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.
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.
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.
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')
PESI
get_pesiid(searchterm = "Salvelinus")
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') )
Search for a Candida boidinii
myco_search(filter='Name CONTAINS "Candida boidinii"')
taxizesoap
in R doing citation(package = 'taxizesoap')
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