Analysis of Convergent Evolution

Documentation for package ‘convevol’ version 1.3

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.
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
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
plotellipse	Plots an ellipse