Fitting Hansen Models to Investigate Convergent Evolution

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Documentation for package ‘surface’ version 0.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

surface-package	Fitting Hansen Models to Investigate Convergent Evolution
addRegime	Adding Regimes to a Hansen Model
collapseRegimes	Collapsing Convergent Regimes in a Hansen Model
convertBack	Utilities for Formatting Objects for SURFACE Analysis
convertTreeData	Utilities for Formatting Objects for SURFACE Analysis
getAIC	Akaike's Information Criterion for SURFACE Models
getBranchTimes	Extract Branching Times from an 'ouch' Tree
nameNodes	Utilities for Formatting Objects for SURFACE Analysis
npSurface	Akaike's Information Criterion for SURFACE Models
ouchDescendants	Obtain Descendants from an 'ouch' Tree
propRegMatch	Similarity of Two Hansen Models
repaint	Paint the Branches of a Tree
runSurface	Run All Steps of a SURFACE Analysis
startingModel	Create an Initial Model for a SURFACE Analysis
surface	Fitting Hansen Models to Investigate Convergent Evolution
surfaceAICMultiPlot	Plot the AIC Throughout a SURFACE Analysis
surfaceAICPlot	Plot the AIC Throughout a SURFACE Analysis
surfaceBackward	Collapsing Convergent Regimes in a Hansen Model
surfaceDemo	Tree and Data for Demonstrating SURFACE
surfaceForward	Adding Regimes to a Hansen Model
surfaceSimulate	Simulate Data for SURFACE
surfaceSummary	Summarize SURFACE Output
surfaceTraitPlot	Visualize Results of a SURFACE Analysis
surfaceTreePlot	Visualize Results of a SURFACE Analysis