aligned_reason: explanation specific taxon name alignment (original name aligned name). alignment_code: code accompanies aligned_reason, indicating relative sequence match alignment process. cleaned_name: original name punctuation infraspecific taxon designation terms standardised function standardise_names; streamlines exact matches. stripped_name: cleaned name punctuation infraspecific taxon designation terms removed function strip_names; improves fuzzy matches. stripped_name2: cleaned name punctuation, infraspecific taxon designation terms, filler words removed function strip_names_extra; required matches first two word first three words. trinomial: first three words stripped_name2, required matches ignore text original_name; improves phrase name matches. binomial: first two words stripped_name2, required matches ignore text original_name; improves phrase name matches. genus: first two words cleaned_name; required genus-rank matches reprocessing genus-rank names. fuzzy_match_genus: fuzzy match genus column best match among APC-accepted names; required fuzzy matches genus-rank names. fuzzy_match_genus_synonym: fuzzy match genus column best match among APC-synonymous names, considering different matches documented APC-accepted genera; required fuzzy matches genus-rank names. fuzzy_match_genus_APNI: fuzzy match genus column best match among APNI names, considering different matches documented APC-accepted APC-known genera; required fuzzy matches genus-rank names. fuzzy_match_family: fuzzy match genus column best match among APC-accepted family names; required fuzzy matches family-rank names. fuzzy_match_family_synonym: fuzzy match genus column best match among APC-synonymous family names; required fuzzy matches family-rank names. fuzzy_match_cleaned_APC: fuzzy match stripped_name APC-accepted names; created yet---aligned names match step 05a function match_taxa. fuzzy_match_cleaned_APC_synonym: fuzzy match stripped_name APC-synonymous names; created yet---aligned names match step 05b function match_taxa. fuzzy_match_cleaned_APC_imprecise: imprecise fuzzy match stripped_name APC-accepted names; created yet---aligned names match step 07a function match_taxa. fuzzy_match_cleaned_APC_synonym_imprecise: imprecise fuzzy match stripped_name APC-accepted names; created yet---aligned names match step 07b function match_taxa. fuzzy_match_binomial: fuzzy match binomial column best match among APC-accepted names; created yet---aligned names match step 10c function match_taxa. fuzzy_match_binomial_APC_synonym: fuzzy match binomial column best match among APC-synonymous names; created yet---aligned names match step 10d function match_taxa. fuzzy_match_trinomial: fuzzy match trinomial column best match among APC-accepted names; created yet---aligned names match step 09c function match_taxa. fuzzy_match_trinomial_synonym: fuzzy match trinomial column best match among APC-synonymous names; created yet---aligned names match step 09d function match_taxa. fuzzy_match_cleaned_APNI: fuzzy match stripped_name APNI names; created yet---aligned names match step 11a function match_taxa. fuzzy_match_cleaned_APNI_imprecise: imprecise fuzzy match stripped_name APNI names; created yet---aligned names match step 11b function match_taxa.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"function finds taxonomic alignments APC scientific name alignments APNI. uses internal function match_taxa attempt match input strings taxon names APC/APNI. sequentially searches matches 20 different string patterns, prioritising exact matches (accepted names well synonyms, orthographic variants) fuzzy matches. prioritises matches taxa APC names APNI. identifies string patterns input names suggest name can aligned genus (hybrids APC/APNI; graded species; taxa identified species), indicates names genus-rank match. Notes: running function APCalign::create_taxonomic_update_lookup many times, best load taxonomic resources separately using resources <- load_taxonomic_resources(), add argument resources = resources name Banksia cerrata align fuzzy matching algorithm allow first letter genus species epithet change. function option changing fuzzy matching parameters. defaults, fuzzy matches allowing changes 3 (fewer) characters 20% (less) characters carefully calibrated catch just typos, , rarely mis-align name. wish introduce less conservative fuzzy matching recommended manually check aligned names. recommended begin imprecise_fuzzy_matches = FALSE (default), quite less precise fuzzy matches likely erroneous. argument turned plan check alignments manually. argument identifier allows add fix text string genus- family- level names, identifier = \"Royal NP\" return \"Acacia sp. [Royal NP]\".","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"","code":"# \\donttest{ resources <- load_taxonomic_resources() #> Downloading... #> File downloaded successfully. #> File downloaded successfully. #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done # example 1 align_taxa(c(\"Poa annua\", \"Abies alba\"), resources=resources) #> Checking alignments of 2 taxa #> -> of these 1 names have a perfect match to a scientific name in the APC. #> Alignments being sought for remaining names. #> # A tibble: 2 × 7 #> original_name cleaned_name aligned_name taxonomic_dataset taxon_rank #> #> 1 Poa annua Poa annua Poa annua APC species #> 2 Abies alba Abies alba NA NA NA #> # ℹ 2 more variables: aligned_reason , alignment_code # example 2 input <- c(\"Banksia serrata\", \"Banksia serrate\", \"Banksia cerrata\", \"Banksia serrrrata\", \"Dryandra sp.\", \"Banksia big red flowers\") aligned_taxa <- APCalign::align_taxa( original_name = input, identifier = \"APCalign test\", full = TRUE, resources=resources ) #> Checking alignments of 6 taxa #> -> of these 1 names have a perfect match to a scientific name in the APC. #> Alignments being sought for remaining names. # }"},{"path":"https://traitecoevo.github.io/APCalign/reference/create_species_state_origin_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"State level native and introduced origin status — create_species_state_origin_matrix","title":"State level native and introduced origin status — create_species_state_origin_matrix","text":"function uses taxon distribution data APC determine state level native introduced origin status. function processes geographic data available APC returns state level native, introduced complicated origins status taxa.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/create_species_state_origin_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"State level native and introduced origin status — create_species_state_origin_matrix","text":"","code":"create_species_state_origin_matrix(resources = load_taxonomic_resources())"},{"path":"https://traitecoevo.github.io/APCalign/reference/create_species_state_origin_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"State level native and introduced origin status — create_species_state_origin_matrix","text":"resources taxonomic resources required make summary statistics. Loading can slow, call load_taxonomic_resources separately greatly speed function pass resources .","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/create_species_state_origin_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"State level native and introduced origin status — create_species_state_origin_matrix","text":"tibble columns representing state rows representing species. values cell represent origin species state.","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/create_species_state_origin_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"State level native and introduced origin status — create_species_state_origin_matrix","text":"","code":"create_species_state_origin_matrix() #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done #> # A tibble: 26,507 × 19 #> species WA NT Qld SA NSW Vic Tas ChI LHI CoI NI #> #> 1 Acanthus e… nati… nati… nati… not … not … not … not … not … not … not … not … #> 2 Acanthus i… not … nati… nati… not … not … not … not … not … not … not … not … #> 3 Acanthus m… natu… not … doub… natu… natu… natu… natu… not … not … not … not … #> 4 Andrograph… not … natu… doub… not … not … not … not … nati… not … not … not … #> 5 Asystasia … not … not … not … not … not … not … not … nati… not … not … not … #> 6 Asystasia … not … not … nati… not … not … not … not … not … not … not … not … #> 7 Asystasia … natu… natu… natu… not … natu… not … not … natu… not … not … not … #> 8 Asystasia … not … not … not … not … not … not … not … natu… not … not … not … #> 9 Asystasia … not … not … nati… not … not … not … not … not … not … not … not … #> 10 Asystasia … not … not … not … not … not … not … not … natu… not … not … not … #> # ℹ 26,497 more rows #> # ℹ 7 more variables: ACT , CSI , AR , MI , HI , #> # MDI , CaI "},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"function takes list Australian plant names need reconciled current taxonomy generates lookup table best-possible scientific name match input name. Usage case: APCalign’s core function, merging together alignment updating taxonomy.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"","code":"create_taxonomic_update_lookup( taxa, stable_or_current_data = \"stable\", version = default_version(), taxonomic_splits = \"most_likely_species\", full = FALSE, fuzzy_abs_dist = 3, fuzzy_rel_dist = 0.2, fuzzy_matches = TRUE, APNI_matches = TRUE, imprecise_fuzzy_matches = FALSE, identifier = NA_character_, resources = load_taxonomic_resources(), quiet = FALSE, output = NULL )"},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"taxa list Australian plant species needs reconciled current taxonomy. stable_or_current_data either \"stable\" consistent version, \"current\" leading edge version. version version number dataset use. taxonomic_splits handle one_to_many taxonomic matches. Default \"return_all\". options \"collapse_to_higher_taxon\" \"most_likely_species\". most_likely_species defaults original_name name accepted APC; right certain species subsets, make errors cases, use caution. full logical whether full lookup table returned just key columns fuzzy_abs_dist number characters allowed different fuzzy match. fuzzy_rel_dist proportion characters allowed different fuzzy match. fuzzy_matches Fuzzy matches turned default. relative absolute distances allowed fuzzy matches species infraspecific taxon names defined parameters fuzzy_abs_dist fuzzy_rel_dist. APNI_matches Name matches APNI (Australian Plant Names Index) turned default. imprecise_fuzzy_matches Imprecise fuzzy matches uses fuzzy matching function lenient levels set (absolute distance 5 characters; relative distance = 0.25). offers way get wider range possible names, possibly corresponding distant spelling mistakes. FALSE default outputs checked often makes erroneous matches. identifier dataset, location identifier, defaults NA. resources taxonomic resources used cleaning, default loading local place computer. called repeatedly, much faster load resources using load_taxonomic_resources separately pass data . quiet Logical indicate whether display messages aligning taxa. output file path save output. file already exists, function check subset species passed try add file. can useful large growing projects.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"lookup table containing accepted suggested names original name input, additional taxonomic information taxon rank, taxonomic status, taxon IDs genera. original_name: original plant name. aligned_name: input plant name aligned taxon name APC APNI align_taxa function. accepted_name: APC-accepted plant name, available. suggested_name: suggested plant name use. Identical accepted_name, accepted_name exists; otherwise suggested_name aligned_name. genus: genus accepted (suggested) name; APC-accepted genus names filled . family: family accepted (suggested) name; APC-accepted family names filled . taxon_rank: taxonomic rank suggested (accepted) name. taxonomic_dataset: source suggested (accepted) names (APC APNI). taxonomic_status: taxonomic status suggested (accepted) name. taxonomic_status_aligned: taxonomic status aligned name, taxonomic updates applied. aligned_reason: explanation specific taxon name alignment (original name aligned name). update_reason: explanation specific taxon name update (aligned name accepted suggested name). subclass: subclass accepted name. taxon_distribution: distribution accepted name; filled APC accepted_name available. scientific_name_authorship: authorship information accepted (synonymous) name; available APC APNI names. taxon_ID: unique taxon concept identifier accepted_name; filled APC accepted_name available. taxon_ID_genus: identifier genus; filled APC-accepted genus name available. scientific_name_ID: identifier nomenclatural (taxonomic) details scientific name; available APC APNI names. row_number: row number specific original_name input. number_of_collapsed_taxa: taxonomic_splits == \"collapse_to_higher_taxon\", number possible taxon names collapsed.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"uses first function align_taxa, function update_taxonomy achieve output. aligned name plant name aligned taxon name APC APNI align_taxa function. Notes: running function APCalign::create_taxonomic_update_lookup many times, best load taxonomic resources separately using resources <- load_taxonomic_resources(), add argument resources = resources name Banksia cerrata align fuzzy matching algorithm allow first letter genus species epithet change. argument taxonomic_splits allows choose outcome updating names taxa ambiguous taxonomic histories; applies scientific names attached broadly circumscribed taxon concept, split several narrowly circumscribed taxon concepts, one retains original name. three options: most_likely_species returns name retained, alternative names documented square brackets; return_all adds additional rows output, one possible taxon concept; collapse_to_higher_taxon returns genus possible names square brackets. argument identifier allows add fix text string genus- family- level names, identifier = \"Royal NP\" return Acacia sp. \\[Royal NP].","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"","code":"# \\donttest{ resources <- load_taxonomic_resources() #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done # example 1 create_taxonomic_update_lookup(c(\"Eucalyptus regnans\", \"Acacia melanoxylon\", \"Banksia integrifolia\", \"Not a species\"), resources = resources) #> Checking alignments of 4 taxa #> -> of these 3 names have a perfect match to a scientific name in the APC. #> Alignments being sought for remaining names. #> # A tibble: 4 × 12 #> original_name aligned_name accepted_name suggested_name genus taxon_rank #> #> 1 Eucalyptus regnans Eucalyptus … Eucalyptus r… Eucalyptus re… Euca… species #> 2 Acacia melanoxylon Acacia mela… Acacia melan… Acacia melano… Acac… species #> 3 Banksia integrifol… Banksia int… Banksia inte… Banksia integ… Bank… species #> 4 Not a species NA NA NA NA NA #> # ℹ 6 more variables: taxonomic_dataset , taxonomic_status , #> # scientific_name , aligned_reason , update_reason , #> # number_of_collapsed_taxa # example 2 input <- c(\"Banksia serrata\", \"Banksia serrate\", \"Banksia cerrata\", \"Banksea serrata\", \"Banksia serrrrata\", \"Dryandra\") create_taxonomic_update_lookup( taxa = input, identifier = \"APCalign test\", full = TRUE, resources = resources ) #> Checking alignments of 6 taxa #> -> of these 1 names have a perfect match to a scientific name in the APC. #> Alignments being sought for remaining names. #> # A tibble: 6 × 21 #> original_name aligned_name accepted_name suggested_name genus family #> #> 1 Banksia serrata Banksia serrata Banksia serr… Banksia serra… Bank… Prote… #> 2 Banksia serrate Banksia serrata Banksia serr… Banksia serra… Bank… Prote… #> 3 Banksia cerrata Banksia sp. [Bank… NA Banksia sp. [… Bank… Prote… #> 4 Banksea serrata Banksia serrata Banksia serr… Banksia serra… Bank… Prote… #> 5 Banksia serrrrata Banksia serrata Banksia serr… Banksia serra… Bank… Prote… #> 6 Dryandra Dryandra sp. [Dry… NA Dryandra sp. … Drya… Eupho… #> # ℹ 15 more variables: taxon_rank , taxonomic_dataset , #> # taxonomic_status , taxonomic_status_aligned , #> # aligned_reason , update_reason , subclass , #> # taxon_distribution , scientific_name , taxon_ID , #> # taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa # example 3 taxon_list <- readr::read_csv( system.file(\"extdata\", \"test_taxa.csv\", package = \"APCalign\"), show_col_types = FALSE) create_taxonomic_update_lookup( taxa = taxon_list$original_name, identifier = taxon_list$notes, full = TRUE, resources = resources ) #> Checking alignments of 32 taxa #> -> of these 10 names have a perfect match to a scientific name in the APC. #> Alignments being sought for remaining names. #> # A tibble: 32 × 21 #> original_name aligned_name accepted_name suggested_name genus family #> #> 1 Banksia serrata Banksia ser… Banksia serr… Banksia serra… Bank… Prote… #> 2 Banksia serrate Banksia ser… Banksia serr… Banksia serra… Bank… Prote… #> 3 Banksee serrate Banksia ser… Banksia serr… Banksia serra… Bank… Prote… #> 4 Banksia cerrata Banksia sp.… NA Banksia sp. [… Bank… Prote… #> 5 Banksia sp. Banksia sp.… NA Banksia sp. [… Bank… Prote… #> 6 Dryandra sp. Dryandra sp… NA Dryandra sp. … Drya… Eupho… #> 7 Argyrodendron (Whyanb… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… #> 8 Argyrodendron ssp. (W… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… #> 9 Argyrodendron Whyanbe… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… #> 10 Argyrodendron sp. (Wh… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… #> # ℹ 22 more rows #> # ℹ 15 more variables: taxon_rank , taxonomic_dataset , #> # taxonomic_status , taxonomic_status_aligned , #> # aligned_reason , update_reason , subclass , #> # taxon_distribution , scientific_name , taxon_ID , #> # taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa # }"},{"path":"https://traitecoevo.github.io/APCalign/reference/default_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the default version for stable data — default_version","title":"Get the default version for stable data — default_version","text":"function returns default version stable data, used version specified.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/default_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the default version for stable data — default_version","text":"","code":"default_version()"},{"path":"https://traitecoevo.github.io/APCalign/reference/default_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the default version for stable data — default_version","text":"character string representing default version stable data.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/default_version.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the default version for stable data — default_version","text":"","code":"default_version() #> [1] \"2024-07+31\""},{"path":"https://traitecoevo.github.io/APCalign/reference/gbif_lite.html","id":null,"dir":"Reference","previous_headings":"","what":"GBIF Australian Plant Data — gbif_lite","title":"GBIF Australian Plant Data — gbif_lite","text":"subset plant data Global Biodiversity Information Facility","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/gbif_lite.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GBIF Australian Plant Data — gbif_lite","text":"","code":"gbif_lite"},{"path":"https://traitecoevo.github.io/APCalign/reference/gbif_lite.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"GBIF Australian Plant Data — gbif_lite","text":"gbif_lite tibble 129 rows 7 columns: species name first species scientificname infraspecificepithet name lowest terminal infraspecific epithet scientificname taxonrank taxonomic rank specific name decimalLongitude Longitude decimal degrees decimalLatitude Latitude decimal degrees scientificname Scientific Name verbatimscientificname Scientific name appeared original record","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/gbif_lite.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"GBIF Australian Plant Data — gbif_lite","text":"https://www.gbif.org/","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/get_apc_genus_family_lookup.html","id":null,"dir":"Reference","previous_headings":"","what":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","title":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","text":"Retrieve family name given genus using taxonomic data Australian Plant Census (APC).","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/get_apc_genus_family_lookup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","text":"","code":"get_apc_genus_family_lookup(genus, resources = load_taxonomic_resources())"},{"path":"https://traitecoevo.github.io/APCalign/reference/get_apc_genus_family_lookup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","text":"genus character vector genus names retrieve corresponding family names. resources taxonomic resources required make lookup. Loading can slow, call load_taxonomic_resources separately speed function pass resources .","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/get_apc_genus_family_lookup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","text":"data frame two columns: \"genus\", indicating genus name, \"family\", indicating corresponding family name APC.","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/get_apc_genus_family_lookup.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","text":"","code":"get_apc_genus_family_lookup(genus = c(\"Acacia\", \"Eucalyptus\")) #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done #> # A tibble: 2 × 2 #> genus family #> #> 1 Acacia Fabaceae #> 2 Eucalyptus Myrtaceae"},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":null,"dir":"Reference","previous_headings":"","what":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"function loads two taxonomic datasets Australia's vascular plants, APC APNI, global environment. creates several data frames filtering selecting data loaded lists.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"","code":"load_taxonomic_resources( stable_or_current_data = \"stable\", version = default_version(), quiet = FALSE )"},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"stable_or_current_data Type dataset access. default \"stable\", loads dataset github archived file. set \"current\", dataset loaded URL cutting edge version, may change time without notice. version version number dataset use. Defaults default version. quiet logical indicating whether print status loading screen. Defaults FALSE.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"taxonomic resources data loaded global environment.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"accesses taxonomic data dataset using provided version number default version. output several dataframes include subsets APC/APNI based taxon rank taxonomic status.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"","code":"# \\donttest{ load_taxonomic_resources(stable_or_current_data=\"stable\", version=\"0.0.2.9000\")# } #> Downloading... #> File downloaded successfully. #> File downloaded successfully. #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done #> $APC #> # A tibble: 109,624 × 38 #> taxon_ID name_type accepted_name_usage_ID accepted_name_usage #> #> 1 https://id.biodiversity… scientif… https://id.biodiversi… Plantae Haeckel #> 2 https://id.biodiversity… scientif… https://id.biodiversi… Charophyta Sachs #> 3 https://id.biodiversity… scientif… https://id.biodiversi… Charophyta Sachs #> 4 https://id.biodiversity… scientif… https://id.biodiversi… Equisetopsida C.Ag… #> 5 https://id.biodiversity… scientif… https://id.biodiversi… Equisetopsida C.Ag… #> 6 https://id.biodiversity… scientif… https://id.biodiversi… Equisetopsida C.Ag… #> 7 https://id.biodiversity… scientif… https://id.biodiversi… Cycadidae Pax #> 8 https://id.biodiversity… scientif… https://id.biodiversi… Cycadales Pers. ex… #> 9 https://id.biodiversity… scientif… https://id.biodiversi… Cycadales Pers. ex… #> 10 https://id.biodiversity… scientif… https://id.biodiversi… Cycadales Pers. ex… #> # ℹ 109,614 more rows #> # ℹ 34 more variables: nomenclaturalStatus , nomIlleg , #> # nomInval , taxonomic_status , pro_parte , #> # scientific_name , scientific_name_ID , canonical_name , #> # scientific_name_authorship , parentNameUsageID , #> # taxon_rank , taxon_rank_sort_order , kingdom , class , #> # subclass , family , taxonConceptID , … #> #> $APNI #> # A tibble: 132,385 × 48 #> scientific_name_ID name_type scientific_name scientificNameHTML #> #> 1 https://id.biodiversity.org.au/… scientif… Acanthus ebrac… 2 https://id.biodiversity.org.au/… autonym Acanthus ebrac… 3 https://id.biodiversity.org.au/… scientif… Acanthus ebrac… 4 https://id.biodiversity.org.au/… autonym Acanthus ilici… 5 https://id.biodiversity.org.au/… scientif… Acanthus ilici… 6 https://id.biodiversity.org.au/… scientif… Acanthus ilici… 7 https://id.biodiversity.org.au/… scientif… Acanthus ilici… 8 https://id.biodiversity.org.au/… scientif… Acanthus molli… 9 https://id.biodiversity.org.au/… scientif… Acanthus volub… 10 https://id.biodiversity.org.au/… scientif… Acanthus L. # ℹ 132,375 more rows #> # ℹ 44 more variables: canonical_name , canonicalNameHTML , #> # name_element , nomenclaturalStatus , #> # scientific_name_authorship , autonym , hybrid , #> # cultivar , formula , scientific , nomInval , #> # nomIlleg , namePublishedIn , namePublishedInID , #> # namePublishedInYear , nameInstanceType , … #> #> $`APC list (accepted)` #> # A tibble: 30,538 × 15 #> canonical_name scientific_name taxonomic_status taxon_ID scientific_name_ID #> #> 1 Cycas angulata Cycas angulata… accepted https:/… https://id.biodiv… #> 2 Cycas arenicola Cycas arenicol… accepted https:/… https://id.biodiv… #> 3 Cycas armstrong… Cycas armstron… accepted https:/… https://id.biodiv… #> 4 Cycas arnhemica Cycas arnhemic… accepted https:/… https://id.biodiv… #> 5 Cycas badensis Cycas badensis… accepted https:/… https://id.biodiv… #> 6 Cycas basaltica Cycas basaltic… accepted https:/… https://id.biodiv… #> 7 Cycas brunnea Cycas brunnea … accepted https:/… https://id.biodiv… #> 8 Cycas cairnsiana Cycas cairnsia… accepted https:/… https://id.biodiv… #> 9 Cycas calcicola Cycas calcicol… accepted https:/… https://id.biodiv… #> 10 Cycas canalis Cycas canalis … accepted https:/… https://id.biodiv… #> # ℹ 30,528 more rows #> # ℹ 10 more variables: accepted_name_usage_ID , name_type , #> # taxon_rank , genus , stripped_canonical , #> # stripped_canonical2 , stripped_scientific , binomial , #> # trinomial , taxonomic_dataset #> #> $`APC list (known names)` #> # A tibble: 69,647 × 15 #> canonical_name scientific_name taxonomic_status taxon_ID scientific_name_ID #> #> 1 Pterostylis cli… Pterostylis cl… alternative name https:/… https://id.biodiv… #> 2 Pterostylis cre… Pterostylis cr… alternative name https:/… https://id.biodiv… #> 3 Eucalyptus resi… Eucalyptus res… alternative name https:/… https://id.biodiv… #> 4 Macrozamia paul… Macrozamia pau… basionym https:/… https://id.biodiv… #> 5 Lycopodium creb… Lycopodium cre… basionym https:/… https://id.biodiv… #> 6 Lycopodium lock… Lycopodium loc… basionym https:/… https://id.biodiv… #> 7 Aralia polaris Aralia polaris… basionym https:/… https://id.biodiv… #> 8 Sium nodiflorum Sium nodifloru… basionym https:/… https://id.biodiv… #> 9 Trachymene koch… Trachymene koc… basionym https:/… https://id.biodiv… #> 10 Pittosporum res… Pittosporum re… basionym https:/… https://id.biodiv… #> # ℹ 69,637 more rows #> # ℹ 10 more variables: accepted_name_usage_ID , name_type , #> # taxon_rank , genus , stripped_canonical , #> # stripped_canonical2 , stripped_scientific , binomial , #> # trinomial , taxonomic_dataset #> #> $`APNI names` #> # A tibble: 15,379 × 13 #> canonical_name scientific_name scientific_name_ID name_type taxon_rank #> #> 1 (Eucalyptus globulus… (Eucalyptus gl… https://id.biodiv… hybrid-f… species #> 2 (Eucalyptus globulus… (Eucalyptus gl… https://id.biodiv… hybrid-f… species #> 3 (Eucalyptus johnston… (Eucalyptus jo… https://id.biodiv… hybrid-f… species #> 4 (Eucalyptus johnston… (Eucalyptus jo… https://id.biodiv… hybrid-f… species #> 5 (Eucalyptus urnigera… (Eucalyptus ur… https://id.biodiv… hybrid-f… species #> 6 (Eucalyptus urnigera… (Eucalyptus ur… https://id.biodiv… hybrid-f… species #> 7 Abacopteris presliana Abacopteris pr… https://id.biodiv… scientif… species #> 8 Abarema clypearia f.… Abarema clypea… https://id.biodiv… scientif… form #> 9 Abarema pruinosa Abarema pruino… https://id.biodiv… scientif… species #> 10 Abelia rupestris Abelia rupestr… https://id.biodiv… scientif… species #> # ℹ 15,369 more rows #> # ℹ 8 more variables: taxonomic_status , stripped_canonical , #> # stripped_canonical2 , stripped_scientific , binomial , #> # trinomial , genus , taxonomic_dataset #> #> $genera_accepted #> # A tibble: 3,094 × 11 #> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name #> #> 1 Cycas Cycas L. https://id.biodiversity.o… Cycas L. #> 2 Bowenia Bowenia Hook.f. https://id.biodiversity.o… Bowenia Hook.f. #> 3 Lepidozamia Lepidozamia Regel https://id.biodiversity.o… Lepidozamia Re… #> 4 Macrozamia Macrozamia Miq. https://id.biodiversity.o… Macrozamia Miq. #> 5 Equisetum Equisetum L. https://id.biodiversity.o… Equisetum L. #> 6 Isoetes Isoetes L. https://id.biodiversity.o… Isoetes L. #> 7 Huperzia Huperzia Bernh. https://id.biodiversity.o… Huperzia Bernh. #> 8 Lycopodiella Lycopodiella Holub https://id.biodiversity.o… Lycopodiella H… #> 9 Lycopodium Lycopodium L. https://id.biodiversity.o… Lycopodium L. #> 10 Phlegmariurus Phlegmariurus Holub https://id.biodiversity.o… Phlegmariurus … #> # ℹ 3,084 more rows #> # ℹ 7 more variables: taxonomic_status , taxon_ID , #> # scientific_name_ID , name_type , taxon_rank , genus , #> # taxonomic_dataset #> #> $genera_synonym #> # A tibble: 2,848 × 11 #> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name #> #> 1 Encephallartes Encephalartos Lehm. https://id.biodiversity… Encephallartes… #> 2 Encephalartus Encephalartos Lehm. https://id.biodiversity… Encephalartus … #> 3 Encephalartos Encephalartos Lehm. https://id.biodiversity… Encephalartos … #> 4 Catakidozamia Lepidozamia Regel https://id.biodiversity… Catakidozamia … #> 5 Zamia Zamia L. https://id.biodiversity… Zamia L. #> 6 Calamaria Isoetes L. https://id.biodiversity… Calamaria Boeh… #> 7 Lateristachys Lycopodiella Holub https://id.biodiversity… Lateristachys … #> 8 Lepidotis Lycopodiella Holub https://id.biodiversity… Lepidotis P.Be… #> 9 Austrolycopodium Lycopodium L. https://id.biodiversity… Austrolycopodi… #> 10 Diphasium Lycopodium L. https://id.biodiversity… Diphasium C.Pr… #> # ℹ 2,838 more rows #> # ℹ 7 more variables: taxonomic_status , taxon_ID , #> # scientific_name_ID , name_type , taxon_rank , genus , #> # taxonomic_dataset #> #> $genera_APNI #> # A tibble: 1,426 × 8 #> canonical_name scientific_name taxonomic_status scientific_name_ID name_type #> #> 1 Beloperone Beloperone Nees unplaced https://id.biodiv… scientif… #> 2 Hemiadelphis Hemiadelphis Ne… unplaced https://id.biodiv… scientif… #> 3 Leptosiphonium Leptosiphonium … unplaced https://id.biodiv… scientif… #> 4 Megaskepasma Megaskepasma Li… unplaced https://id.biodiv… scientif… #> 5 Meyenia Meyenia Nees unplaced https://id.biodiv… scientif… #> 6 Simonachne Simonachne E.J.… unplaced https://id.biodiv… scientif… #> 7 Thyrsacanthus Thyrsacanthus N… unplaced https://id.biodiv… scientif… #> 8 Synarrhena Synarrhena F.Mu… unplaced https://id.biodiv… scientif… #> 9 Allosorus Allosorus Bernh. unplaced https://id.biodiv… scientif… #> 10 Austrogramme Austrogramme E.… unplaced https://id.biodiv… scientif… #> # ℹ 1,416 more rows #> # ℹ 3 more variables: taxon_rank , genus , taxonomic_dataset #> #> $genera_all #> # A tibble: 7,368 × 12 #> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name #> #> 1 Cycas Cycas L. https://id.biodiversity.o… Cycas L. #> 2 Bowenia Bowenia Hook.f. https://id.biodiversity.o… Bowenia Hook.f. #> 3 Lepidozamia Lepidozamia Regel https://id.biodiversity.o… Lepidozamia Re… #> 4 Macrozamia Macrozamia Miq. https://id.biodiversity.o… Macrozamia Miq. #> 5 Equisetum Equisetum L. https://id.biodiversity.o… Equisetum L. #> 6 Isoetes Isoetes L. https://id.biodiversity.o… Isoetes L. #> 7 Huperzia Huperzia Bernh. https://id.biodiversity.o… Huperzia Bernh. #> 8 Lycopodiella Lycopodiella Holub https://id.biodiversity.o… Lycopodiella H… #> 9 Lycopodium Lycopodium L. https://id.biodiversity.o… Lycopodium L. #> 10 Phlegmariurus Phlegmariurus Holub https://id.biodiversity.o… Phlegmariurus … #> # ℹ 7,358 more rows #> # ℹ 8 more variables: taxonomic_status , taxon_ID , #> # scientific_name_ID , name_type , taxon_rank , genus , #> # taxonomic_dataset , cleaned_name #> #> $family_accepted #> # A tibble: 307 × 38 #> taxon_ID name_type accepted_name_usage_ID accepted_name_usage #> #> 1 https://id.biodiversity… scientif… https://id.biodiversi… Cycadaceae Pers. #> 2 https://id.biodiversity… scientif… https://id.biodiversi… Zamiaceae Horan. #> 3 https://id.biodiversity… scientif… https://id.biodiversi… Equisetaceae Michx… #> 4 https://id.biodiversity… scientif… https://id.biodiversi… Isoetaceae Rchb. #> 5 https://id.biodiversity… scientif… https://id.biodiversi… Lycopodiaceae P.Be… #> 6 https://id.biodiversity… scientif… https://id.biodiversi… Selaginellaceae Wi… #> 7 https://id.biodiversity… scientif… https://id.biodiversi… Apiaceae Lindl. #> 8 https://id.biodiversity… scientif… https://id.biodiversi… Araliaceae Juss. #> 9 https://id.biodiversity… scientif… https://id.biodiversi… Griseliniaceae J.R… #> 10 https://id.biodiversity… scientif… https://id.biodiversi… Myodocarpaceae Dow… #> # ℹ 297 more rows #> # ℹ 34 more variables: nomenclaturalStatus , nomIlleg , #> # nomInval , taxonomic_status , pro_parte , #> # scientific_name , scientific_name_ID , canonical_name , #> # scientific_name_authorship , parentNameUsageID , #> # taxon_rank , taxon_rank_sort_order , kingdom , class , #> # subclass , family , taxonConceptID , … #> #> $family_synonym #> # A tibble: 244 × 11 #> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name #> #> 1 Boweniaceae Zamiaceae Horan. https://id.biodiversi… Boweniaceae D.… #> 2 Lycopodia Lycopodiaceae P.Bea… https://id.biodiversi… Lycopodia Mirb. #> 3 Umbelliferae Apiaceae Lindl. https://id.biodiversi… Umbelliferae J… #> 4 Araliae Araliaceae Juss. https://id.biodiversi… Araliae Juss. #> 5 Griselineae Griseliniaceae J.R.… https://id.biodiversi… Griselineae A.… #> 6 Pittosporeae Pittosporaceae R.Br. https://id.biodiversi… Pittosporeae R… #> 7 Cardiopterideae Cardiopteridaceae B… https://id.biodiversi… Cardiopteridea… #> 8 Quintiniaceae Paracryphiaceae Air… https://id.biodiversi… Quintiniaceae … #> 9 Sphenostemonaceae Paracryphiaceae Air… https://id.biodiversi… Sphenostemonac… #> 10 Compositae Asteraceae Bercht. … https://id.biodiversi… Compositae Gis… #> # ℹ 234 more rows #> # ℹ 7 more variables: taxonomic_status , taxon_ID , #> # scientific_name_ID , name_type , taxon_rank , genus , #> # taxonomic_dataset #>"},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":null,"dir":"Reference","previous_headings":"","what":"Native anywhere in Australia — native_anywhere_in_australia","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"function checks species list thought native anywhere Australia according APC.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"","code":"native_anywhere_in_australia(species, resources = load_taxonomic_resources())"},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"species character string typically representing binomial species. resources optional list taxonomic resources use lookup. provided, function load default taxonomic resources using load_taxonomic_resources() function.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"tibble two columns: species, unique values input species, native_anywhere_in_aus, vector indicating whether species native anywhere Australia, introduced humans elsewhere, unknown respect APC resource.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"Important caveats: function detect within-Australia introductions, e.g. species Western Australia invasive east coast. recent invasions unlikely documented yet APC. Ideally check spelling taxonomy updates first via create_taxonomic_update_lookup. complete matrix species states also represents within-Australia invasions, use create_species_state_origin_matrix.","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"","code":"native_anywhere_in_australia(c(\"Eucalyptus globulus\",\"Pinus radiata\",\"Banksis notaspecies\")) #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done #> Warning: At least one input not found in APC; make sure inputs are at the species level and consider using `create_taxonomic_update_lookup` first. #> # A tibble: 3 × 2 #> species native_anywhere_in_aus #> #> 1 Eucalyptus globulus native #> 2 Pinus radiata introduced #> 3 Banksis notaspecies unknown"},{"path":"https://traitecoevo.github.io/APCalign/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. dplyr %>%","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardise taxon names — standardise_names","title":"Standardise taxon names — standardise_names","text":"Standardises taxon names performing series text substitutions remove common inconsistencies taxonomic nomenclature. function takes character vector taxon names input returns character vector taxon names using standardised taxonomic syntax output.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standardise taxon names — standardise_names","text":"","code":"standardise_names(taxon_names)"},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standardise taxon names — standardise_names","text":"taxon_names character vector taxon names need standardised.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standardise taxon names — standardise_names","text":"character vector standardised taxon names.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standardise taxon names — standardise_names","text":"removes stray punctuation start end character string. standardises unusual characters symbols ASCII equivalents. standardises taxon rank abbreviations qualifiers (subsp., var., f.), people use many variants terms. standardises removes additional filler words used within taxon names (affinis becomes aff.; s.l. s.s. removed).","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Standardise taxon names — standardise_names","text":"","code":"standardise_names(c(\"Quercus suber\", \"Eucalyptus sp.\", \"Eucalyptus spp.\", \"Agave americana var. marginata\", \"Agave americana v marginata\", \"Notelaea longifolia forma longifolia\", \"Notelaea longifolia f longifolia\")) #> [1] \"Quercus suber\" \"Eucalyptus sp.\" #> [3] \"Eucalyptus sp.\" \"Agave americana var. marginata\" #> [5] \"Agave americana var. marginata\" \"Notelaea longifolia f. longifolia\" #> [7] \"Notelaea longifolia f. longifolia\""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardise taxon ranks — standardise_taxon_rank","title":"Standardise taxon ranks — standardise_taxon_rank","text":"Standardise taxon ranks Latin English.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standardise taxon ranks — standardise_taxon_rank","text":"","code":"standardise_taxon_rank(taxon_rank)"},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standardise taxon ranks — standardise_taxon_rank","text":"taxon_rank character vector Latin taxon ranks.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standardise taxon ranks — standardise_taxon_rank","text":"character vector English taxon ranks.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standardise taxon ranks — standardise_taxon_rank","text":"function takes character vector Latin taxon ranks input returns character vector taxon ranks using standardised English terms.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Standardise taxon ranks — standardise_taxon_rank","text":"","code":"standardise_taxon_rank(c(\"regnum\", \"kingdom\", \"classis\", \"class\")) #> [1] \"kingdom\" \"kingdom\" \"class\" \"class\""},{"path":"https://traitecoevo.github.io/APCalign/reference/state_diversity_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"State- and territory-level diversity — state_diversity_counts","title":"State- and territory-level diversity — state_diversity_counts","text":"Australian states territories, use geographic distribution data APC calculate state-level diversity native, introduced, complicated species origins","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/state_diversity_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"State- and territory-level diversity — state_diversity_counts","text":"","code":"state_diversity_counts(state, resources = load_taxonomic_resources())"},{"path":"https://traitecoevo.github.io/APCalign/reference/state_diversity_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"State- and territory-level diversity — state_diversity_counts","text":"state character string indicating Australian state territory calculate diversity . Possible values \"NSW\", \"NT\", \"Qld\", \"WA\", \"ChI\", \"SA\", \"Vic\", \"Tas\", \"ACT\", \"NI\", \"LHI\", \"MI\", \"HI\", \"MDI\", \"CoI\", \"CSI\", \"AR\". resources taxonomic resources required make summary statistics. loading can slow, call load_taxonomic_resources separately greatly speed function pass resources .","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/state_diversity_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"State- and territory-level diversity — state_diversity_counts","text":"tibble diversity counts specified state territory, including native, introduced, complicated species origins. tibble three columns: \"origin\" indicating origin species, \"state\" indicating Australian state territory, \"num_species\" indicating number species origin state.","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/state_diversity_counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"State- and territory-level diversity — state_diversity_counts","text":"","code":"state_diversity_counts(state = \"NSW\") #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done #> # A tibble: 7 × 3 #> origin state num_species #> #> 1 doubtfully naturalised NSW 94 #> 2 formerly naturalised NSW 8 #> 3 native NSW 5959 #> 4 native and doubtfully naturalised NSW 2 #> 5 native and naturalised NSW 34 #> 6 naturalised NSW 1583 #> 7 presumed extinct NSW 9"},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Strip taxon names — strip_names","title":"Strip taxon names — strip_names","text":"Strip taxonomic names taxon rank abbreviations qualifiers special characters","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Strip taxon names — strip_names","text":"","code":"strip_names(taxon_names)"},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Strip taxon names — strip_names","text":"taxon_names character vector taxonomic names stripped.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Strip taxon names — strip_names","text":"character vector stripped taxonomic names, subtaxa designations, special characters, extra whitespace removed, letters converted lowercase.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Strip taxon names — strip_names","text":"Given vector taxonomic names, function removes: subtaxa designations (\"subsp.\", \"var.\", \"f.\", \"ser\") special characters (e.g., \"-\", \".\", \"(\", \")\", \"?\") extra whitespace resulting vector names also converted lowercase.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Strip taxon names — strip_names","text":"","code":"strip_names(c(\"Abies lasiocarpa subsp. lasiocarpa\", \"Quercus kelloggii\", \"Pinus contorta var. latifolia\")) #> [1] \"abies lasiocarpa lasiocarpa\" \"quercus kelloggii\" #> [3] \"pinus contorta latifolia\""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":null,"dir":"Reference","previous_headings":"","what":"Strip taxon names, extra — strip_names_extra","title":"Strip taxon names, extra — strip_names_extra","text":"Strip taxonomic names sp. hybrid symbols. function assumes character function already run strip_names.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Strip taxon names, extra — strip_names_extra","text":"","code":"strip_names_extra(taxon_names)"},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Strip taxon names, extra — strip_names_extra","text":"taxon_names character vector taxonomic names stripped.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Strip taxon names, extra — strip_names_extra","text":"character vector stripped taxonomic names, sp. hybrid symbols removed.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Strip taxon names, extra — strip_names_extra","text":"Given vector taxonomic names, function removes additional filler words (\" x \" hybrid taxa, \"sp.\") removed function strip_names","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Strip taxon names, extra — strip_names_extra","text":"","code":"strip_names_extra(c(\"Abies lasiocarpa subsp. lasiocarpa\", \"Quercus kelloggii\", \"Pinus contorta var. latifolia\", \"Acacia sp.\", \"Lepidium sp. Tanguin Hill (K.R.Newbey 10501)\")) #> [1] \"Abies lasiocarpa subsp. lasiocarpa\" #> [2] \"Quercus kelloggii\" #> [3] \"Pinus contorta var. latifolia\" #> [4] \"Acacia sp.\" #> [5] \"Lepidium sp. Tanguin Hill (K.R.Newbey 10501)\""},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":null,"dir":"Reference","previous_headings":"","what":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"list taxon names aligned APC, update name accepted taxon concept per APC add scientific name taxon concept metadata names aligned either APC APNI.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"","code":"update_taxonomy( aligned_data, taxonomic_splits = \"most_likely_species\", quiet = TRUE, output = NULL, resources = load_taxonomic_resources() )"},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"aligned_data tibble plant names update. table must include 5 columns, original_name, aligned_name, taxon_rank, taxonomic_dataset, aligned_reason. columns created function align_taxa. columns original_name aligned_name must format scientific name, genus species, may contain additional qualifiers subspecies varieties. names case insensitive. taxonomic_splits Variable determines protocol use update taxon names ambiguous due taxonomic splits. three options : most_likely_species, returns species name use split; alternative names returned separate column return_all, returns possible names collapse_to_higher_taxon, declares ambiguous name aligned accepted species/infraspecific name name demoted genus rank quiet Logical indicate whether display messages updating taxa. output (optional) Name file results saved. default NULL file created. specified, output saved CSV file given name. resources taxonomic resources required make summary statistics. Loading can slow, call load_taxonomic_resources separately greatly speed function pass resources .","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"tibble updated taxonomy specified plant names. tibble contains following columns: original_name: original plant name. aligned_name: input plant name aligned taxon name APC APNI align_taxa function. accepted_name: APC-accepted plant name, available. suggested_name: suggested plant name use. Identical accepted_name, accepted_name exists; otherwise suggested_name aligned_name. genus: genus accepted (suggested) name; APC-accepted genus names filled . family: family accepted (suggested) name; APC-accepted family names filled . taxon_rank: taxonomic rank suggested (accepted) name. taxonomic_dataset: source suggested (accepted) names (APC APNI). taxonomic_status: taxonomic status suggested (accepted) name. taxonomic_status_aligned: taxonomic status aligned name, taxonomic updates applied. aligned_reason: explanation specific taxon name alignment (original name aligned name). update_reason: explanation specific taxon name update (aligned name accepted suggested name). subclass: subclass accepted name. taxon_distribution: distribution accepted name; filled APC accepted_name available. scientific_name_authorship: authorship information accepted (synonymous) name; available APC APNI names. taxon_ID: unique taxon concept identifier accepted_name; filled APC accepted_name available. taxon_ID_genus: identifier genus; filled APC-accepted genus name available. scientific_name_ID: identifier nomenclatural (taxonomic) details scientific name; available APC APNI names. row_number: row number specific original_name input. number_of_collapsed_taxa: taxonomic_splits == \"collapse_to_higher_taxon\", number possible taxon names collapsed.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"function uses APC update taxonomy names aligned taxon concept listed APC currently accepted name taxon concept. aligned_data data frame input must contain 5 columns, original_name, aligned_name, taxon_rank, taxonomic_dataset, aligned_reason. (columns output function align_taxa.) aligned name plant name aligned taxon name APC APNI align_taxa function. Notes: input function table 5 columns (output align_taxa), function used explicitly want separate alignment updating components APCalign. function second half create_taxonomic_update_lookup.","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"","code":"# Update taxonomy for two plant names and print the result # \\donttest{ resources <- load_taxonomic_resources() #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done update_taxonomy( dplyr::tibble( original_name = c(\"Dryandra preissii\", \"Banksia acuminata\"), aligned_name = c(\"Dryandra preissii\", \"Banksia acuminata\"), taxon_rank = c(\"species\", \"species\"), taxonomic_dataset = c(\"APC\", \"APC\"), aligned_reason = c(NA_character_, NA_character_) ), resources = resources ) #> # A tibble: 2 × 21 #> original_name aligned_name accepted_name suggested_name genus family #> #> 1 Dryandra preissii Dryandra preissii Banksia acumi… Banksia acumi… Bank… Prote… #> 2 Banksia acuminata Banksia acuminata Banksia acumi… Banksia acumi… Bank… Prote… #> # ℹ 15 more variables: taxon_rank , taxonomic_dataset , #> # taxonomic_status , taxonomic_status_aligned , #> # aligned_reason , update_reason , subclass , #> # taxon_distribution , scientific_name , taxon_ID , #> # taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa # }"},{"path":"https://traitecoevo.github.io/APCalign/news/index.html","id":"apcalign-110","dir":"Changelog","previous_headings":"","what":"APCalign 1.1.0","title":"APCalign 1.1.0","text":"CRAN release: 2024-08-19 Create genus->family lookup specified APC release","code":""},{"path":"https://traitecoevo.github.io/APCalign/news/index.html","id":"apcalign-102","dir":"Changelog","previous_headings":"","what":"APCalign 1.0.2","title":"APCalign 1.0.2","text":"CRAN release: 2024-08-17 Minor update fix Deal vignette issues emerged CRAN Improve “graceful failing”, based issues come github CI minor formatting","code":""},{"path":"https://traitecoevo.github.io/APCalign/news/index.html","id":"apcalign-101","dir":"Changelog","previous_headings":"","what":"APCalign 1.0.1","title":"APCalign 1.0.1","text":"CRAN release: 2024-05-30 First major release APCalign. preprint available https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1. Article accepted publication Australian journal Botany. Following review, number changes implemented. sped & streamlined package. Update function documentation Speed extract_genus Write replacement function stringr::word much faster. Restricting reference list names first letter input string. Switch using utils::adist stringdist::stringdist(method = \"dl\") Rework standardise_names remove punctuation start string Rework strip_names_extra (previously strip_names_2) just perform additional functions strip_names, rather repeating performed strip_names. Avoid importing entire packages using package::function format throughout removing functions @import Add fuzzy match arguments create_taxonomic_update_lookup Add 3 additional family-level APC matches match_taxa. Refine tests Make messages console optional Fix issue fails github (https://github.com/traitecoevo/APCalign/issues/205) Update installation instructions Added cite version APCalign article Exported default_version Add citing method R package Update GitHub Actions Improved family alignments Added standardise_taxon_rank Improved messaging alignment","code":""}] +[{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"APCalign","text":"demonstrate use APCalign, use example dataset gbif_lite documented ?gbif_lite","code":"install.packages(\"remotes\") remotes::install_github(\"traitecoevo/APCalign\") library(APCalign) dim(gbif_lite) #> [1] 129 7 gbif_lite |> print(n = 6) #> # A tibble: 129 × 7 #> species infraspecificepithet taxonrank decimalLongitude decimalLatitude scientificname #> #> 1 Tetratheca… SPECIES 145. -37.4 Tetratheca ci… #> 2 Peganum ha… SPECIES 139. -33.3 Peganum harma… #> 3 Calotis mu… SPECIES 115. -24.3 Calotis multi… #> 4 Leptosperm… SPECIES 151. -34.0 Leptospermum … #> 5 Lepidosper… SPECIES 142. -37.3 Lepidosperma … #> 6 Enneapogon… SPECIES 129. -17.8 Enneapogon po… #> # ℹ 123 more rows #> # ℹ 1 more variable: verbatimscientificname "},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"retrieve-taxonomic-resources","dir":"Articles","previous_headings":"","what":"Retrieve taxonomic resources","title":"APCalign","text":"first step retrieve entire APC APNI name databases store locally taxonomic resources. achieve using load_taxonomic_resources(). resources compressed parquet files speed download local loading. two versions databases can retrieve stable_or_current_data argument. Calling: stable retrieve recent, archived version databases GitHub releases. set default option. current retrieve --date databases directly APC APNI website. Note databases reasonably large initial retrieval core data take minutes. taxonomic resources stored locally, subsequent retrievals take less time. Retrieving current resources always take longer since accessing latest information website uncompressed format. reproducible workflow, recommend specifying exact stable version want use.","code":"# Benchmarking the retrieval of `stable` or `current` resources stable_start_time <- Sys.time() stable_resources <- load_taxonomic_resources(stable_or_current_data = \"stable\") #> Loading resources......done stable_end_time <- Sys.time() current_start_time <- Sys.time() current_resources <- load_taxonomic_resources(stable_or_current_data = \"current\") #> Loading resources......done current_end_time <- Sys.time() # Compare times stable_end_time - stable_start_time #> Time difference of 16.48976 secs resources <- load_taxonomic_resources(stable_or_current_data = \"stable\", version = \"0.0.2.9000\") #> Loading resources......done"},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"align-and-update-plant-taxon-names","dir":"Articles","previous_headings":"","what":"Align and update plant taxon names","title":"APCalign","text":"Now can query taxonomic names taxonomic resources just retrieved using create_taxonomic_update_lookup(). --one function : Align taxonomic names APC APNI using matching algorithms Update names APC-accepted species infraspecific name whenever possible. Return suggested name names, defaulting accepted_name available, otherwise providing APNI name name genus-level alignment possible. like learn step, take look section Closer look name alignment updating ‘APCalign’ original_name taxon name used original data. aligned_name taxon name used link APC identify synonyms. accepted_name currently, accepted taxon name used Australian Plant Census. suggested_name best possible name option original_name.","code":"library(dplyr) updated_gbif_names <- gbif_lite |> pull(species) |> create_taxonomic_update_lookup(resources = resources) #> Checking alignments of 121 taxa #> -> 0 names already matched; 0 names checked but without a match; 121 taxa yet to be checked updated_gbif_names |> print(n = 6) #> # A tibble: 129 × 12 #> original_name aligned_name accepted_name suggested_name genus taxon_rank taxonomic_dataset #> #> 1 Tetratheca c… Tetratheca … Tetratheca c… Tetratheca ci… Tetr… species APC #> 2 Peganum harm… Peganum har… Peganum harm… Peganum harma… Pega… species APC #> 3 Calotis mult… Calotis mul… Calotis mult… Calotis multi… Calo… species APC #> 4 Leptospermum… Leptospermu… Leptospermum… Leptospermum … Lept… species APC #> 5 Lepidosperma… Lepidosperm… Lepidosperma… Lepidosperma … Lepi… species APC #> 6 Enneapogon p… Enneapogon … Enneapogon p… Enneapogon po… Enne… species APC #> # ℹ 123 more rows #> # ℹ 5 more variables: taxonomic_status , scientific_name_authorship , #> # aligned_reason , update_reason , number_of_collapsed_taxa "},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"plant-established-status-across-statesterritories","dir":"Articles","previous_headings":"","what":"Plant established status across states/territories","title":"APCalign","text":"‘APCalign’ can also provide state/territory distribution established status (native/introduced) APC. can access established status data state/territory using create_species_state_origin_matrix() breakdown possible values origin can also obtain breakdown species established status particular state/territory using state_diversity_counts() Using established status data state/territory information, can check plant taxa native using native_anywhere_in_australia()","code":"# Retrieve status data by state/territory status_matrix <- create_species_state_origin_matrix(resources = resources) library(purrr) library(janitor) # Obtain unique values status_matrix |> select(-species) |> flatten_chr() |> tabyl() #> flatten_chr(select(status_matrix, -species)) n percent #> doubtfully naturalised 1120 2.371003e-03 #> formerly naturalised 277 5.863998e-04 #> native 40336 8.538997e-02 #> native and doubtfully naturalised 9 1.905270e-05 #> native and naturalised 136 2.879075e-04 #> native and uncertain origin 2 4.233933e-06 #> naturalised 8765 1.855521e-02 #> not present 421606 8.925258e-01 #> presumed extinct 101 2.138136e-04 #> uncertain origin 22 4.657327e-05 state_diversity_counts(\"NSW\", resources = resources) #> # A tibble: 7 × 3 #> origin state num_species #> #> 1 doubtfully naturalised NSW 93 #> 2 formerly naturalised NSW 8 #> 3 native NSW 5958 #> 4 native and doubtfully naturalised NSW 2 #> 5 native and naturalised NSW 34 #> 6 naturalised NSW 1580 #> 7 presumed extinct NSW 8 library(dplyr) updated_gbif_names |> sample_n(1) |> # Choosing a random species pull(suggested_name) |> # Extracting this APC accepted name native_anywhere_in_australia(resources = resources) #> # A tibble: 1 × 2 #> species native_anywhere_in_aus #> #> 1 Solanum prinophyllum considered native to Australia by APC"},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"closer-look","dir":"Articles","previous_headings":"","what":"Closer look at name standardisation with ‘APCalign’","title":"APCalign","text":"create_taxonomic_update_lookup simple, wrapper, function novice users want quickly check standardise taxon names. experienced users, can take look sub functions match_taxa(), align_taxa() update_taxonomy() see taxon names processed, aligned updated.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"aligning-names-to-apc-and-apni","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’","what":"Aligning names to APC and APNI","title":"APCalign","text":"function align_taxa : functions standardise_names, strip_names strip_names_extra standardise infraspecific taxon designations clean punctuation whitespaces taxonomic name flows progression 50 match algorithms able aligned name either APC APNI list. include exact fuzzy matches. Fuzzy matches designed capture small spelling mistakes syntax errors phrase names. include matches entire name string matches just select words sequence. sequence matches carefully curated align names fewest mistakes. names can resolved genus, reformats name offer standardised genus sp. name, additional information/notes provided part original name square brackets, Acacia sp. [skinny leaves] Acacia sp. [Broken Hill] Determine taxonomic_reference (APC APNI) name-alignment. Note align_taxa seek update outdated taxonomy. process occurs update_taxonomy process. align_taxa instead aligns name input closest match amongst names documented APC APNI. every aligned_name, align_taxa() provide aligned_reason can review table counts:","code":"library(dplyr) aligned_gbif_taxa <- gbif_lite |> pull(species) |> align_taxa(resources = resources) #> Checking alignments of 121 taxa #> -> 0 names already matched; 0 names checked but without a match; 121 taxa yet to be checked aligned_gbif_taxa |> print(n = 6) #> # A tibble: 129 × 7 #> original_name cleaned_name aligned_name taxonomic_dataset taxon_rank aligned_reason #> #> 1 Tetratheca ciliata Tetratheca … Tetratheca … APC species Exact match o… #> 2 Peganum harmala Peganum har… Peganum har… APC species Exact match o… #> 3 Calotis multicaulis Calotis mul… Calotis mul… APC species Exact match o… #> 4 Leptospermum triner… Leptospermu… Leptospermu… APC species Exact match o… #> 5 Lepidosperma latera… Lepidosperm… Lepidosperm… APC species Exact match o… #> 6 Enneapogon polyphyl… Enneapogon … Enneapogon … APC species Exact match o… #> # ℹ 123 more rows #> # ℹ 1 more variable: alignment_code library(janitor) aligned_gbif_taxa |> pull(aligned_reason) |> tabyl() |> tibble() #> # A tibble: 6 × 4 #> `pull(aligned_gbif_taxa, aligned_reason)` n percent valid_percent #> #> 1 Exact match of taxon name to an APC-accepted canonical name o… 118 0.915 0.929 #> 2 Exact match of taxon name to an APC-known canonical name once… 6 0.0465 0.0472 #> 3 Exact match of taxon name to an APNI-listed canonical name on… 1 0.00775 0.00787 #> 4 Exact match of the first two words of the taxon name to an AP… 1 0.00775 0.00787 #> 5 Exact match of the first word of the taxon name to an APC-acc… 1 0.00775 0.00787 #> 6 2 0.0155 NA"},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"fuzzy-match","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’ > Aligning names to APC and APNI","what":"Configuring matching precision and aligned output","title":"APCalign","text":"arguments align_taxa allows select 50 matching algorithms activated/deactivated degree fuzziness fuzzy matching function fuzzy_matches turns fuzzy matching / (defaults TRUE). fuzzy_abs_dist fuzzy_rel_dist control degree fuzzy matching (default fuzzy_abs_dist = 3 & fuzzy_rel_dist = 0.2). imprecise_fuzzy_matches turns imprecise fuzzy matching / (defaults FALSE; true set fuzzy_abs_dist = 5 & fuzzy_rel_dist = 0.25). APNI_matches turns matches APNI list /(defaults TRUE). identifier allows specify text string added genus-level matches, indicating site, study, etc e.g. Acacia sp. [Blue Mountains]","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"update","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’","what":"Updating to APC-accepted names","title":"APCalign","text":"update_taxonomy() uses information generated align_taxa() , whenever possible, update names APC-accepted names.","code":"updated_gbif_taxa <- aligned_gbif_taxa |> update_taxonomy(resources = resources) updated_gbif_taxa |> print(n = 6) #> # A tibble: 129 × 21 #> original_name aligned_name accepted_name suggested_name genus family taxon_rank #> #> 1 Tetratheca ciliata Tetratheca c… Tetratheca c… Tetratheca ci… Tetr… Elaeo… species #> 2 Peganum harmala Peganum harm… Peganum harm… Peganum harma… Pega… Nitra… species #> 3 Calotis multicaulis Calotis mult… Calotis mult… Calotis multi… Calo… Aster… species #> 4 Leptospermum trinervium Leptospermum… Leptospermum… Leptospermum … Lept… Myrta… species #> 5 Lepidosperma laterale Lepidosperma… Lepidosperma… Lepidosperma … Lepi… Cyper… species #> 6 Enneapogon polyphyllus Enneapogon p… Enneapogon p… Enneapogon po… Enne… Poace… species #> # ℹ 123 more rows #> # ℹ 14 more variables: taxonomic_dataset , taxonomic_status , #> # taxonomic_status_aligned , aligned_reason , update_reason , #> # subclass , taxon_distribution , scientific_name_authorship , #> # taxon_ID , taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa "},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"taxonomic-resources-used-for-updating-names","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’ > Updating to APC-accepted names","what":"Taxonomic resources used for updating names","title":"APCalign","text":"APC includes previously recorded taxonomic names current taxon concept, designating currently-accepted name taxonomic_status: accepted, previously used inappropriately used names taxon concept alternative taxonomic statuses documented (e.g. taxonomic synonym, orthographic variant, misapplied). APC includes column acceptedNameUsageID links taxon name alternative taxonomic status current taxon name, allowing outdated/inappropriately used names synced current name. Note: Names listed APNI absent APC designated taxonomic_dataset: APNI APCalign. names currently unknown APC. time, list shrinks, taxonomists link ever occasionally used name variants APC-accepted taxon. However, now, names listed APNI updated","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"name-updates-at-different-taxonomic-levels","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’ > Updating to APC-accepted names","what":"Name updates at different taxonomic levels","title":"APCalign","text":"update_taxonomy() divides names lists based taxon_rank taxonomic_dataset assigned align_taxa, list requires different updating algorithms. taxonomic names designated taxon_rank = species/infraspecific taxonomic_dataset = APC can updated APC-accepted name. taxa, may possible align genus-name APC-accepted genus. taxa, suggested_name provided, selecting accepted_name available, otherwise aligned_name, , possible, updated, APC-accepted genus name.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/APCalign.html","id":"taxonomic-splits","dir":"Articles","previous_headings":"Closer look at name standardisation with ‘APCalign’ > Updating to APC-accepted names","what":"Taxonomic splits","title":"APCalign","text":"Taxonomic splits refers instances single taxon concept subsequently split multiple taxon concepts. taxa, aligned_name “old” taxon concept name, impossible know currently accepted taxon concepts name represents. function update_taxonomy includes argument taxonomic_splits, offering three alternative outputs taxon concepts split. most_likely_species default value, returns accepted_name original taxon_concept; alternative names documented square brackets part suggested name (Acacia aneura [alternative possible names: Acacia minyura (pro parte misapplied) | Acacia paraneura (pro parte misapplied) | Acacia quadrimarginea (misapplied)). return_all returns currently accepted names split original taxon_concept; leads increase number rows output table. (Acacia aneura, Acacia minyura Acacia paraneura output separate row, unique taxon_ID) collapse_to_higher_taxon declares split names, way certain accepted name appropriate therefore best possible match genus level; accepted_name returned, taxon_rank demoted genus suggested name documents possible species-level names square brackets (Acacia sp. [collapsed names: Acacia aneura (accepted) | Acacia minyura (pro parte misapplied) | Acacia paraneura (pro parte misapplied)])","code":"library(dplyr) aligned_gbif_taxa |> update_taxonomy(taxonomic_splits = \"most_likely_species\", resources = resources) |> filter(original_name == \"Acacia aneura\") # Subsetting Acacia aneura as an example #> # A tibble: 1 × 21 #> original_name aligned_name accepted_name suggested_name genus family taxon_rank #> #> 1 Acacia aneura Acacia aneura Acacia aneura Acacia aneura [alternat… Acac… Fabac… species #> # ℹ 14 more variables: taxonomic_dataset , taxonomic_status , #> # taxonomic_status_aligned , aligned_reason , update_reason , #> # subclass , taxon_distribution , scientific_name_authorship , #> # taxon_ID , taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa aligned_gbif_taxa |> update_taxonomy(taxonomic_splits = \"return_all\", resources = resources) |> filter(original_name == \"Acacia aneura\") # Subsetting Acacia aneura as an example #> # A tibble: 3 × 21 #> original_name aligned_name accepted_name suggested_name genus family taxon_rank #> #> 1 Acacia aneura Acacia aneura Acacia aneura Acacia aneura Acacia Fabaceae species #> 2 Acacia aneura Acacia aneura Acacia minyura Acacia minyura Acacia Fabaceae species #> 3 Acacia aneura Acacia aneura Acacia paraneura Acacia paraneura Acacia Fabaceae species #> # ℹ 14 more variables: taxonomic_dataset , taxonomic_status , #> # taxonomic_status_aligned , aligned_reason , update_reason , #> # subclass , taxon_distribution , scientific_name_authorship , #> # taxon_ID , taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa aligned_gbif_taxa |> update_taxonomy(taxonomic_splits = \"collapse_to_higher_taxon\", resources = resources) |> filter(original_name == \"Acacia aneura\") # Subsetting Acacia aneura as an example #> # A tibble: 1 × 21 #> original_name aligned_name accepted_name suggested_name genus family taxon_rank #> #> 1 Acacia aneura Acacia aneura Acacia sp. Acacia sp. [collapsed n… Acac… Fabac… species #> # ℹ 14 more variables: taxonomic_dataset , taxonomic_status , #> # taxonomic_status_aligned , aligned_reason , update_reason , #> # subclass , taxon_distribution , scientific_name_authorship , #> # taxon_ID , taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa "},{"path":"https://traitecoevo.github.io/APCalign/articles/data-providers.html","id":"australian-plant-census-apc","dir":"Articles","previous_headings":"","what":"Australian Plant Census (APC)","title":"Data Providers","text":"Australian Plant Census (APC) national taxonomic database accepted names Australian vascular plants. APC includes information synonyms, misapplications , well established status (native/introduced) distribution across states territories. ‘APCalign’ first attempt align plant names scientific names exist APC.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/data-providers.html","id":"australian-plant-names-index-apni","dir":"Articles","previous_headings":"","what":"Australian Plant Names Index (APNI)","title":"Data Providers","text":"Australian Plant Names Index (APNI) database containing names used Australian plants scientific literature. primarily used botanical community standardising synonyms. Importantly, APNI provide recommendations taxonomy nomenclature; APC indicates taxonomy considered accepted. ‘APCalign’ uses APNI alignment found APC.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/data-providers.html","id":"data-standards-and-meta-data","dir":"Articles","previous_headings":"","what":"Data standards and meta-data","title":"Data Providers","text":"Data APNI APC formatted according Darwin Core standard, widely used data standard biodiversity data. can find meta-data APC APNI : Meta-data APC output Meta-data APNI output details APNI APC, recommend taking read extensive documentation.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/reproducibility.html","id":"apcalign-r-package-version","dir":"Articles","previous_headings":"","what":"APCalign R package version","title":"How to be more reproducible with APCalign","text":"determine version APCalign package :","code":"packageVersion(\"APCalign\")"},{"path":"https://traitecoevo.github.io/APCalign/articles/reproducibility.html","id":"taxonomic-resources","dir":"Articles","previous_headings":"","what":"Taxonomic Resources","title":"How to be more reproducible with APCalign","text":"APCalign allows users load static downloads taxonomic resources APC APNI latest version National Species List website. functionality specified using stable_or_current_data argument load_taxonomic_resources(). want taxonomic alignment update reproducible, recommend always use stable_or_current_data = \"stable\". default value stable_or_current_data = \"stable\". static downloads version controlled stored repository releases. default, load_taxonomic_resources() load latest version static downloads. order transparent, recommend check latest default_version alignment copying pasting output load_taxonomic_resources() directly. way makes version taxonomic resources explicit code. ensure specific version taxonomic resources available subsequent functions make sure assign object: alignment update, make sure supply version taxonomic resources using resources argument:","code":"load_taxonomic_resources(stable_or_current_data = \"stable\") load_taxonomic_resources( stable_or_current_data = \"stable\", version = default_version() ) default_version() #> [1] \"2024-09-25\" resources_0.0.4.9000 <- load_taxonomic_resources( stable_or_current_data = \"stable\", version = \"0.0.4.9000\" ) # Align taxa aligned_taxa <- align_taxa(gbif_lite$species, resources = resources_0.0.4.9000) # Update taxonomy updated_taxa <- update_taxonomy(aligned_taxa, resources = resources_0.0.4.9000) # Align and update all-in-one aligned_updated_taxa <- create_taxonomic_update_lookup(gbif_lite$species, resources = resources_0.0.4.9000)"},{"path":"https://traitecoevo.github.io/APCalign/articles/reproducibility.html","id":"citing-the-r-package","dir":"Articles","previous_headings":"","what":"Citing the R package","title":"How to be more reproducible with APCalign","text":"completion, can also cite R package calling citation(). also research article introducing APCalign, share details citation press.","code":"citation(\"APCalign\") #> To cite package 'APCalign' in publications use: #> #> Wenk E, Cornwell W, Fuchs A, Kar F, Monro A, Sauquet H, Stephens R, #> Falster D (2024). \"APCalign: an R package workflow and app for #> aligning and updating flora names to the Australian Plant Census.\" #> _Australian Journal of Botany_. R package version: 1.0.1, #> . #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census}, #> journal = {Australian Journal of Botany}, #> author = {Elizabeth Wenk and Will Cornwell and Ann Fuchs and Fonti Kar and Anna Monro and Herve Sauquet and Ruby Stephens and Daniel Falster}, #> year = {2024}, #> note = {R package version: 1.0.1}, #> url = {https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1}, #> }"},{"path":"https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html","id":"aligning-taxon-names-with-taxon-conceptsnames-in-apc-and-apni","dir":"Articles","previous_headings":"","what":"Aligning taxon names with taxon concepts/names in APC and APNI","title":"Methods for updating taxon names in APCalign","text":"following table indicates rules 51 separate algorithms sequentially applied attempt align submitted name taxon concept APC scientific names APNI. Note, table truncated screen, use horizontal scroll view entire table.","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html","id":"updating-taxonomy","dir":"Articles","previous_headings":"","what":"Updating taxonomy","title":"Methods for updating taxon names in APCalign","text":"following table indicates separate functions used : update aligned names accepted names APC add best-practice suggested names submitted names add identifiers taxon concepts (APC) scientific names (APC APNI) Different functions used depending taxon rank aligned name taxonomic dataset name aligned (APC vs APNI). -* genus updated APC accepted genus possible; ** species infraspecific taxon name","code":""},{"path":"https://traitecoevo.github.io/APCalign/articles/updating-taxon-names.html","id":"outputs-of-apcalign","dir":"Articles","previous_headings":"","what":"Outputs of APCalign","title":"Methods for updating taxon names in APCalign","text":"following columns output core function create_taxonomic_update_lookup two component functions align_taxa update_taxonomy.","code":""},{"path":"https://traitecoevo.github.io/APCalign/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Daniel Falster. Author, maintainer, copyright holder. Elizabeth Wenk. Author, contributor. Cornwell. Author, contributor. Fonti Kar. Author, contributor. Carl Boettiger. Contributor.","code":""},{"path":"https://traitecoevo.github.io/APCalign/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Wenk E, Cornwell W, Fuchs , Kar F, Monro , Sauquet H, Stephens R, Falster D (2024). “APCalign: R package workflow app aligning updating flora names Australian Plant Census.” Australian Journal Botany. R package version: 1.0.1, https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1.","code":"@Article{, title = {APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census}, journal = {Australian Journal of Botany}, author = {Elizabeth Wenk and Will Cornwell and Ann Fuchs and Fonti Kar and Anna Monro and Herve Sauquet and Ruby Stephens and Daniel Falster}, year = {2024}, note = {R package version: 1.0.1}, url = {https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1}, }"},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"apcalign-","dir":"","previous_headings":"","what":"Resolving Plant Taxon Names Using the Australian Plant Census","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"APCalign uses Australian Plant Census (APC) Australian Plant Name Index align update Australian plant taxon name strings. ‘APCalign’ also supplies information established status (native/introduced) plant taxa across different states/territories. ’s useful updating species list intersecting APC consensus understanding established status (native/introduced).","code":""},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"CRAN: github version:","code":"install.packages(\"APCalign\") install.packages(\"remotes\") remotes::install_github(\"traitecoevo/APCalign\")"},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"a-quick-demo","dir":"","previous_headings":"","what":"A quick demo","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"Generating look-table can done just one function: ’re going use APCalign , save time load taxonomic resources memory first: Checking list species see classified Australian natives: Getting family lookup table genera specified taxonomy:","code":"library(APCalign) create_taxonomic_update_lookup( taxa = c( \"Banksia integrifolia\", \"Acacia longifolia\", \"Commersonia rosea\" ) ) #> ================================================================================================================================================================ #> # A tibble: 3 × 12 #> original_name aligned_name accepted_name suggested_name genus taxon_rank #> #> 1 Banksia integrifol… Banksia int… Banksia inte… Banksia integ… Bank… species #> 2 Acacia longifolia Acacia long… Acacia longi… Acacia longif… Acac… species #> 3 Commersonia rosea Commersonia… Androcalva r… Androcalva ro… Andr… species #> # ℹ 6 more variables: taxonomic_dataset , taxonomic_status , #> # scientific_name , aligned_reason , update_reason , #> # number_of_collapsed_taxa tax_resources <- load_taxonomic_resources() #> ================================================================================================================================================================ create_taxonomic_update_lookup( taxa = c( \"Banksia integrifolia\", \"Acacia longifolia\", \"Commersonia rosea\", \"not a species\" ), resources = tax_resources ) #> # A tibble: 4 × 12 #> original_name aligned_name accepted_name suggested_name genus taxon_rank #> #> 1 Banksia integrifol… Banksia int… Banksia inte… Banksia integ… Bank… species #> 2 Acacia longifolia Acacia long… Acacia longi… Acacia longif… Acac… species #> 3 Commersonia rosea Commersonia… Androcalva r… Androcalva ro… Andr… species #> 4 not a species #> # ℹ 6 more variables: taxonomic_dataset , taxonomic_status , #> # scientific_name , aligned_reason , update_reason , #> # number_of_collapsed_taxa native_anywhere_in_australia(c(\"Eucalyptus globulus\",\"Pinus radiata\"), resources = tax_resources) #> # A tibble: 2 × 2 #> species native_anywhere_in_aus #> #> 1 Eucalyptus globulus native #> 2 Pinus radiata introduced get_apc_genus_family_lookup(c(\"Eucalyptus\", \"Pinus\", \"Actinotus\", \"Banksia\", \"Acacia\", \"Triodia\"), resources = tax_resources) #> # A tibble: 6 × 2 #> genus family #> #> 1 Eucalyptus Myrtaceae #> 2 Pinus Pinaceae #> 3 Actinotus Apiaceae #> 4 Banksia Proteaceae #> 5 Acacia Fabaceae #> 6 Triodia Poaceae"},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"shiny-application","dir":"","previous_headings":"","what":"Shiny application","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"also developed shiny application non-R users update align taxonomic names. can find application : https://unsw.shinyapps.io/APCalign-app","code":""},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"learn-more","dir":"","previous_headings":"","what":"Learn more","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"Highly recommend looking Getting Started vignette learn use APCalign. can also learn taxa matching algorithm.","code":""},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"found-a-bug","dir":"","previous_headings":"","what":"Found a bug?","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"come across unexpected taxon name change? Elusive error can’t debug - submit issue try best help.","code":""},{"path":"https://traitecoevo.github.io/APCalign/index.html","id":"comments-and-contributions","dir":"","previous_headings":"","what":"Comments and contributions","title":"Resolving Plant Taxon Names Using the Australian Plant Census","text":"welcome comments contributions package, start submit issue can take !","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/APCalign.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardising Taxonomic Names in Australian Plants — APCalign","title":"Standardising Taxonomic Names in Australian Plants — APCalign","text":"process standardising taxon names necessary working biodiversity data. 'APCalign' uses Australian Plant Name Index (APNI) Australian Plant Census (APC) align update plant taxon names current, accepted standards. 'APCalign' can also supply information established status plant taxa across different states/territories.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/APCalign.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Standardising Taxonomic Names in Australian Plants — APCalign","text":"Standarise taxon names load_taxonomic_resources create_taxonomic_update_lookup align_taxa update_taxonomy Established status region state_diversity_counts create_species_state_origin_matrix native_anywhere_in_australia","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/APCalign.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Standardising Taxonomic Names in Australian Plants — APCalign","text":"questions, comments suggestions, please submit issue GitHub repository","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/APCalign.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Standardising Taxonomic Names in Australian Plants — APCalign","text":"Maintainer: Daniel Falster daniel.falster@unsw.edu.au (ORCID) [copyright holder] Authors: Elizabeth Wenk e.wenk@unsw.edu.au (ORCID) [contributor] Cornwell w.cornwell@unsw.edu.au (ORCID) [contributor] Fonti Kar f.kar@unsw.edu.au (ORCID) [contributor] contributors: Carl Boettiger cboettig@gmail.com (ORCID) [contributor]","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":null,"dir":"Reference","previous_headings":"","what":"Align Australian plant scientific names to the APC or APNI — align_taxa","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"list Australian plant names, find taxonomic scientific name alignments APC APNI standardizing formatting fixing spelling errors. Usage case: Users run function wish see details matching algorithms, many output columns matching function compares seeks best alignment. may also select function want adjust “fuzziness” level fuzzy matches, options allowed create_taxonomic_update_lookup. function first half create_taxonomic_update_lookup.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"","code":"align_taxa( original_name, output = NULL, full = FALSE, resources = load_taxonomic_resources(), quiet = FALSE, fuzzy_abs_dist = 3, fuzzy_rel_dist = 0.2, fuzzy_matches = TRUE, imprecise_fuzzy_matches = FALSE, APNI_matches = TRUE, identifier = NA_character_ )"},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"original_name list names query taxonomic alignments. output (optional) name file save results . full Parameter determine many columns output resources taxonomic resources used align taxa names. Loading can slow, call load_taxonomic_resources separately greatly speed function pass resources . quiet Logical indicate whether display messages aligning taxa. fuzzy_abs_dist number characters allowed different fuzzy match. fuzzy_rel_dist proportion characters allowed different fuzzy match. fuzzy_matches Fuzzy matches turned default. relative absolute distances allowed fuzzy matches species infraspecific taxon names defined parameters fuzzy_abs_dist fuzzy_rel_dist imprecise_fuzzy_matches Imprecise fuzzy matches uses fuzzy matching function lenient levels set (absolute distance 5 characters; relative distance = 0.25). offers way get wider range possible names, possibly corresponding distant spelling mistakes. FALSE default outputs checked often makes erroneous matches. APNI_matches Name matches APNI (Australian Plant Names Index) turned default. identifier dataset, location identifier, defaults NA.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"tibble columns include original_name, aligned_name, taxonomic_dataset, taxon_rank, aligned_reason, alignment_code. original_name: original plant name input. aligned_name: original plant name function standardise_names standardised syntax infraspecific taxon designations. taxonomic_dataset: source aligned names (APC APNI). taxon_rank: taxonomic rank aligned name. aligned_reason: explanation specific taxon name alignment (original name aligned name). alignment_code: code accompanies aligned_reason, indicating relative sequence match alignment process. cleaned_name: original name punctuation infraspecific taxon designation terms standardised function standardise_names; streamlines exact matches. stripped_name: cleaned name punctuation infraspecific taxon designation terms removed function strip_names; improves fuzzy matches. stripped_name2: cleaned name punctuation, infraspecific taxon designation terms, filler words removed function strip_names_extra; required matches first two word first three words. trinomial: first three words stripped_name2, required matches ignore text original_name; improves phrase name matches. binomial: first two words stripped_name2, required matches ignore text original_name; improves phrase name matches. genus: first two words cleaned_name; required genus-rank matches reprocessing genus-rank names. fuzzy_match_genus: fuzzy match genus column best match among APC-accepted names; required fuzzy matches genus-rank names. fuzzy_match_genus_synonym: fuzzy match genus column best match among APC-synonymous names, considering different matches documented APC-accepted genera; required fuzzy matches genus-rank names. fuzzy_match_genus_APNI: fuzzy match genus column best match among APNI names, considering different matches documented APC-accepted APC-known genera; required fuzzy matches genus-rank names. fuzzy_match_family: fuzzy match genus column best match among APC-accepted family names; required fuzzy matches family-rank names. fuzzy_match_family_synonym: fuzzy match genus column best match among APC-synonymous family names; required fuzzy matches family-rank names. fuzzy_match_cleaned_APC: fuzzy match stripped_name APC-accepted names; created yet---aligned names match step 05a function match_taxa. fuzzy_match_cleaned_APC_synonym: fuzzy match stripped_name APC-synonymous names; created yet---aligned names match step 05b function match_taxa. fuzzy_match_cleaned_APC_imprecise: imprecise fuzzy match stripped_name APC-accepted names; created yet---aligned names match step 07a function match_taxa. fuzzy_match_cleaned_APC_synonym_imprecise: imprecise fuzzy match stripped_name APC-accepted names; created yet---aligned names match step 07b function match_taxa. fuzzy_match_binomial: fuzzy match binomial column best match among APC-accepted names; created yet---aligned names match step 10c function match_taxa. fuzzy_match_binomial_APC_synonym: fuzzy match binomial column best match among APC-synonymous names; created yet---aligned names match step 10d function match_taxa. fuzzy_match_trinomial: fuzzy match trinomial column best match among APC-accepted names; created yet---aligned names match step 09c function match_taxa. fuzzy_match_trinomial_synonym: fuzzy match trinomial column best match among APC-synonymous names; created yet---aligned names match step 09d function match_taxa. fuzzy_match_cleaned_APNI: fuzzy match stripped_name APNI names; created yet---aligned names match step 11a function match_taxa. fuzzy_match_cleaned_APNI_imprecise: imprecise fuzzy match stripped_name APNI names; created yet---aligned names match step 11b function match_taxa.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"function finds taxonomic alignments APC scientific name alignments APNI. uses internal function match_taxa attempt match input strings taxon names APC/APNI. sequentially searches matches 20 different string patterns, prioritising exact matches (accepted names well synonyms, orthographic variants) fuzzy matches. prioritises matches taxa APC names APNI. identifies string patterns input names suggest name can aligned genus (hybrids APC/APNI; graded species; taxa identified species), indicates names genus-rank match. Notes: running function APCalign::create_taxonomic_update_lookup many times, best load taxonomic resources separately using resources <- load_taxonomic_resources(), add argument resources = resources name Banksia cerrata align fuzzy matching algorithm allow first letter genus species epithet change. function option changing fuzzy matching parameters. defaults, fuzzy matches allowing changes 3 (fewer) characters 20% (less) characters carefully calibrated catch just typos, , rarely mis-align name. wish introduce less conservative fuzzy matching recommended manually check aligned names. recommended begin imprecise_fuzzy_matches = FALSE (default), quite less precise fuzzy matches likely erroneous. argument turned plan check alignments manually. argument identifier allows add fix text string genus- family- level names, identifier = \"Royal NP\" return \"Acacia sp. [Royal NP]\".","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/align_taxa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Align Australian plant scientific names to the APC or APNI — align_taxa","text":"","code":"# \\donttest{ resources <- load_taxonomic_resources() #> Downloading... #> File downloaded successfully. #> File downloaded successfully. #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done # example 1 align_taxa(c(\"Poa annua\", \"Abies alba\"), resources=resources) #> Checking alignments of 2 taxa #> -> of these 1 names have a perfect match to a scientific name in the APC. #> Alignments being sought for remaining names. #> # A tibble: 2 × 7 #> original_name cleaned_name aligned_name taxonomic_dataset taxon_rank #> #> 1 Poa annua Poa annua Poa annua APC species #> 2 Abies alba Abies alba NA NA NA #> # ℹ 2 more variables: aligned_reason , alignment_code # example 2 input <- c(\"Banksia serrata\", \"Banksia serrate\", \"Banksia cerrata\", \"Banksia serrrrata\", \"Dryandra sp.\", \"Banksia big red flowers\") aligned_taxa <- APCalign::align_taxa( original_name = input, identifier = \"APCalign test\", full = TRUE, resources=resources ) #> Checking alignments of 6 taxa #> -> of these 1 names have a perfect match to a scientific name in the APC. #> Alignments being sought for remaining names. # }"},{"path":"https://traitecoevo.github.io/APCalign/reference/create_species_state_origin_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"State level native and introduced origin status — create_species_state_origin_matrix","title":"State level native and introduced origin status — create_species_state_origin_matrix","text":"function uses taxon distribution data APC determine state level native introduced origin status. function processes geographic data available APC returns state level native, introduced complicated origins status taxa.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/create_species_state_origin_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"State level native and introduced origin status — create_species_state_origin_matrix","text":"","code":"create_species_state_origin_matrix(resources = load_taxonomic_resources())"},{"path":"https://traitecoevo.github.io/APCalign/reference/create_species_state_origin_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"State level native and introduced origin status — create_species_state_origin_matrix","text":"resources taxonomic resources required make summary statistics. Loading can slow, call load_taxonomic_resources separately greatly speed function pass resources .","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/create_species_state_origin_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"State level native and introduced origin status — create_species_state_origin_matrix","text":"tibble columns representing state rows representing species. values cell represent origin species state.","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/create_species_state_origin_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"State level native and introduced origin status — create_species_state_origin_matrix","text":"","code":"create_species_state_origin_matrix() #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done #> # A tibble: 26,509 × 19 #> species WA NT Qld SA NSW Vic Tas ChI LHI CoI NI #> #> 1 Acanthus e… nati… nati… nati… not … not … not … not … not … not … not … not … #> 2 Acanthus i… not … nati… nati… not … not … not … not … not … not … not … not … #> 3 Acanthus m… natu… not … doub… natu… natu… natu… natu… not … not … not … not … #> 4 Andrograph… not … natu… doub… not … not … not … not … nati… not … not … not … #> 5 Asystasia … not … not … not … not … not … not … not … nati… not … not … not … #> 6 Asystasia … not … not … nati… not … not … not … not … not … not … not … not … #> 7 Asystasia … natu… natu… natu… not … natu… not … not … natu… not … not … not … #> 8 Asystasia … not … not … not … not … not … not … not … natu… not … not … not … #> 9 Asystasia … not … not … nati… not … not … not … not … not … not … not … not … #> 10 Asystasia … not … not … not … not … not … not … not … natu… not … not … not … #> # ℹ 26,499 more rows #> # ℹ 7 more variables: ACT , CSI , AR , MI , HI , #> # MDI , CaI "},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"function takes list Australian plant names need reconciled current taxonomy generates lookup table best-possible scientific name match input name. Usage case: APCalign’s core function, merging together alignment updating taxonomy.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"","code":"create_taxonomic_update_lookup( taxa, stable_or_current_data = \"stable\", version = default_version(), taxonomic_splits = \"most_likely_species\", full = FALSE, fuzzy_abs_dist = 3, fuzzy_rel_dist = 0.2, fuzzy_matches = TRUE, APNI_matches = TRUE, imprecise_fuzzy_matches = FALSE, identifier = NA_character_, resources = load_taxonomic_resources(), quiet = FALSE, output = NULL )"},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"taxa list Australian plant species needs reconciled current taxonomy. stable_or_current_data either \"stable\" consistent version, \"current\" leading edge version. version version number dataset use. taxonomic_splits handle one_to_many taxonomic matches. Default \"return_all\". options \"collapse_to_higher_taxon\" \"most_likely_species\". most_likely_species defaults original_name name accepted APC; right certain species subsets, make errors cases, use caution. full logical whether full lookup table returned just key columns fuzzy_abs_dist number characters allowed different fuzzy match. fuzzy_rel_dist proportion characters allowed different fuzzy match. fuzzy_matches Fuzzy matches turned default. relative absolute distances allowed fuzzy matches species infraspecific taxon names defined parameters fuzzy_abs_dist fuzzy_rel_dist. APNI_matches Name matches APNI (Australian Plant Names Index) turned default. imprecise_fuzzy_matches Imprecise fuzzy matches uses fuzzy matching function lenient levels set (absolute distance 5 characters; relative distance = 0.25). offers way get wider range possible names, possibly corresponding distant spelling mistakes. FALSE default outputs checked often makes erroneous matches. identifier dataset, location identifier, defaults NA. resources taxonomic resources used cleaning, default loading local place computer. called repeatedly, much faster load resources using load_taxonomic_resources separately pass data . quiet Logical indicate whether display messages aligning taxa. output file path save output. file already exists, function check subset species passed try add file. can useful large growing projects.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"lookup table containing accepted suggested names original name input, additional taxonomic information taxon rank, taxonomic status, taxon IDs genera. original_name: original plant name. aligned_name: input plant name aligned taxon name APC APNI align_taxa function. accepted_name: APC-accepted plant name, available. suggested_name: suggested plant name use. Identical accepted_name, accepted_name exists; otherwise suggested_name aligned_name. genus: genus accepted (suggested) name; APC-accepted genus names filled . family: family accepted (suggested) name; APC-accepted family names filled . taxon_rank: taxonomic rank suggested (accepted) name. taxonomic_dataset: source suggested (accepted) names (APC APNI). taxonomic_status: taxonomic status suggested (accepted) name. taxonomic_status_aligned: taxonomic status aligned name, taxonomic updates applied. aligned_reason: explanation specific taxon name alignment (original name aligned name). update_reason: explanation specific taxon name update (aligned name accepted suggested name). subclass: subclass accepted name. taxon_distribution: distribution accepted name; filled APC accepted_name available. scientific_name_authorship: authorship information accepted (synonymous) name; available APC APNI names. taxon_ID: unique taxon concept identifier accepted_name; filled APC accepted_name available. taxon_ID_genus: identifier genus; filled APC-accepted genus name available. scientific_name_ID: identifier nomenclatural (taxonomic) details scientific name; available APC APNI names. row_number: row number specific original_name input. number_of_collapsed_taxa: taxonomic_splits == \"collapse_to_higher_taxon\", number possible taxon names collapsed.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"uses first function align_taxa, function update_taxonomy achieve output. aligned name plant name aligned taxon name APC APNI align_taxa function. Notes: running function APCalign::create_taxonomic_update_lookup many times, best load taxonomic resources separately using resources <- load_taxonomic_resources(), add argument resources = resources name Banksia cerrata align fuzzy matching algorithm allow first letter genus species epithet change. argument taxonomic_splits allows choose outcome updating names taxa ambiguous taxonomic histories; applies scientific names attached broadly circumscribed taxon concept, split several narrowly circumscribed taxon concepts, one retains original name. three options: most_likely_species returns name retained, alternative names documented square brackets; return_all adds additional rows output, one possible taxon concept; collapse_to_higher_taxon returns genus possible names square brackets. argument identifier allows add fix text string genus- family- level names, identifier = \"Royal NP\" return Acacia sp. \\[Royal NP].","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/create_taxonomic_update_lookup.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a table with the best-possible scientific name match for Australian plant names — create_taxonomic_update_lookup","text":"","code":"# \\donttest{ resources <- load_taxonomic_resources() #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done # example 1 create_taxonomic_update_lookup(c(\"Eucalyptus regnans\", \"Acacia melanoxylon\", \"Banksia integrifolia\", \"Not a species\"), resources = resources) #> Checking alignments of 4 taxa #> -> of these 3 names have a perfect match to a scientific name in the APC. #> Alignments being sought for remaining names. #> # A tibble: 4 × 12 #> original_name aligned_name accepted_name suggested_name genus taxon_rank #> #> 1 Eucalyptus regnans Eucalyptus … Eucalyptus r… Eucalyptus re… Euca… species #> 2 Acacia melanoxylon Acacia mela… Acacia melan… Acacia melano… Acac… species #> 3 Banksia integrifol… Banksia int… Banksia inte… Banksia integ… Bank… species #> 4 Not a species NA NA NA NA NA #> # ℹ 6 more variables: taxonomic_dataset , taxonomic_status , #> # scientific_name , aligned_reason , update_reason , #> # number_of_collapsed_taxa # example 2 input <- c(\"Banksia serrata\", \"Banksia serrate\", \"Banksia cerrata\", \"Banksea serrata\", \"Banksia serrrrata\", \"Dryandra\") create_taxonomic_update_lookup( taxa = input, identifier = \"APCalign test\", full = TRUE, resources = resources ) #> Checking alignments of 6 taxa #> -> of these 1 names have a perfect match to a scientific name in the APC. #> Alignments being sought for remaining names. #> # A tibble: 6 × 21 #> original_name aligned_name accepted_name suggested_name genus family #> #> 1 Banksia serrata Banksia serrata Banksia serr… Banksia serra… Bank… Prote… #> 2 Banksia serrate Banksia serrata Banksia serr… Banksia serra… Bank… Prote… #> 3 Banksia cerrata Banksia sp. [Bank… NA Banksia sp. [… Bank… Prote… #> 4 Banksea serrata Banksia serrata Banksia serr… Banksia serra… Bank… Prote… #> 5 Banksia serrrrata Banksia serrata Banksia serr… Banksia serra… Bank… Prote… #> 6 Dryandra Dryandra sp. [Dry… NA Dryandra sp. … Drya… Eupho… #> # ℹ 15 more variables: taxon_rank , taxonomic_dataset , #> # taxonomic_status , taxonomic_status_aligned , #> # aligned_reason , update_reason , subclass , #> # taxon_distribution , scientific_name , taxon_ID , #> # taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa # example 3 taxon_list <- readr::read_csv( system.file(\"extdata\", \"test_taxa.csv\", package = \"APCalign\"), show_col_types = FALSE) create_taxonomic_update_lookup( taxa = taxon_list$original_name, identifier = taxon_list$notes, full = TRUE, resources = resources ) #> Checking alignments of 32 taxa #> -> of these 10 names have a perfect match to a scientific name in the APC. #> Alignments being sought for remaining names. #> # A tibble: 32 × 21 #> original_name aligned_name accepted_name suggested_name genus family #> #> 1 Banksia serrata Banksia ser… Banksia serr… Banksia serra… Bank… Prote… #> 2 Banksia serrate Banksia ser… Banksia serr… Banksia serra… Bank… Prote… #> 3 Banksee serrate Banksia ser… Banksia serr… Banksia serra… Bank… Prote… #> 4 Banksia cerrata Banksia sp.… NA Banksia sp. [… Bank… Prote… #> 5 Banksia sp. Banksia sp.… NA Banksia sp. [… Bank… Prote… #> 6 Dryandra sp. Dryandra sp… NA Dryandra sp. … Drya… Eupho… #> 7 Argyrodendron (Whyanb… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… #> 8 Argyrodendron ssp. (W… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… #> 9 Argyrodendron Whyanbe… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… #> 10 Argyrodendron sp. (Wh… Argyrodendr… Argyrodendro… Argyrodendron… Argy… Malva… #> # ℹ 22 more rows #> # ℹ 15 more variables: taxon_rank , taxonomic_dataset , #> # taxonomic_status , taxonomic_status_aligned , #> # aligned_reason , update_reason , subclass , #> # taxon_distribution , scientific_name , taxon_ID , #> # taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa # }"},{"path":"https://traitecoevo.github.io/APCalign/reference/default_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the default version for stable data — default_version","title":"Get the default version for stable data — default_version","text":"function returns default version stable data, used version specified.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/default_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the default version for stable data — default_version","text":"","code":"default_version()"},{"path":"https://traitecoevo.github.io/APCalign/reference/default_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the default version for stable data — default_version","text":"character string representing default version stable data.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/default_version.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the default version for stable data — default_version","text":"","code":"default_version() #> [1] \"2024-09-25\""},{"path":"https://traitecoevo.github.io/APCalign/reference/gbif_lite.html","id":null,"dir":"Reference","previous_headings":"","what":"GBIF Australian Plant Data — gbif_lite","title":"GBIF Australian Plant Data — gbif_lite","text":"subset plant data Global Biodiversity Information Facility","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/gbif_lite.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GBIF Australian Plant Data — gbif_lite","text":"","code":"gbif_lite"},{"path":"https://traitecoevo.github.io/APCalign/reference/gbif_lite.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"GBIF Australian Plant Data — gbif_lite","text":"gbif_lite tibble 129 rows 7 columns: species name first species scientificname infraspecificepithet name lowest terminal infraspecific epithet scientificname taxonrank taxonomic rank specific name decimalLongitude Longitude decimal degrees decimalLatitude Latitude decimal degrees scientificname Scientific Name verbatimscientificname Scientific name appeared original record","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/gbif_lite.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"GBIF Australian Plant Data — gbif_lite","text":"https://www.gbif.org/","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/get_apc_genus_family_lookup.html","id":null,"dir":"Reference","previous_headings":"","what":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","title":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","text":"Retrieve family name given genus using taxonomic data Australian Plant Census (APC).","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/get_apc_genus_family_lookup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","text":"","code":"get_apc_genus_family_lookup(genus, resources = load_taxonomic_resources())"},{"path":"https://traitecoevo.github.io/APCalign/reference/get_apc_genus_family_lookup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","text":"genus character vector genus names retrieve corresponding family names. resources taxonomic resources required make lookup. Loading can slow, call load_taxonomic_resources separately speed function pass resources .","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/get_apc_genus_family_lookup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","text":"data frame two columns: \"genus\", indicating genus name, \"family\", indicating corresponding family name APC.","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/get_apc_genus_family_lookup.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lookup Family by Genus from APC — get_apc_genus_family_lookup","text":"","code":"get_apc_genus_family_lookup(genus = c(\"Acacia\", \"Eucalyptus\")) #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done #> # A tibble: 2 × 2 #> genus family #> #> 1 Acacia Fabaceae #> 2 Eucalyptus Myrtaceae"},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":null,"dir":"Reference","previous_headings":"","what":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"function loads two taxonomic datasets Australia's vascular plants, APC APNI, global environment. creates several data frames filtering selecting data loaded lists.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"","code":"load_taxonomic_resources( stable_or_current_data = \"stable\", version = default_version(), quiet = FALSE )"},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"stable_or_current_data Type dataset access. default \"stable\", loads dataset github archived file. set \"current\", dataset loaded URL cutting edge version, may change time without notice. version version number dataset use. Defaults default version. quiet logical indicating whether print status loading screen. Defaults FALSE.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"taxonomic resources data loaded global environment.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"accesses taxonomic data dataset using provided version number default version. output several dataframes include subsets APC/APNI based taxon rank taxonomic status.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/load_taxonomic_resources.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load taxonomic reference lists, APC & APNI — load_taxonomic_resources","text":"","code":"# \\donttest{ load_taxonomic_resources(stable_or_current_data=\"stable\", version=\"0.0.2.9000\")# } #> Downloading... #> File downloaded successfully. #> File downloaded successfully. #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done #> $APC #> # A tibble: 109,624 × 38 #> taxon_ID name_type accepted_name_usage_ID accepted_name_usage #> #> 1 https://id.biodiversity… scientif… https://id.biodiversi… Plantae Haeckel #> 2 https://id.biodiversity… scientif… https://id.biodiversi… Charophyta Sachs #> 3 https://id.biodiversity… scientif… https://id.biodiversi… Charophyta Sachs #> 4 https://id.biodiversity… scientif… https://id.biodiversi… Equisetopsida C.Ag… #> 5 https://id.biodiversity… scientif… https://id.biodiversi… Equisetopsida C.Ag… #> 6 https://id.biodiversity… scientif… https://id.biodiversi… Equisetopsida C.Ag… #> 7 https://id.biodiversity… scientif… https://id.biodiversi… Cycadidae Pax #> 8 https://id.biodiversity… scientif… https://id.biodiversi… Cycadales Pers. ex… #> 9 https://id.biodiversity… scientif… https://id.biodiversi… Cycadales Pers. ex… #> 10 https://id.biodiversity… scientif… https://id.biodiversi… Cycadales Pers. ex… #> # ℹ 109,614 more rows #> # ℹ 34 more variables: nomenclaturalStatus , nomIlleg , #> # nomInval , taxonomic_status , pro_parte , #> # scientific_name , scientific_name_ID , canonical_name , #> # scientific_name_authorship , parentNameUsageID , #> # taxon_rank , taxon_rank_sort_order , kingdom , class , #> # subclass , family , taxonConceptID , … #> #> $APNI #> # A tibble: 132,385 × 48 #> scientific_name_ID name_type scientific_name scientificNameHTML #> #> 1 https://id.biodiversity.org.au/… scientif… Acanthus ebrac… 2 https://id.biodiversity.org.au/… autonym Acanthus ebrac… 3 https://id.biodiversity.org.au/… scientif… Acanthus ebrac… 4 https://id.biodiversity.org.au/… autonym Acanthus ilici… 5 https://id.biodiversity.org.au/… scientif… Acanthus ilici… 6 https://id.biodiversity.org.au/… scientif… Acanthus ilici… 7 https://id.biodiversity.org.au/… scientif… Acanthus ilici… 8 https://id.biodiversity.org.au/… scientif… Acanthus molli… 9 https://id.biodiversity.org.au/… scientif… Acanthus volub… 10 https://id.biodiversity.org.au/… scientif… Acanthus L. # ℹ 132,375 more rows #> # ℹ 44 more variables: canonical_name , canonicalNameHTML , #> # name_element , nomenclaturalStatus , #> # scientific_name_authorship , autonym , hybrid , #> # cultivar , formula , scientific , nomInval , #> # nomIlleg , namePublishedIn , namePublishedInID , #> # namePublishedInYear , nameInstanceType , … #> #> $`APC list (accepted)` #> # A tibble: 30,538 × 15 #> canonical_name scientific_name taxonomic_status taxon_ID scientific_name_ID #> #> 1 Cycas angulata Cycas angulata… accepted https:/… https://id.biodiv… #> 2 Cycas arenicola Cycas arenicol… accepted https:/… https://id.biodiv… #> 3 Cycas armstrong… Cycas armstron… accepted https:/… https://id.biodiv… #> 4 Cycas arnhemica Cycas arnhemic… accepted https:/… https://id.biodiv… #> 5 Cycas badensis Cycas badensis… accepted https:/… https://id.biodiv… #> 6 Cycas basaltica Cycas basaltic… accepted https:/… https://id.biodiv… #> 7 Cycas brunnea Cycas brunnea … accepted https:/… https://id.biodiv… #> 8 Cycas cairnsiana Cycas cairnsia… accepted https:/… https://id.biodiv… #> 9 Cycas calcicola Cycas calcicol… accepted https:/… https://id.biodiv… #> 10 Cycas canalis Cycas canalis … accepted https:/… https://id.biodiv… #> # ℹ 30,528 more rows #> # ℹ 10 more variables: accepted_name_usage_ID , name_type , #> # taxon_rank , genus , stripped_canonical , #> # stripped_canonical2 , stripped_scientific , binomial , #> # trinomial , taxonomic_dataset #> #> $`APC list (known names)` #> # A tibble: 69,647 × 15 #> canonical_name scientific_name taxonomic_status taxon_ID scientific_name_ID #> #> 1 Pterostylis cli… Pterostylis cl… alternative name https:/… https://id.biodiv… #> 2 Pterostylis cre… Pterostylis cr… alternative name https:/… https://id.biodiv… #> 3 Eucalyptus resi… Eucalyptus res… alternative name https:/… https://id.biodiv… #> 4 Macrozamia paul… Macrozamia pau… basionym https:/… https://id.biodiv… #> 5 Lycopodium creb… Lycopodium cre… basionym https:/… https://id.biodiv… #> 6 Lycopodium lock… Lycopodium loc… basionym https:/… https://id.biodiv… #> 7 Aralia polaris Aralia polaris… basionym https:/… https://id.biodiv… #> 8 Sium nodiflorum Sium nodifloru… basionym https:/… https://id.biodiv… #> 9 Trachymene koch… Trachymene koc… basionym https:/… https://id.biodiv… #> 10 Pittosporum res… Pittosporum re… basionym https:/… https://id.biodiv… #> # ℹ 69,637 more rows #> # ℹ 10 more variables: accepted_name_usage_ID , name_type , #> # taxon_rank , genus , stripped_canonical , #> # stripped_canonical2 , stripped_scientific , binomial , #> # trinomial , taxonomic_dataset #> #> $`APNI names` #> # A tibble: 15,379 × 13 #> canonical_name scientific_name scientific_name_ID name_type taxon_rank #> #> 1 (Eucalyptus globulus… (Eucalyptus gl… https://id.biodiv… hybrid-f… species #> 2 (Eucalyptus globulus… (Eucalyptus gl… https://id.biodiv… hybrid-f… species #> 3 (Eucalyptus johnston… (Eucalyptus jo… https://id.biodiv… hybrid-f… species #> 4 (Eucalyptus johnston… (Eucalyptus jo… https://id.biodiv… hybrid-f… species #> 5 (Eucalyptus urnigera… (Eucalyptus ur… https://id.biodiv… hybrid-f… species #> 6 (Eucalyptus urnigera… (Eucalyptus ur… https://id.biodiv… hybrid-f… species #> 7 Abacopteris presliana Abacopteris pr… https://id.biodiv… scientif… species #> 8 Abarema clypearia f.… Abarema clypea… https://id.biodiv… scientif… form #> 9 Abarema pruinosa Abarema pruino… https://id.biodiv… scientif… species #> 10 Abelia rupestris Abelia rupestr… https://id.biodiv… scientif… species #> # ℹ 15,369 more rows #> # ℹ 8 more variables: taxonomic_status , stripped_canonical , #> # stripped_canonical2 , stripped_scientific , binomial , #> # trinomial , genus , taxonomic_dataset #> #> $genera_accepted #> # A tibble: 3,094 × 11 #> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name #> #> 1 Cycas Cycas L. https://id.biodiversity.o… Cycas L. #> 2 Bowenia Bowenia Hook.f. https://id.biodiversity.o… Bowenia Hook.f. #> 3 Lepidozamia Lepidozamia Regel https://id.biodiversity.o… Lepidozamia Re… #> 4 Macrozamia Macrozamia Miq. https://id.biodiversity.o… Macrozamia Miq. #> 5 Equisetum Equisetum L. https://id.biodiversity.o… Equisetum L. #> 6 Isoetes Isoetes L. https://id.biodiversity.o… Isoetes L. #> 7 Huperzia Huperzia Bernh. https://id.biodiversity.o… Huperzia Bernh. #> 8 Lycopodiella Lycopodiella Holub https://id.biodiversity.o… Lycopodiella H… #> 9 Lycopodium Lycopodium L. https://id.biodiversity.o… Lycopodium L. #> 10 Phlegmariurus Phlegmariurus Holub https://id.biodiversity.o… Phlegmariurus … #> # ℹ 3,084 more rows #> # ℹ 7 more variables: taxonomic_status , taxon_ID , #> # scientific_name_ID , name_type , taxon_rank , genus , #> # taxonomic_dataset #> #> $genera_synonym #> # A tibble: 2,848 × 11 #> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name #> #> 1 Encephallartes Encephalartos Lehm. https://id.biodiversity… Encephallartes… #> 2 Encephalartus Encephalartos Lehm. https://id.biodiversity… Encephalartus … #> 3 Encephalartos Encephalartos Lehm. https://id.biodiversity… Encephalartos … #> 4 Catakidozamia Lepidozamia Regel https://id.biodiversity… Catakidozamia … #> 5 Zamia Zamia L. https://id.biodiversity… Zamia L. #> 6 Calamaria Isoetes L. https://id.biodiversity… Calamaria Boeh… #> 7 Lateristachys Lycopodiella Holub https://id.biodiversity… Lateristachys … #> 8 Lepidotis Lycopodiella Holub https://id.biodiversity… Lepidotis P.Be… #> 9 Austrolycopodium Lycopodium L. https://id.biodiversity… Austrolycopodi… #> 10 Diphasium Lycopodium L. https://id.biodiversity… Diphasium C.Pr… #> # ℹ 2,838 more rows #> # ℹ 7 more variables: taxonomic_status , taxon_ID , #> # scientific_name_ID , name_type , taxon_rank , genus , #> # taxonomic_dataset #> #> $genera_APNI #> # A tibble: 1,426 × 8 #> canonical_name scientific_name taxonomic_status scientific_name_ID name_type #> #> 1 Beloperone Beloperone Nees unplaced https://id.biodiv… scientif… #> 2 Hemiadelphis Hemiadelphis Ne… unplaced https://id.biodiv… scientif… #> 3 Leptosiphonium Leptosiphonium … unplaced https://id.biodiv… scientif… #> 4 Megaskepasma Megaskepasma Li… unplaced https://id.biodiv… scientif… #> 5 Meyenia Meyenia Nees unplaced https://id.biodiv… scientif… #> 6 Simonachne Simonachne E.J.… unplaced https://id.biodiv… scientif… #> 7 Thyrsacanthus Thyrsacanthus N… unplaced https://id.biodiv… scientif… #> 8 Synarrhena Synarrhena F.Mu… unplaced https://id.biodiv… scientif… #> 9 Allosorus Allosorus Bernh. unplaced https://id.biodiv… scientif… #> 10 Austrogramme Austrogramme E.… unplaced https://id.biodiv… scientif… #> # ℹ 1,416 more rows #> # ℹ 3 more variables: taxon_rank , genus , taxonomic_dataset #> #> $genera_all #> # A tibble: 7,368 × 12 #> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name #> #> 1 Cycas Cycas L. https://id.biodiversity.o… Cycas L. #> 2 Bowenia Bowenia Hook.f. https://id.biodiversity.o… Bowenia Hook.f. #> 3 Lepidozamia Lepidozamia Regel https://id.biodiversity.o… Lepidozamia Re… #> 4 Macrozamia Macrozamia Miq. https://id.biodiversity.o… Macrozamia Miq. #> 5 Equisetum Equisetum L. https://id.biodiversity.o… Equisetum L. #> 6 Isoetes Isoetes L. https://id.biodiversity.o… Isoetes L. #> 7 Huperzia Huperzia Bernh. https://id.biodiversity.o… Huperzia Bernh. #> 8 Lycopodiella Lycopodiella Holub https://id.biodiversity.o… Lycopodiella H… #> 9 Lycopodium Lycopodium L. https://id.biodiversity.o… Lycopodium L. #> 10 Phlegmariurus Phlegmariurus Holub https://id.biodiversity.o… Phlegmariurus … #> # ℹ 7,358 more rows #> # ℹ 8 more variables: taxonomic_status , taxon_ID , #> # scientific_name_ID , name_type , taxon_rank , genus , #> # taxonomic_dataset , cleaned_name #> #> $family_accepted #> # A tibble: 307 × 38 #> taxon_ID name_type accepted_name_usage_ID accepted_name_usage #> #> 1 https://id.biodiversity… scientif… https://id.biodiversi… Cycadaceae Pers. #> 2 https://id.biodiversity… scientif… https://id.biodiversi… Zamiaceae Horan. #> 3 https://id.biodiversity… scientif… https://id.biodiversi… Equisetaceae Michx… #> 4 https://id.biodiversity… scientif… https://id.biodiversi… Isoetaceae Rchb. #> 5 https://id.biodiversity… scientif… https://id.biodiversi… Lycopodiaceae P.Be… #> 6 https://id.biodiversity… scientif… https://id.biodiversi… Selaginellaceae Wi… #> 7 https://id.biodiversity… scientif… https://id.biodiversi… Apiaceae Lindl. #> 8 https://id.biodiversity… scientif… https://id.biodiversi… Araliaceae Juss. #> 9 https://id.biodiversity… scientif… https://id.biodiversi… Griseliniaceae J.R… #> 10 https://id.biodiversity… scientif… https://id.biodiversi… Myodocarpaceae Dow… #> # ℹ 297 more rows #> # ℹ 34 more variables: nomenclaturalStatus , nomIlleg , #> # nomInval , taxonomic_status , pro_parte , #> # scientific_name , scientific_name_ID , canonical_name , #> # scientific_name_authorship , parentNameUsageID , #> # taxon_rank , taxon_rank_sort_order , kingdom , class , #> # subclass , family , taxonConceptID , … #> #> $family_synonym #> # A tibble: 244 × 11 #> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name #> #> 1 Boweniaceae Zamiaceae Horan. https://id.biodiversi… Boweniaceae D.… #> 2 Lycopodia Lycopodiaceae P.Bea… https://id.biodiversi… Lycopodia Mirb. #> 3 Umbelliferae Apiaceae Lindl. https://id.biodiversi… Umbelliferae J… #> 4 Araliae Araliaceae Juss. https://id.biodiversi… Araliae Juss. #> 5 Griselineae Griseliniaceae J.R.… https://id.biodiversi… Griselineae A.… #> 6 Pittosporeae Pittosporaceae R.Br. https://id.biodiversi… Pittosporeae R… #> 7 Cardiopterideae Cardiopteridaceae B… https://id.biodiversi… Cardiopteridea… #> 8 Quintiniaceae Paracryphiaceae Air… https://id.biodiversi… Quintiniaceae … #> 9 Sphenostemonaceae Paracryphiaceae Air… https://id.biodiversi… Sphenostemonac… #> 10 Compositae Asteraceae Bercht. … https://id.biodiversi… Compositae Gis… #> # ℹ 234 more rows #> # ℹ 7 more variables: taxonomic_status , taxon_ID , #> # scientific_name_ID , name_type , taxon_rank , genus , #> # taxonomic_dataset #>"},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":null,"dir":"Reference","previous_headings":"","what":"Native anywhere in Australia — native_anywhere_in_australia","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"function checks species list thought native anywhere Australia according APC.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"","code":"native_anywhere_in_australia(species, resources = load_taxonomic_resources())"},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"species character string typically representing binomial species. resources optional list taxonomic resources use lookup. provided, function load default taxonomic resources using load_taxonomic_resources() function.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"tibble two columns: species, unique values input species, native_anywhere_in_aus, vector indicating whether species native anywhere Australia, introduced humans elsewhere, unknown respect APC resource.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"Important caveats: function detect within-Australia introductions, e.g. species Western Australia invasive east coast. recent invasions unlikely documented yet APC. Ideally check spelling taxonomy updates first via create_taxonomic_update_lookup. complete matrix species states also represents within-Australia invasions, use create_species_state_origin_matrix.","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/native_anywhere_in_australia.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Native anywhere in Australia — native_anywhere_in_australia","text":"","code":"native_anywhere_in_australia(c(\"Eucalyptus globulus\",\"Pinus radiata\",\"Banksis notaspecies\")) #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done #> Warning: At least one input not found in APC; make sure inputs are at the species level and consider using `create_taxonomic_update_lookup` first. #> # A tibble: 3 × 2 #> species native_anywhere_in_aus #> #> 1 Eucalyptus globulus native #> 2 Pinus radiata introduced #> 3 Banksis notaspecies unknown"},{"path":"https://traitecoevo.github.io/APCalign/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. dplyr %>%","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardise taxon names — standardise_names","title":"Standardise taxon names — standardise_names","text":"Standardises taxon names performing series text substitutions remove common inconsistencies taxonomic nomenclature. function takes character vector taxon names input returns character vector taxon names using standardised taxonomic syntax output.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standardise taxon names — standardise_names","text":"","code":"standardise_names(taxon_names)"},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standardise taxon names — standardise_names","text":"taxon_names character vector taxon names need standardised.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standardise taxon names — standardise_names","text":"character vector standardised taxon names.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standardise taxon names — standardise_names","text":"removes stray punctuation start end character string. standardises unusual characters symbols ASCII equivalents. standardises taxon rank abbreviations qualifiers (subsp., var., f.), people use many variants terms. standardises removes additional filler words used within taxon names (affinis becomes aff.; s.l. s.s. removed).","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Standardise taxon names — standardise_names","text":"","code":"standardise_names(c(\"Quercus suber\", \"Eucalyptus sp.\", \"Eucalyptus spp.\", \"Agave americana var. marginata\", \"Agave americana v marginata\", \"Notelaea longifolia forma longifolia\", \"Notelaea longifolia f longifolia\")) #> [1] \"Quercus suber\" \"Eucalyptus sp.\" #> [3] \"Eucalyptus sp.\" \"Agave americana var. marginata\" #> [5] \"Agave americana var. marginata\" \"Notelaea longifolia f. longifolia\" #> [7] \"Notelaea longifolia f. longifolia\""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardise taxon ranks — standardise_taxon_rank","title":"Standardise taxon ranks — standardise_taxon_rank","text":"Standardise taxon ranks Latin English.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standardise taxon ranks — standardise_taxon_rank","text":"","code":"standardise_taxon_rank(taxon_rank)"},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standardise taxon ranks — standardise_taxon_rank","text":"taxon_rank character vector Latin taxon ranks.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standardise taxon ranks — standardise_taxon_rank","text":"character vector English taxon ranks.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standardise taxon ranks — standardise_taxon_rank","text":"function takes character vector Latin taxon ranks input returns character vector taxon ranks using standardised English terms.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/standardise_taxon_rank.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Standardise taxon ranks — standardise_taxon_rank","text":"","code":"standardise_taxon_rank(c(\"regnum\", \"kingdom\", \"classis\", \"class\")) #> [1] \"kingdom\" \"kingdom\" \"class\" \"class\""},{"path":"https://traitecoevo.github.io/APCalign/reference/state_diversity_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"State- and territory-level diversity — state_diversity_counts","title":"State- and territory-level diversity — state_diversity_counts","text":"Australian states territories, use geographic distribution data APC calculate state-level diversity native, introduced, complicated species origins","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/state_diversity_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"State- and territory-level diversity — state_diversity_counts","text":"","code":"state_diversity_counts(state, resources = load_taxonomic_resources())"},{"path":"https://traitecoevo.github.io/APCalign/reference/state_diversity_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"State- and territory-level diversity — state_diversity_counts","text":"state character string indicating Australian state territory calculate diversity . Possible values \"NSW\", \"NT\", \"Qld\", \"WA\", \"ChI\", \"SA\", \"Vic\", \"Tas\", \"ACT\", \"NI\", \"LHI\", \"MI\", \"HI\", \"MDI\", \"CoI\", \"CSI\", \"AR\". resources taxonomic resources required make summary statistics. loading can slow, call load_taxonomic_resources separately greatly speed function pass resources .","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/state_diversity_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"State- and territory-level diversity — state_diversity_counts","text":"tibble diversity counts specified state territory, including native, introduced, complicated species origins. tibble three columns: \"origin\" indicating origin species, \"state\" indicating Australian state territory, \"num_species\" indicating number species origin state.","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/state_diversity_counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"State- and territory-level diversity — state_diversity_counts","text":"","code":"state_diversity_counts(state = \"NSW\") #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done #> # A tibble: 7 × 3 #> origin state num_species #> #> 1 doubtfully naturalised NSW 94 #> 2 formerly naturalised NSW 8 #> 3 native NSW 5959 #> 4 native and doubtfully naturalised NSW 2 #> 5 native and naturalised NSW 34 #> 6 naturalised NSW 1583 #> 7 presumed extinct NSW 9"},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Strip taxon names — strip_names","title":"Strip taxon names — strip_names","text":"Strip taxonomic names taxon rank abbreviations qualifiers special characters","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Strip taxon names — strip_names","text":"","code":"strip_names(taxon_names)"},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Strip taxon names — strip_names","text":"taxon_names character vector taxonomic names stripped.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Strip taxon names — strip_names","text":"character vector stripped taxonomic names, subtaxa designations, special characters, extra whitespace removed, letters converted lowercase.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Strip taxon names — strip_names","text":"Given vector taxonomic names, function removes: subtaxa designations (\"subsp.\", \"var.\", \"f.\", \"ser\") special characters (e.g., \"-\", \".\", \"(\", \")\", \"?\") extra whitespace resulting vector names also converted lowercase.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Strip taxon names — strip_names","text":"","code":"strip_names(c(\"Abies lasiocarpa subsp. lasiocarpa\", \"Quercus kelloggii\", \"Pinus contorta var. latifolia\")) #> [1] \"abies lasiocarpa lasiocarpa\" \"quercus kelloggii\" #> [3] \"pinus contorta latifolia\""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":null,"dir":"Reference","previous_headings":"","what":"Strip taxon names, extra — strip_names_extra","title":"Strip taxon names, extra — strip_names_extra","text":"Strip taxonomic names sp. hybrid symbols. function assumes character function already run strip_names.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Strip taxon names, extra — strip_names_extra","text":"","code":"strip_names_extra(taxon_names)"},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Strip taxon names, extra — strip_names_extra","text":"taxon_names character vector taxonomic names stripped.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Strip taxon names, extra — strip_names_extra","text":"character vector stripped taxonomic names, sp. hybrid symbols removed.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Strip taxon names, extra — strip_names_extra","text":"Given vector taxonomic names, function removes additional filler words (\" x \" hybrid taxa, \"sp.\") removed function strip_names","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/strip_names_extra.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Strip taxon names, extra — strip_names_extra","text":"","code":"strip_names_extra(c(\"Abies lasiocarpa subsp. lasiocarpa\", \"Quercus kelloggii\", \"Pinus contorta var. latifolia\", \"Acacia sp.\", \"Lepidium sp. Tanguin Hill (K.R.Newbey 10501)\")) #> [1] \"Abies lasiocarpa subsp. lasiocarpa\" #> [2] \"Quercus kelloggii\" #> [3] \"Pinus contorta var. latifolia\" #> [4] \"Acacia sp.\" #> [5] \"Lepidium sp. Tanguin Hill (K.R.Newbey 10501)\""},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":null,"dir":"Reference","previous_headings":"","what":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"list taxon names aligned APC, update name accepted taxon concept per APC add scientific name taxon concept metadata names aligned either APC APNI.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"","code":"update_taxonomy( aligned_data, taxonomic_splits = \"most_likely_species\", quiet = TRUE, output = NULL, resources = load_taxonomic_resources() )"},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"aligned_data tibble plant names update. table must include 5 columns, original_name, aligned_name, taxon_rank, taxonomic_dataset, aligned_reason. columns created function align_taxa. columns original_name aligned_name must format scientific name, genus species, may contain additional qualifiers subspecies varieties. names case insensitive. taxonomic_splits Variable determines protocol use update taxon names ambiguous due taxonomic splits. three options : most_likely_species, returns species name use split; alternative names returned separate column return_all, returns possible names collapse_to_higher_taxon, declares ambiguous name aligned accepted species/infraspecific name name demoted genus rank quiet Logical indicate whether display messages updating taxa. output (optional) Name file results saved. default NULL file created. specified, output saved CSV file given name. resources taxonomic resources required make summary statistics. Loading can slow, call load_taxonomic_resources separately greatly speed function pass resources .","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"tibble updated taxonomy specified plant names. tibble contains following columns: original_name: original plant name. aligned_name: input plant name aligned taxon name APC APNI align_taxa function. accepted_name: APC-accepted plant name, available. suggested_name: suggested plant name use. Identical accepted_name, accepted_name exists; otherwise suggested_name aligned_name. genus: genus accepted (suggested) name; APC-accepted genus names filled . family: family accepted (suggested) name; APC-accepted family names filled . taxon_rank: taxonomic rank suggested (accepted) name. taxonomic_dataset: source suggested (accepted) names (APC APNI). taxonomic_status: taxonomic status suggested (accepted) name. taxonomic_status_aligned: taxonomic status aligned name, taxonomic updates applied. aligned_reason: explanation specific taxon name alignment (original name aligned name). update_reason: explanation specific taxon name update (aligned name accepted suggested name). subclass: subclass accepted name. taxon_distribution: distribution accepted name; filled APC accepted_name available. scientific_name_authorship: authorship information accepted (synonymous) name; available APC APNI names. taxon_ID: unique taxon concept identifier accepted_name; filled APC accepted_name available. taxon_ID_genus: identifier genus; filled APC-accepted genus name available. scientific_name_ID: identifier nomenclatural (taxonomic) details scientific name; available APC APNI names. row_number: row number specific original_name input. number_of_collapsed_taxa: taxonomic_splits == \"collapse_to_higher_taxon\", number possible taxon names collapsed.","code":""},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"function uses APC update taxonomy names aligned taxon concept listed APC currently accepted name taxon concept. aligned_data data frame input must contain 5 columns, original_name, aligned_name, taxon_rank, taxonomic_dataset, aligned_reason. (columns output function align_taxa.) aligned name plant name aligned taxon name APC APNI align_taxa function. Notes: input function table 5 columns (output align_taxa), function used explicitly want separate alignment updating components APCalign. function second half create_taxonomic_update_lookup.","code":""},{"path":[]},{"path":"https://traitecoevo.github.io/APCalign/reference/update_taxonomy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update to currently accepted APC name and add APC/APNI name metadata — update_taxonomy","text":"","code":"# Update taxonomy for two plant names and print the result # \\donttest{ resources <- load_taxonomic_resources() #> #> Loading resources into memory... #> =========================== ===================================================== ================================================================================ #> ...done update_taxonomy( dplyr::tibble( original_name = c(\"Dryandra preissii\", \"Banksia acuminata\"), aligned_name = c(\"Dryandra preissii\", \"Banksia acuminata\"), taxon_rank = c(\"species\", \"species\"), taxonomic_dataset = c(\"APC\", \"APC\"), aligned_reason = c(NA_character_, NA_character_) ), resources = resources ) #> # A tibble: 2 × 21 #> original_name aligned_name accepted_name suggested_name genus family #> #> 1 Dryandra preissii Dryandra preissii Banksia acumi… Banksia acumi… Bank… Prote… #> 2 Banksia acuminata Banksia acuminata Banksia acumi… Banksia acumi… Bank… Prote… #> # ℹ 15 more variables: taxon_rank , taxonomic_dataset , #> # taxonomic_status , taxonomic_status_aligned , #> # aligned_reason , update_reason , subclass , #> # taxon_distribution , scientific_name , taxon_ID , #> # taxon_ID_genus , scientific_name_ID , canonical_name , #> # row_number , number_of_collapsed_taxa # }"},{"path":"https://traitecoevo.github.io/APCalign/news/index.html","id":"apcalign-110","dir":"Changelog","previous_headings":"","what":"APCalign 1.1.0","title":"APCalign 1.1.0","text":"CRAN release: 2024-08-19 Create genus->family lookup specified APC release","code":""},{"path":"https://traitecoevo.github.io/APCalign/news/index.html","id":"apcalign-102","dir":"Changelog","previous_headings":"","what":"APCalign 1.0.2","title":"APCalign 1.0.2","text":"CRAN release: 2024-08-17 Minor update fix Deal vignette issues emerged CRAN Improve “graceful failing”, based issues come github CI minor formatting","code":""},{"path":"https://traitecoevo.github.io/APCalign/news/index.html","id":"apcalign-101","dir":"Changelog","previous_headings":"","what":"APCalign 1.0.1","title":"APCalign 1.0.1","text":"CRAN release: 2024-05-30 First major release APCalign. preprint available https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1. Article accepted publication Australian journal Botany. Following review, number changes implemented. sped & streamlined package. Update function documentation Speed extract_genus Write replacement function stringr::word much faster. Restricting reference list names first letter input string. Switch using utils::adist stringdist::stringdist(method = \"dl\") Rework standardise_names remove punctuation start string Rework strip_names_extra (previously strip_names_2) just perform additional functions strip_names, rather repeating performed strip_names. Avoid importing entire packages using package::function format throughout removing functions @import Add fuzzy match arguments create_taxonomic_update_lookup Add 3 additional family-level APC matches match_taxa. Refine tests Make messages console optional Fix issue fails github (https://github.com/traitecoevo/APCalign/issues/205) Update installation instructions Added cite version APCalign article Exported default_version Add citing method R package Update GitHub Actions Improved family alignments Added standardise_taxon_rank Improved messaging alignment","code":""}]