is.invasive.R

## is.invasive.R
is.invasive()

##Description##

#This function check which species (both plants and animals) are considered "invaders" somewhere in the
# world.  For that end, it checks GISD (http://www.issg.org/database/welcome/) and returns a value, either
#"Not invasive" or the brief description presented in GISD. Note that the webpage contains more
#information. Also note that the function won't tell you if it's exotic in your area, a lot of exotic
#species are not considered invaders (yet). As expected, the function is as good as the database is, which
#I find quite reliable and well maintained. The database is also able to recognize a lot (but not all) of
#the species synonyms. This function worked for me, but I didn't test it intensively, and any changes on
#the webpage html design will return wrong values. Apply the usual disclaimers when using it.
#The function is slow (not optimized at all), so be patient with long lists of species.

#Author Ignasi Bartomeus (nacho.bartomeus#gmail.com). Last updated 23 Nov 2012.

#Usage:
is.invasive(sp, simplified.df = FALSE)

#Arguments:
#sp: a vector of species names in latin (Genus species)

#simplified.df: Returns a data.frame with the species name and the values "Invasive", "Not Invasive". I
#recomend to check first the not simplified version (default), which contains raw information about the
#level of invasiveness.

#The function:
is.invasive <- function(sp, simplified.df = FALSE){
	require(plyr)
	require(XML)
	require(RCurl)
	#reformat sp list
	species <- gsub(" ","+",sp)
	#create urls to parse
	urls <- paste("http://www.issg.org/database/species/search.asp?sts=sss&st=sss&fr=1&x=13&y=9&sn=",
  	species,"&rn=&hci=-1&ei=-1&lang=EN", sep = "")
	#create a data.frame to store the Output
	Out <- data.frame(species = sp, status = c(1:length(urls)))
	#loop through all species
	for(i in 1:length(urls)){
		#Parse url and extract table
		doc <- htmlTreeParse(urls[i], useInternalNodes = TRUE)
		tables <- getNodeSet(doc, "//table")
		t <- readHTMLTable(tables[[4]])
		tt <- as.matrix(t)
		if(length(grep("No invasive species currently recorded",tt, value = TRUE)) > 0){
			Out[i,2] <- "Not invasive"
		}
		else{
			if(simplified.df == FALSE){Out[i,2] <- tt[12,1]}
			else{Out[i,2] <- "Invasive"}
		}
		print(paste("Checking species", i+1))
	}
	print("Done")
	Out
}

#Example:
sp <- c("Carpobrotus edulis", "Rosmarinus officinalis")
## first species is invasive, second one is not.

d <- is.invasive(sp)
d
d <- is.invasive(sp, simplified.df = TRUE)
d