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Comparative Methods in R How To

Getting started with R:

R is freely available statistical software, which can be run in various environments (MacOSX, Windows, Linux). For a general description of R, visit its its introductory page. To download R, go to its homepage and select one of the CRAN mirrors. Most users will want to choose a precompiled binary distributions for their system (Mac, Windows, Linux). For PC users, select the "base" subdirectory and download and run the setup program (.exe file). MAC users will download the .dmg file and double-click the icon to install the program.

In order to run comparative analyses in R, the user will need to download one or more additional packages. To install R packages, open R (by double-clicking the desktop icon, via the start menu for PC users, or within the applications folder for Mac users). The first window users will see is the R Console. Mac users can download packages via the Package Installer in the Packages & Data menu. PC users can download packages by selecting install packages from the Packages menu. Packages can also be downloaded by using the command line. At the prompt >, type install.packages("ape") to install ape. There are a large number of packages for phylogenetic and comparative analyses; a useful comparison of these packages and their functions has been compiled by Brian O'Meara (available here).

These packages must be loaded at the beginning of each session in R. To load a package, type library("ape") at the command prompt. Basic information about the package can obtained by typing"ape").


  • How to load a tree
  • How to load a dataset
  • How to....


  • How to calculate Independent Contrasts
  • How to calculate Ancestral State Reconstructions
  • How to calculate measures of phylogenetic patterning
  • How to.....

Tree & Data Manipulation

  • How to run analysis across multiple trees
  • How to subset trees and data
  • How to resolve polytomies
  • How to change branch lengths
  • How to .....