I am using R to reconstruct the phylogenetic hypothesis of a family of flies and I want to map some discrete characters to analyze their evolution. The characters I am using are four states for a foreleg character ("0", "A", "B", and "C") and four states for a sternite character ("0", "A", "B", and "C"). What is the easiest way to do this (preferably in R)?
I would be forever grateful if you could help!
There are several packages in R that deal with phylogenetic mapping and inference. Look up adephylo, ape and phangorn. They are well documented, and have a solid user base so a lot of questions can be answered with adequate googling. Good luck!
I'd like to second the above recommendations, especially phangorn. It's an excellent package and I have used it occasionally to map characters to trees.
I centered my answer based on your specific request for R packages, but I have also found very useful and quite user-friendly the packages developed by Mark Pagel's group, which can be found at http://www.evolution.rdg.ac.uk/SoftwareMain.html
For these kinds of analyses, I recommend you to use different methods and packages to replicate the same analysis, and to avoid the temptation of cherry-picking the one option that yields the results you wanted/like/can explain, and instead use the results from multiple methods to discuss the robustness of your results.
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