Learn R Programming

surface (version 0.6)

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) .

Copy Link

Version

Install

install.packages('surface')

Monthly Downloads

327

Version

0.6

License

GPL (>= 2)

Maintainer

Travis Ingram

Last Published

August 19th, 2024

Functions in surface (0.6)

propRegMatch

Similarity of Two Hansen Models
surfaceForward

Adding Regimes to a Hansen Model
surfaceSimulate

Simulate Data for SURFACE
runSurface

Run All Steps of a SURFACE Analysis
convertTreeData

Utilities for Formatting Objects for SURFACE Analysis
startingModel

Create an Initial Model for a SURFACE Analysis
surfaceBackward

Collapsing Convergent Regimes in a Hansen Model
surfaceDemo

Tree and Data for Demonstrating SURFACE
ouchDescendants

Obtain Descendants from an ouch Tree
getAIC

Akaike's Information Criterion for SURFACE Models
surfaceSummary

Summarize SURFACE Output
surface-package

Fitting Hansen Models to Investigate Convergent Evolution
surfaceTreePlot

Visualize Results of a SURFACE Analysis
surfaceAICPlot

Plot the AIC Throughout a SURFACE Analysis
getBranchTimes

Extract Branching Times from an ouch Tree
repaint

Paint the Branches of a Tree