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surface (version 0.5)

Fitting Hansen Models to Investigate Convergent Evolution

Description

This data-driven phylogenetic comparative method fits stabilizing selection models to continuous trait data, building on the 'ouch' methodology of Butler and King (2004) . The main functions fit a series of Hansen models using stepwise AIC, then identify cases of convergent evolution where multiple lineages have shifted to the same adaptive peak. For more information see Ingram and Mahler (2013) .

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Version

Install

install.packages('surface')

Monthly Downloads

313

Version

0.5

License

GPL (>= 2)

Maintainer

Travis Ingram

Last Published

December 18th, 2020

Functions in surface (0.5)

ouchDescendants

Obtain Descendants from an ouch Tree
startingModel

Create an Initial Model for a SURFACE Analysis
surfaceAICPlot

Plot the AIC Throughout a SURFACE Analysis
repaint

Paint the Branches of a Tree
propRegMatch

Similarity of Two Hansen Models
surface-package

Fitting Hansen Models to Investigate Convergent Evolution
getBranchTimes

Extract Branching Times from an ouch Tree
runSurface

Run All Steps of a SURFACE Analysis
surfaceSummary

Summarize SURFACE Output
convertTreeData

Utilities for Formatting Objects for SURFACE Analysis
getAIC

Akaike's Information Criterion for SURFACE Models
surfaceBackward

Collapsing Convergent Regimes in a Hansen Model
surfaceTreePlot

Visualize Results of a SURFACE Analysis
surfaceDemo

Tree and Data for Demonstrating SURFACE
surfaceForward

Adding Regimes to a Hansen Model
surfaceSimulate

Simulate Data for SURFACE