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

Description Usage Arguments Details Value Examples

View source: R/getSynonyms.R

Description

This function looks up any listed synonyms on the ASW website (http://research.amnh.org/vz/herpetology/amphibia/index.php/). 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 ~7000 species webpages for upwards of 20 000 synonyms), but additional arguments can be included to restrict searches to a specified taxonomic group.

Usage

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getSynonyms(asw_taxonomy = defrostR::asw_taxonomy, Order = NA,
  Superfamily = NA, Family = NA, Subfamily = NA, Genus = NA,
  Species = NA)

Arguments

asw_taxonomy

the ASW taxonomy table obtained with getTaxonomy(). 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 this version of the amphibian taxonomy may be outdated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 dataframe listing all species and their listed synonyms

Examples

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

defrostR documentation built on Jan. 20, 2018, 9:01 a.m.