In ropensci/taxizesoap: Taxonomic Information from Around the Soap Web

taxizesoap

knitr::opts_chunk$set(
  comment = "#>",
  collapse = TRUE,
  warning = FALSE,
  message = FALSE
)

UPDATE: WORMS data source is now in taxize - for PESI and Mycobank continue to use this package.

taxizesoap is an extension to taxize, but for data sources that use SOAP data transfer protocol, which is hard to support in R. This package won't go on CRAN.

Most functions in this package are different from those in taxize, but there are some of the same (e.g,. classification()). In this package, where a function is named the same as in taxize, I've added a _s at the end of the function representing the version of that function in the taxizesoap package. This is to avoid confounding effects when both packages are loaded at the same time.

Currently implemented in taxizesoap

Souce	Function prefix	API Docs	API key
Pan-European Species directories Infrastructure (PESI)	pesi	link	none
Mycobank	myco	link	none

Note: Euro+Med is available through PESI.

R versions

We previously had problems with this package, where it didn't work on R > 3.2. But now those problems seem to have been solved. let us know if you run into any more problems.

Install taxizesoap

devtools::install_github("ropensci/taxizesoap")

That should install two dependencies not on CRAN (XMLSchema, SSOAP). If they aren't installed correctly for you, try installing from our Drat repo.

install.packages(c("XMLSchema", "SSOAP"), repos = c("http://packages.ropensci.org", "http://cran.rstudio.com"))

If that doesn't work, try insatlling from GitHub:

install.packages("devtools")
devtools::install_github("omegahat/XMLSchema")
devtools::install_github("sckott/SSOAP")

Load the package

library('taxizesoap')

Get taxonomic ids

PESI

get_pesiid(searchterm = "Salvelinus")

PESI

Search for PESI scientific names and associated metadata.

pesi_search(scientific='Ternatea vulgaris')

Get PESI scientific names from GUIDs

pesi_name_scientific(guid='67C3CC9C-624A-40C5-B63A-AB880E0300D1')

Get PESI synonyms from GUIDs

head( pesi_synonyms(guid='A0433E13-D7B5-49F2-86BA-A1777364C559') )

Mycobank

Search for a Candida boidinii

myco_search(filter='Name CONTAINS "Candida boidinii"')

Contributors

• Scott Chamberlain https://github.com/sckott
• Francois Michonneau https://github.com/fmichonneau

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for taxizesoap in R doing citation(package = 'taxizesoap')
• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

ropensci/taxizesoap documentation built on May 18, 2022, 7:33 p.m.