Fitting Hansen Models to Investigate Convergent Evolution
Collapsing Convergent Regimes in a Hansen Model
Adding Regimes to a Hansen Model
Simulate Data for SURFACE
Utilities for Formatting Objects for SURFACE Analysis
Akaike's Information Criterion for SURFACE Models
Extract Branching Times from an ouch Tree
Obtain Descendants from an ouch Tree
Similarity of Two Hansen Models
Paint the Branches of a Tree
Run All Steps of a SURFACE Analysis
Create an Initial Model for a SURFACE Analysis
Fitting Hansen Models to Investigate Convergent Evolution
Plot the AIC Throughout a SURFACE Analysis
Summarize SURFACE Output
Visualize Results of a SURFACE Analysis
This data-driven phylogenetic comparative method fits stabilizing selection models to continuous trait data, building on the 'ouch' methodology of Butler and King (2004) <doi:10.1086/426002>. 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) <doi:10.1111/2041-210X.12034>.