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Instructions for installing the aRbor package.
We have a number of test cases where we built workflows both in R and Arbor to analyze trait evolution.
Anolis lizards are famous as an example of convergent evolution. Ecomorphs, which are habitat specialists types found in anoles like "trunk-crown," "crown-giant", and "twig." These ecomorphs have evolved repeatedly on islands in the Greater Antilles.
For Anolis, we envision the scenario where a researcher wants to reconstruct the historical patterns of ecomorph evolution in a phylogenetic context. The researcher might come to us with a list of anole species classified by ecomorph. They want to know if each of these ecomorphs have evolved more than once on the phylogenetic tree. We can address this question with two steps: (1) obtain a tree of anoles from open tree, and (2) use ancestral state reconstruction, which calculates relative likelihoods for each ecomorph on every node in the tree given some model of evolution.
Our work on anoles can be seen here.