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# By Martin Jung (2015) | |
# http://conservationecology.wordpress.com/ | |
# Takes a IUCN species id code as input, which | |
# can ether be queried from the api (http://api.iucnredlist.org/) | |
# or directly from the full database downloadable here: | |
# http://api.iucnredlist.org/index/all.csv | |
isForestSpecialist <- function (inputID) | |
{ | |
print(paste("Now processing ID",inputID)) | |
# Input data need to be joined first with IUCN ids | |
# Queries the IUCN database if a species is associated with forests and has major importance = yes | |
library(XML) | |
library(RCurl) | |
library(stringr) | |
if(is.na(inputID)) return(NA) else | |
{ | |
# Generate the link | |
link <- paste("http://www.iucnredlist.org/details/classify/",inputID, "/0", sep = "") | |
# Download the html file | |
webpage <- getURL(link) | |
webpage <- readLines(tc <- textConnection(webpage)); close(tc) | |
# Parse site structure and extract body | |
pagetree <- htmlTreeParse(webpage, error=function(...){}) | |
body <- pagetree$children$html$children$body | |
# Then extract habitat container | |
b <- try( xpathApply(body, "//div[@id='habitat']")[[1]] ) | |
if(class(b)[1] =="try-error") { | |
print(paste("Species ID",inputID,"does not seem to have habitat info...")) | |
return(NA) | |
} | |
# get text | |
bb <- toString.XMLNode(b) | |
# split at hr | |
h2 <- unlist(str_split(bb,"<hr",n = Inf)) | |
# check if forest and mayor importance occur | |
res <- vector() | |
for(i in 1:length(h2)){ | |
# Reduce does the trick | |
ix <- c( Reduce('&', lapply(c("Forest","Yes"), grepl, h2[i])), | |
Reduce('&', lapply(c("forest","yes"), grepl, h2[i])), | |
Reduce('&', lapply(c("Forest","yes"), grepl, h2[i])), | |
Reduce('&', lapply(c("forest","Yes"), grepl, h2[i])) | |
) | |
if(any(ix)) res <- c(res,"Forest-specialist") | |
iy <- c( Reduce('&', lapply(c("Forest","No"), grepl, h2[i])), | |
Reduce('&', lapply(c("forest","no"), grepl, h2[i])), | |
Reduce('&', lapply(c("Forest","no"), grepl, h2[i])), | |
Reduce('&', lapply(c("forest","No"), grepl, h2[i])) | |
) | |
if(any(iy)) res <- c(res,"Forest-associated") | |
} | |
# Check if one clear association. | |
if( "Forest-specialist" %in% res) return("Forest-specialist") else | |
if( length(unique(res)) == 2 ) return("Forest-specialist") else | |
if( length(unique(res) == 1)) return("Forest-associated") else | |
return("Other Habitats") # If none return NA by default if nothing else works | |
} | |
} |
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