Tag Archive | plants

Taxonomy in R

Hi there,
here is a r-snippet which i wrote to get new data out of a species list.
I have a species-list of insect-pollinated european grassland plants, which is a little to detailed for me.
Through filtering i want to get a subset list with only small herbs.
First i consulted the PESI-Portal for a taxamatch only to find out, that only 75% of my species are currently in the database (Acer campestre is not found?)
After that i searched for a smart solution in r and i found taxize, a newly package which queries different databases and has nice functions for taxonomic data management.
First i want to get familynames for each genus-species combination. My species list contains two columns with the genus and the species name.
See below my solution how to get a family name for each species.

# Load in the source package taxize and get familynames for taxa in splist
install_github("taxize_", "ropensci")

splist <- paste(data$Genus,data$Species,sep="_")
mat <- matrix(nrow=length(splist),ncol=2)
mat[,2] <- splist
for(i in seq(1:length(splist))){
 # I had to use a try, because some entries produce strange errors.
res <- try(expr=get_tsn(splist[i],"sciname", by_="name"),silent=T)
if(is.vector(res)) {
fam <- get_familyname(res)
mat[i,1] <- fam
print(paste(fam,splist[i],sep=" - "))

It’s kind of rough, but it works. Currently it runs through my plant-species list with over 1500 entries.
The output looks like this…

[1] "Asteraceae - Artemisia_scoparia"

[1] "Asteraceae - Artemisia_vulgaris"

[1] "Araceae - Arum_maculatum"

[1] "Rosaceae - Aruncus_dioicus"

[1] "Asclepiadaceae - Asclepias_syriaca"

[1] "Asparagaceae - Asparagus_officinalis"

Iam still looking for a solution how to get specific traits for every species, such as “Perennial or Annual” or “Grow height”.
Will report back, if i find something.

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