is_invasive( ) got a new best friend: is_native( )

May 7, 2015
By

(This article was first published on Bartomeus lab » Rstats, and kindly contributed to R-bloggers)

A while ago I did a function to check if a species was among the worst invaders. I am really happy this function was used and ropensci put it in a package. However the function does not tell you if a species is exotic in a particular place, and this is what most people want to know. Scott Chamberlain found a couple of other resources to get invasive species lists and we where discussing where to find those reliable, complete “lists of exotic species per region”, but we where thinking the problem from the wrong approach.

Exotic species lists will be always incomplete and hard to maintain. For most research questions the reverse question is also suited. Instead of “is exotic?”, you can ask “is not native?” Lists of natives species are easier to get and stable through time. Moreover, It conveys the message that any non native species is potentially harmful, rather than restricting to “worst invaders” or “known exotic species”.

So here it is. Its implemented for animals and plants in the US (using ITIS database) and for Plants in Europe (Using Flora Europaea)*. You can use it with the following R code:

install.packages("devtools")
library(devtools)
install_github("ibartomeus/traits")
library("traits")

#make a species list
sp <- c("Lavandula stoechas", "Carpobrotus edulis", "Rhododendron ponticum", "Alkanna lutea", "Anchusa arvensis")

#ask in which countries the first species is native by querying in Flora Europaea
fe_native(sp[1])
?fe_native #to see the help page.

#use sapply for querying all species at once
sapply(sp, fe_native, simplify = FALSE)

#ask if the first species is native in a particular region
is_native(sp[1], where = "Islas_Baleares", region = "europe")
?is_native #to see the help page and country names used

#or all species at once
sapply(sp, is_native, where = "Continental US", region = "america")
sapply(sp, is_native, where = "Islas_Baleares", region = "europe")

#for america I am calling itis_native function from taxize package.

The function will be available from ropensci/traits soon, and probably Scott will make it faster and more usable. Let me know if it breaks with any species or if the help pages needs clarifications and I can try to fix it.

*If you know/have a list of all native species for your region of interest, we can add it.

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