Hello
This Elaine. I tried to prune a phylogeny tree using two methods based on the code attached. Method 1 returned the tip.label sharing between birddata and birdtree. Method 2 returned nothing. Please kindly indicate why Method 2 failed to prune the tree. Also, please kindly explain the command birdtree$tip.label[-na.omit Thank you again. Code Method 1 Library(ape) birddata <- read.csv("H:/ birddata_family_20130405.csv", header = TRUE) birdtree <- read.nexus("H:/ birddata_family_20130405.nexus") setwd("H:) ## prune the phylogeny to include only species which are in the data set species.to.keep<-read.csv("H:/ birddata_family_20130405.csv", header = TRUE) birdtree.pruned<-drop.tip(birdtree,birdtree$tip.label[-na.omit(match(species.to.keep[,1],birdtree$tip.label))]) Method 2 Library(ape) birddata <- read.csv("H:/ birddata_family_20130405.csv", header = TRUE) birdtree <- read.nexus("H:/ birddata_family_20130405.nexus") setwd("H:) ## prune the phylogeny to include only species which are in the data set temp <- name.check(birdtree, birddata) birdtree.pruned <- drop.tip(birdtree, tip=temp$Tree.not.data) [[alternative HTML version deleted]]
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