APCalign

‘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.

Installation

‘APCalign’ is current not on CRAN. Install the currently development version:

# install.packages("remotes")
# remotes::install_github("traitecoevo/APCalign")

library(APCalign)

A quick demo

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>

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 and how APC/APNI data is cached behind-the-scenes.

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!