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opts_chunk$set(warning=FALSE, message=FALSE, comment=NA, cache=FALSE)


name: is-invasive layout: post title: Is invasive? date: 2012-12-13 author: Scott Chamberlain tags:

  • R
  • ropensci
  • taxize
  • invasive

The Global Invasive Species Database (GISD) (see their website for more info here) has data on the invasiveness status of many species. From taxize you can now query the GISD database.

Introducing the function gisd_isinvasive. This function was contributed to taxize by Ignasi Bartomeus, a postdoc at the Swedish University Agricultural Sciences.

There are two possible outputs from using gisd_isinvasive: "Invasive" or "Not in GISD". If you use simplify=TRUE in the function you get "Invasive" or "Not in GISD", but if you use simplify=FALSE you get verbose description of the invasive species instead of just "Invasive" (and you still just get "Not in GISD").


Install taxize from GitHub

# install_github('taxize_', 'ropensci') # install if you don't already have the GitHub version
library(taxize)

Make a vector of species

sp <- c("Carpobrotus edulis", "Rosmarinus officinalis", "Nasua nasua", "Martes melampus", "Centaurea solstitialis")

Using the function gisd_isinvasive you can query the GISD database for the invasiveness status of your species, at least according to GISD. Calling gisd_isinvasive with the second parameter set to default simplify=FALSE, you get verbose output, with details on the species.

gisd_isinvasive(sp)

Simpler output, just the invasive status.

gisd_isinvasive(sp, simplify = TRUE)

Get the .Rmd file used to create this post at my github account - or .md file.

Written in Markdown, with help from knitr.