When working with biodiversity data, it is important to verify taxonomic names with an authoritative list and correct any out-of-date names or names with typos.
The ‘APCalign’ package simplifies this process by:
- Accessing up-to-date taxonomic information from the Australian Plant Census and the Australia Plant Name Index.
- Aligning authoritative names to your taxonomic names using our fuzzy matching algorithm
- Updating your taxonomic names in a transparent, reproducible manner
- Because APCalign was developed explicitly for the Australian flora it handles phrase names and aligns disparate phrase name syntax
- Indicating when a split leads to uncertainty in a name alignment
‘APCalign’ also supplies information about the established status (i.e., native/introduced) of plant taxa within different states/territories as compiled by the APC. It’s useful for updating species list and intersecting them with the APC consensus for both taxonomy and establishment status.
Read the APCalign paper to learn more about the motivations for this project and our fuzzy matching and aligning algorithms.
Installation 🛠️
From CRAN:
install.packages("APCalign")
library(APCalign)OR for the GitHub version:
install.packages("remotes")
remotes::install_github("traitecoevo/APCalign")Or for the ShinyApp head to unsw.shinyapps.io/APCalign-app
A quick demo
Generating a look-up table can be done with just one function:
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
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 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 <chr>, taxonomic_status <chr>,
#> # scientific_name <chr>, aligned_reason <chr>, update_reason <chr>,
#> # number_of_collapsed_taxa <dbl>You can alternatively load the taxonomic resources into memory first:
tax_resources <- load_taxonomic_resources()
create_taxonomic_update_lookup(
taxa = c(
"Banksia integrifolia",
"Banksya integrifolla",
"Banksya integriifolla",
"Banksyya integriifolla",
"Banksia red flowers",
"Banksia sp.",
"Banksia catoglypta",
"Dryandra catoglypta",
"Dryandra cataglypta",
"Dryandra australis",
"Acacia longifolia",
"Commersonia rosea",
"Panicum sp. Hairy glumes (C.R.Michell 4192)",
"Panicum sp. Hairy glumes (Michell)",
"Panicum sp. Hairy glumes",
"not a species"
),
resources = tax_resources
)
#> # A tibble: 16 × 12
#> original_name aligned_name accepted_name suggested_name genus taxon_rank
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Banksia integrifo… Banksia int… Banksia inte… Banksia integ… Bank… species
#> 2 Banksya integrifo… Banksia int… Banksia inte… Banksia integ… Bank… species
#> 3 Banksya integriif… Banksia int… Banksia inte… Banksia integ… Bank… species
#> 4 Banksyya integrii… Banksia sp.… <NA> Banksia sp. [… Bank… genus
#> 5 Banksia red flowe… Banksia sp.… <NA> Banksia sp. [… Bank… genus
#> 6 Banksia sp. Banksia sp. <NA> Banksia sp. Bank… genus
#> 7 Banksia catoglypta Banksia cat… Banksia cato… Banksia catog… Bank… species
#> 8 Dryandra catoglyp… Dryandra ca… Banksia cato… Banksia catog… Bank… species
#> 9 Dryandra cataglyp… Dryandra ca… Banksia cato… Banksia catog… Bank… species
#> 10 Dryandra australis Dryandra sp… <NA> Dryandra sp. … Drya… genus
#> 11 Acacia longifolia Acacia long… Acacia longi… Acacia longif… Acac… species
#> 12 Commersonia rosea Commersonia… Androcalva r… Androcalva ro… Andr… species
#> 13 Panicum sp. Hairy… Panicum sp.… Panicum sp. … Panicum sp. H… Pani… species
#> 14 Panicum sp. Hairy… Panicum sp.… Panicum sp. … Panicum sp. H… Pani… species
#> 15 Panicum sp. Hairy… Panicum sp.… Panicum sp. … Panicum sp. H… Pani… species
#> 16 not a species <NA> <NA> <NA> <NA> <NA>
#> # ℹ 6 more variables: taxonomic_dataset <chr>, taxonomic_status <chr>,
#> # scientific_name <chr>, aligned_reason <chr>, update_reason <chr>,
#> # number_of_collapsed_taxa <dbl>Checking for a list of species to see if they are classified as Australian natives:
native_anywhere_in_australia(c("Eucalyptus globulus","Pinus radiata"), resources = tax_resources)
#> # A tibble: 2 × 2
#> species native_anywhere_in_aus
#> <chr> <chr>
#> 1 Eucalyptus globulus native
#> 2 Pinus radiata introducedDetermining the number of species present in NSW and their establishment means:
state_diversity_counts("NSW", resources = tax_resources)
#> # A tibble: 7 × 3
#> origin state num_species
#> <chr> <chr> <table[1d]>
#> 1 doubtfully naturalised NSW 94
#> 2 formerly naturalised NSW 8
#> 3 native NSW 5980
#> 4 native and doubtfully naturalised NSW 2
#> 5 native and naturalised NSW 34
#> 6 naturalised NSW 1584
#> 7 presumed extinct NSW 9The related function create_species_state_origin_matrix() generates a table for all taxa in Australia, indicating their distribution and establishment means, by state.
Getting a family lookup table for genera from the specified taxonomy:
get_apc_genus_family_lookup(c("Eucalyptus",
"Pinus",
"Actinotus",
"Banksia",
"Acacia",
"Triodia"),
resources = tax_resources)
#> # A tibble: 6 × 2
#> genus family
#> <chr> <chr>
#> 1 Eucalyptus Myrtaceae
#> 2 Pinus Pinaceae
#> 3 Actinotus Apiaceae
#> 4 Banksia Proteaceae
#> 5 Acacia Fabaceae
#> 6 Triodia PoaceaeCompiling a list of outdated synonyms for currently accepted names:
names_to_check <- c("Acacia aneura", "Banksia nivea", "Cardamine gunnii", "Stenocarpus sinuatus")
synonyms_for_accepted_names(resources = tax_resources, accepted_names = names_to_check, collapse = T)
#> # A tibble: 4 × 5
#> family accepted_name synonyms scientific_name accepted_name_usage_ID
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Brassicaceae Cardamine gunnii Cardami… Cardamine gunn… https://id.biodiversi…
#> 2 Fabaceae Acacia aneura Acacia … Acacia aneura … https://id.biodiversi…
#> 3 Proteaceae Banksia nivea Dryandr… Banksia nivea … https://id.biodiversi…
#> 4 Proteaceae Stenocarpus sinu… Stenoca… Stenocarpus si… https://id.biodiversi…
Learn more 📚
Highly recommend looking at our Getting Started vignette to learn about how to use APCalign. You can also learn more about our taxa matching algorithm.
Show us support 💛
Please consider citing our work, we are really proud of it!
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_, *72*(4). R package version: 1.1.4,
#> <https://doi.org/10.1071/BT24014>.
#>
#> 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},
#> volume = {72},
#> number = {4},
#> year = {2024},
#> publisher = {CSIRO Publishing},
#> note = {R package version: 1.1.4},
#> url = {https://doi.org/10.1071/BT24014},
#> }Found a bug? 🐛
Did you come across an unexpected taxon name change? Elusive error you can’t debug - submit an issue and we will try our best to help.
Comments and contributions
We welcome any comments and contributions to the package, start by submit an issue and we can take it from there!