README.md

In bstaggmartin/contsimmap: Stochastic Character Maps of Continuous Trait Data on Phylogenies

contsimmap

An R package for making stochastic character maps of continuous trait data on phylogenies

A "stochastic character map", often called a "simulation map" or "Simmap" for short, is a means of better understanding/exploring trait evolution dynamics on phylogenies, introduced by Nielsen and expanded on by Hulsenbeck, Bollback, and others in the 2000s. The popularity of Simmaps exploded with Revell's user-friendly implementation in his phytools package for R. Unlike conventional ancestral state reconstruction, the goal of Simmapping is not to come up with the most likely ancestral states at particular nodes in a phylogeny, but simulate probable trajectories of trait evolution across the entire evolutionary history depicted in a phylogeny. In a nutshell, this means sampling ancestral states under some fitted model of evolution. Simmaps have various uses in visualization, permutation-based hypothesis testing, and integrating over uncertainty in ancestral states in a conceptually straight-forward way (e.g., musscrat, ratematrix, mvmorph).

A current limitation of Simmapping methods/implementations is that they are limited to discrete traits (e.g., colors, presence/absence of novel phenotypes, habitat). The goal of this package is implement an analogous method for continuous traits (e.g., lengths, masses), and develop a few new visualization and modeling frameworks based off of them. This method is now available via the function make.contsimmap() in the current vesion of the package, but documentation and many convenience features are still missing!

If you find yourself here and want to get started using contsimmaps, feel free to reach out to me at: [e-mail].

bstaggmartin/contsimmap documentation built on Aug. 12, 2024, 5:16 a.m.