R: Fitting Hansen Models to Investigate Convergent Evolution

# Fitting Hansen Models to Investigate Convergent Evolution

## Documentation for package ‘surface’ version 0.6

- 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