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convevol (version 2.0.1)

Analysis of Convergent Evolution

Description

Quantifies and assesses the significance of convergent evolution using multiple methods and measures as described in Stayton (2015) and Grossnickle et al. 2023. Also displays results in various ways.

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Version

Install

install.packages('convevol')

Monthly Downloads

439

Version

2.0.1

License

GPL-2

Maintainer

C Tristan Stayton

Last Published

June 30th, 2023

Functions in convevol (2.0.1)

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)

convnum

Quantify convergence by the number of convergent events

multianc

Reconstructs ancestral states for multiple characters

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)

calcCsCt

Computes Ct values for a pair of tips. Internal, called in calcConv.

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.

plotCt

Plots calcConv or convSig output.

convnumsig

Assess the significance of convergent evolution using simulations and the convnum metric

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)

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.

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).