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:
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.
Simpler output, just the invasive status.
gisd_isinvasive(sp, simplify = TRUE)