R/PLANTS_regenerate_lookup.R

In GioBo/TR8: A Tool for Downloading Functional Traits Data for Plant Species

## ## url<-"http://bricol.net/downloads/data/PLANTSdatabase/09-02-02PLANTSdata.csv"
## PLANTS<-read.table(url,fileEncoding="iso-8859-1")

## PLANTS<-read.table("~/Downloads/09-02-02PLANTSdata.csv",fileEncoding="iso-8859-1")

## ## remove commas in species names since they conflict with TNRS

## PLANTS$Scientific.Name<-as.character(PLANTS$Scientific.Name)
## PLANTS$Scientific.Name<-gsub(","," ",PLANTS$Scientific.Name)

## go<-tnrs(PLANTS$Scientific.Name ,source = "iPlant_TNRS",verbose=FALSE)
## go$score<-as.numeric(go$score)
## dai<-go[,c("submittedname","acceptedname","score","matchedname","authority")]
## dai<-dai[dai$score>=.6,]
## names(dai)<-revalue(names(dai),c("submittedname"="Scientific.Name"))
## ref_PLANTS<-merge(dai,PLANTS)

## ref_PLANTS<-ref_PLANTS[,c("acceptedname","score","matchedname","Symbol")]

##remove non ascii characters in acceptedname column
## "small" x (code "<c3><97>" in iso-859-1, used un Citrus x aurantium
## tp<-iconv(ref_PLANTS$acceptedname,"iso-8859-1","ASCII",sub="byte")
## ## replace "small x"  with "x"
## tp<-gsub("<c3><97>","x",tp)
## ref_PLANTS$acceptedname<-tp


##save(file="~/Work/src/tr8_github/data/ref_PLANTS.rda",ref_PLANTS)