Assessing the adequacy of phylogenetic models of quantitative trait evolution
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README.md

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arbutus logo

This package was developed to assess the adequacy of continuous trait models. The package includes functions to parse the output of various model-fitting functions in R, rescale phylogenies according to fitted parameters, simulate datasets, calculate summary statistics and plot results. The methods is described in a our paper: "Model adequacy and the macroevolution of angiosperm functional traits" published in The American Naturalist (see link; pdf; and manuscript repo).

Installation

To install the package from github, the easiest way is to install using devtools. Install devtools, then type

devtools::install_github("mwpennell/arbutus")

The package depends on the ape library

Supported packages

The idea behind arbutus is that models are fit to comparative data using other packages and arbutus is used to assess the adequacy of the fitted model. There are no native functions for fitting models or performing model selection within this package. Currently, arbutus can handle objects of the following classes:

  • gfit objects from fitContinuous in geiger (>= 2.0)
  • fit.mle objects from find.mle in diversitree (>= 0.9.7)
  • mcmcsamples objects from mcmc in diversitree (>= 0.9.7)`
  • gls objects from gls in nlme
  • pgls objects from pgls in caper
  • phylolm objects from phylolm in phylolm
  • phylo objects in ape format (does not rescale phylogeny)
  • multiPhylo objects in ape format (does not rescale phylogeny)

We plan to add more package interfaces as this project progresses.