Dear all,
This is Elaine.
I am using drop.tip (ape) to prune a phylogeny tree and
get the data of the pruned tree.
The original data encompassed two types of information:
family name and migration status.
However, using two methods below got different results.
method 1 (from tree.pruned$tip.label) : family name only
method 2 (from data.pruned): migration status only
Please kindly explain why it is not possible to retrieve both family name
and migration status together using method 1 or 2.
Further, please kindly advise any modification to get both information.
Thank you.
Elaine
Code
Library(ape)
birddata <- read.csv("H:/ birddata_family.csv", header = TRUE)
birdtree <- read.nexus("H:/ birddata_family.nexus")
setwd("H:)
## prune the phylogeny to include only species which are in the data set
species.to.keep<-read.csv("H:/ birddata_family_20130405.csv", header = TRUE)
tree.pruned<-drop.tip(birdtree,tree.pruned<-drop.tip(tree,**
setdiff(tree$tip.label,ss))
# tree.pruned csv (method 1)
write.csv<-(tree.pruned$tip.label,"H:/treepruned_tiplabel.csv")
# prune the data to include only those taxa in the pruned tree
data.pruned <- birddata[tree.pruned$tip.label, ]
# data.pruned csv (method 2)
write.csv <-(data.pruned,"H:/datapruned.csv")
birddata
https://www.box.com/files/0/f/766727938/1/f_7323300929
treepruned_tiplabel (method 1)
https://www.box.com/files/0/f/766727938/1/f_7353351839
datapruned (method 1)
https://www.box.com/files/0/f/766727938/1/f_7353351839
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