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convevol (version 2.2.1)

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

319

Version

2.2.1

License

GPL-3

Maintainer

C Tristan Stayton

Last Published

August 16th, 2024

Functions in convevol (2.2.1)

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
phy

Sample phylogeny for use in convevol examples and tutorial
findanc

Find the ancestor of a given node in a phylogeny
convratsig

Tests the signifiance of convergent evolution by the ratio of the current to maximum past phenotypic distance
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.
plot2D

Plots calcConv or convSig output as a two-dimensional time series.
trait

Sample data for use in convevol examples and tutorial
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)
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).
labelstonumbers

Converts taxon names to tip/edge numbers
maxdist

Calculates the maximum phenotypic distance between the lineages leading to a pair of taxa.
calcCsCt

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

Calculates all phenotypic changes that occur on all branches of a phylogeny.
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)
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.
allmaxdist

Calculates maxdist for all pairs of taxa in a phylogeny.
convnum

Quantify convergence by the number of convergent events
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)
ancestrallineages

Extracts lineages leading to two tips, t1 and t2, from their most recent common ancestor.