R: Analysis of Convergent Evolution

# Analysis of Convergent Evolution

## Documentation for package ‘convevol’ version 2.0.1

- DESCRIPTION file.

## Help Pages

calcConv | Quantifies convergent evolution by the ratio of the current to maximum past phenotypic distance between two or more lineages, as described in Stayton (2015). Code written by Jonathan S. Mitchell for Zelditch et al. (2017).
calcConvCt | Computes Ct-metric scores for putatively convergent tips (or groups of tips) given a set of user provided phenotypic characters and a time calibrated phylogeny.
calcCs | Calculates the C1-C4 measures of convergent evolution between two lineages as described in Stayton (2015). All measures quantify convergence by the ratio of current to maximum past phenotypic distance between lineages. Can be used as-is but more often will be used within the calcConv script. Code written by Jonathan S. Mitchell for Zelditch et al. (2017)
calcCsCt | Computes Ct values for a pair of tips. Internal, called in calcConv.
convnum | Quantify convergence by the number of convergent events
convnumsig | Assess the significance of convergent evolution using simulations and the convnum metric
convSig | Uses simulations to assess the significance of C1-C4 measures of convergent evolution as described in Stayton (2015). Code written by Jonathan S. Mitchell for Zelditch et al. (2017)
convSigCt | Computes and conducts significance tests on Ct-metric scores for putatively convergent tips (or groups of tips) given a set of user provided phenotypic characters and a time calibrated phylogeny.
multianc | Reconstructs ancestral states for multiple characters
plotCt | Plots calcConv or convSig output.
plotellipse | Plots an ellipse
pullNodeSeq | Extracts a vector of ancestors for a given taxon. Code written by Jonathan S. Mitchell for Zelditch et al. (2017)