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surface (version 0.4-1)

Fitting Hansen Models to Investigate Convergent Evolution

Description

SURFACE is a data-driven phylogenetic comparative method for fitting stabilizing selection models to continuous trait data, building on the ouch package. 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.

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Version

Install

install.packages('surface')

Monthly Downloads

247

Version

0.4-1

License

GPL (>= 2)

Maintainer

Travis Ingram

Last Published

February 14th, 2014

Functions in surface (0.4-1)

runSurface

Run All Steps of a SURFACE Analysis
ouchDescendants

Obtain Descendants from an ouch Tree
surfaceTreePlot

Visualize Results of a SURFACE Analysis
surface-package

Fitting Hansen Models to Investigate Convergent Evolution
getBranchTimes

Extract Branching Times from an ouch Tree
repaint

Paint the Branches of a Tree
startingModel

Create an Initial Model for a SURFACE Analysis
surfaceSimulate

Simulate Data for SURFACE
surfaceBackward

Collapsing Convergent Regimes in a Hansen Model
surfaceForward

Adding Regimes to a Hansen Model
surfaceSummary

Summarize SURFACE Output
convertTreeData

Utilities for Formatting Objects for SURFACE Analysis
surfaceAICPlot

Plot the AIC Throughout a SURFACE Analysis
surfaceDemo

Tree and Data for Demonstrating SURFACE
propRegMatch

Similarity of Two Hansen Models
getAIC

Akaike's Information Criterion for SURFACE Models