# Analysis of Convergent Evolution

## Documentation for package ‘convevol’ version 2.2.1

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

## Help Pages

allmaxdist | Calculates maxdist for all pairs of taxa in a phylogeny.
ancestrallineages | Extracts lineages leading to two tips, t1 and t2, from their most recent common ancestor.
calcchanges | Calculates all phenotypic changes that occur on all branches of a phylogeny.
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
convrat | Quantifies convergent evolution using the C1, C2, C3, and C4 measures as described by Stayton (2015).
convratsig | Tests the signifiance of convergent evolution by the ratio of the current to maximum past phenotypic distance
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.
findanc | Find the ancestor of a given node in a phylogeny
labelstonumbers | Converts taxon names to tip/edge numbers
maxdist | Calculates the maximum phenotypic distance between the lineages leading to a pair of taxa.
multianc | Reconstructs ancestral states for multiple characters
phy | Sample phylogeny for use in convevol examples and tutorial
plot2D | Plots calcConv or convSig output as a two-dimensional time series.
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)
pwCheck | Calculates the number of measurements that can be made between two lineages for each pairwise comparison within a set of putatively convergent tips (group identity may also be taken into account). Useful for determining which comparisons are not informative, and constructing a group object before running calcConvCt or convSigCt.
trait | Sample data for use in convevol examples and tutorial