get_synonyms: Compile dataframe of all synonyms listed on Amphibian Species...

In hcliedtke/AmphiNom: An Amphibian Systematics Tool

Compile dataframe of all synonyms listed on Amphibian Species of the World

Description

This function looks up any listed synonyms on the ASW website (https://amphibiansoftheworld.amnh.org/). It takes a minimum of one argument: the asw_taxonomy table generated with the function getTaxonomy(). If a full search is performed, this can take quite long (looking through ~8800 species webpages for upwards of 31 000 synonyms), but additional arguments can be included to restrict searches to a specified taxonomic group.

Usage

get_synonyms(
  asw_taxonomy = AmphiNom::asw_taxonomy,
  Order = NA,
  Superfamily = NA,
  Family = NA,
  Subfamily = NA,
  Genus = NA,
  Species = NA
)

Arguments

asw_taxonomy	the ASW taxonomy table obtained with get_taxonomy(). If no table is provided, by default it will use the internally stored data set. WARNING! this version of the amphibian taxonomy may be outdated
Order	limit search to a user-specified amphibian order
Superfamily	limit search to a user-specified amphibian superfamily
Family	limit search to a user-specified amphibian family
Subfamily	limit search to a user-specified amphibian subfamily
Genus	limit search to a user-specified amphibian genus
Species	limit search to a user-specified amphibian species

Details

Users may experience issues with umlauts that are not supported by their system language. On Mac OSX, this can be changed by running the following line of code in R:

system("defaults write org.R-project.R force.LANG en_US.UTF-8")

and then restarting the session. Read more here: https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Internationalization-of-the-R_002eapp

Value

returns a data frame listing all species and their listed synonyms

Examples

#to get a full list of synonyms for all species, run:
## Not run: asw_synonyms<-get_synonyms()
#to get synonyms for a specific taxonomic group only:
## Not run: get_synonyms(Family="Sooglossidae")

hcliedtke/AmphiNom documentation built on Nov. 8, 2024, 8:10 a.m.