R Hackathon 1/InputtingData
The commands referenced below are all part of special phylogenetic packages in R, not the basic R install. Be sure that you have installed and loaded the packages containing the commands referenced below before continuing. For example:
This loads the package ape and its required packages gee, lattice and ade4 into your R session.
How do I input a phylogeny into R?
The package APE can read phylogenies in either Newick or NEXUS format using the read.tree and read.nexus commands, respectively.
MyTree <- read.tree("MyNewickTreefile.tre") MyTree <- read.nexus("MyNexusTreefile.nex")
Either of these commands will create an identical object in R containing your tree. Taxon names should appear without quotes. Note that the NEXUS format supports the use of a translation table for taxon names.
How do I export a phylogeny out of R?
The package APE can export phylogenies in either Newick or Nexus format using the write.tree and write.nexus commands, respectivly.
write.tree(geospiza$geospiza.tree, file="geospiza.tre" write.nexus(geospiza$geospiza.tree, file="geospiza.nex"
How do I input data corresponding to the tips of my phylogeny into R?
First, assemble your data into a tab delimited text file (this can be done, for example, in a simple text editor or in MS Excel)
In what ways can I manipulate phylogenies in R?