Hi Elaine, you should try to subset your data set data set and not the function data! Try: data.pruned <- birddata[tree.pruned$tip.label, ]
Regards, Klaus On 4/5/13, Elaine Kuo <[email protected]> wrote: > Hello, > > I am using the following code to prune a phylogeny tree of bird family. > However, an error appeared when running the last line of the code, saying: > > Error in data[tree.pruned$tip.label, ] : > object of type 'closure' is not subsettable > > > I do not understand the error message. > Please kindly help explain and advise if any further information > is in need to solve the issue. > > Thank you. > Elaine > > > Code > library(geiger) > > # read data and tree > birddata <-read.csv("H:/birddata_family_20130405.csv", header = TRUE) > birdtree <- read.nexus("H:/birddata_family_20130405.nexus") > setwd("H:") > > #temp <- name.check(birdtree, birddata) > tree.pruned <- drop.tip(birdtree, tip=temp$Tree.not.data) > > ## prune the data to include only those taxa in the pruned tree > data.pruned <- data[tree.pruned$tip.label, ] > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/[email protected]/ > -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
