Taxize

taxize_classification.md

Using taxize to get a classification

Install taxize

install.packages("taxize")

Load taxize

library(taxize)

Get a set of species names

sp <- names_list("species", 10)

Get classifications for each species

res <- classification(sp, db = "col")

Remove missing taxa

res <- res[!is.na(res)]

Combine results to a data.frame, and select only certain ranks

library(plyr)
ldply(res, function(x) x[x$rank %in% c('Kingdom','Family','Genus'),])

Or this way

library(plyr)
library(reshape2)
ldply(res, function(x){
  tmp <- data.frame(t(x$name))
  names(tmp) <- x$rank
  tmp
})

                          .id Kingdom       Phylum         Class      Order         Family     Genus
1       Pohlia camptotrachela Plantae    Bryophyta     Bryopsida    Bryales       Bryaceae    Pohlia
2       Spiridens vieillardii Plantae    Bryophyta     Bryopsida    Bryales Spiridentaceae Spiridens
3 Gunnera katherine-wilsoniae Plantae Tracheophyta Magnoliopsida Gunnerales    Gunneraceae   Gunnera
4          Encalypta vulgaris Plantae    Bryophyta     Bryopsida  Pottiales  Encalyptaceae Encalypta
5           Hampeella pallens Plantae    Bryophyta     Bryopsida Isobryales Ptychomniaceae Hampeella

write.csv(df, file="awafsdsdf.csv", row.names=FALSE)