‘APCalign’ uses the Australian Plant Census (APC) and Australian Plant Name Index to align and update Australian plant taxon name strings. ‘APCalign’ also supplies information about the established status (native/introduced) of plant taxa across different states/territories.
‘APCalign’ is current not on CRAN. Install the currently development version:
# install.packages("remotes")
# remotes::install_github("traitecoevo/APCalign", dependencies = TRUE, upgrade = "ask")
library(APCalign)
Generating a look-up table can be done with just one function
# Load APC/APNI resources into R
resources <- load_taxonomic_resources()
# Create lookup
create_taxonomic_update_lookup(
taxa = c(
"Banksia integrifolia",
"Acacia longifolia",
"Commersonia rosea"
),
resources = resources
)
#> # 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>
We also developed a shiny application for non-R users to update and align their taxonomic names. You can find the application here: https://unsw.shinyapps.io/APCalign-app
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.
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
We welcome any comments and contributions to the package, start by submit an issue and we can take it from there!