Package: convevol 2.2.1

C. Tristan Stayton

convevol: Analysis of Convergent Evolution

Quantifies and assesses the significance of convergent evolution using multiple methods and measures as described in Stayton (2015) <doi:10.1111/evo.12729> and Grossnickle et al. 2023. Also displays results in various ways.

Authors:William Brightly [aut], C. Tristan Stayton [aut, cre]

convevol_2.2.1.tar.gz
convevol_2.2.1.tar.gz(r-4.7-any)convevol_2.2.1.tar.gz(r-4.6-any)
convevol_2.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
convevol/json (API)

# Install 'convevol' in R:

install.packages('convevol', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

phy - Sample phylogeny for use in convevol examples and tutorial
trait - Sample data for use in convevol examples and tutorial

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.52 score 33 scripts 285 downloads 16 mentions 22 exports 44 dependencies

Last updated from:8e05ddcdf4. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	145
source / vignettes	OK	176
linux-release-x86_64	OK	146
wasm-release	OK	117

Exports:allmaxdist ancestrallineages calcchanges calcConv calcConvCt calcCs calcCsCt convnum convnumsig convrat convratsig convSig convSigCt findanc labelstonumbers maxdist multianc plot2D plotCt plotellipse pullNodeSeq pwCheck

Dependencies:ape cli cluster clusterGeneration coda codetools colorspace combinat cpp11 curl DEoptim deSolve digest doParallel expm fastmatch foreach geiger generics glue igraph iterators lattice lifecycle magick magrittr maps MASS Matrix mnormt mvtnorm ncbit nlme numDeriv optimParallel phangorn phytools pkgconfig quadprog Rcpp rlang scatterplot3d subplex vctrs

R packages: Static PDF and HTML vignettes

Rendered fromTM_Tutorial_v5.pdf.asisusingR.rsp::asis

Last update: 2024-08-17
Started: 2024-08-17

Citation

Readme and manuals

Help Manual

Help page	Topics
Calculates maxdist for all pairs of taxa in a phylogeny.	allmaxdist
Extracts lineages leading to two tips, t1 and t2, from their most recent common ancestor.	ancestrallineages
Calculates all phenotypic changes that occur on all branches of a phylogeny.	calcchanges
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).	calcConv
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.	calcConvCt
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)	calcCs
Computes Ct values for a pair of tips. Internal, called in calcConv.	calcCsCt
Quantify convergence by the number of convergent events	convnum
Assess the significance of convergent evolution using simulations and the convnum metric	convnumsig
Quantifies convergent evolution using the C1, C2, C3, and C4 measures as described by Stayton (2015).	convrat
Tests the signifiance of convergent evolution by the ratio of the current to maximum past phenotypic distance	convratsig
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)	convSig
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.	convSigCt
Find the ancestor of a given node in a phylogeny	findanc
Converts taxon names to tip/edge numbers	labelstonumbers
Calculates the maximum phenotypic distance between the lineages leading to a pair of taxa.	maxdist
Reconstructs ancestral states for multiple characters	multianc
Sample phylogeny for use in convevol examples and tutorial	phy
Plots calcConv or convSig output as a two-dimensional time series.	plot2D
Plots calcConv or convSig output.	plotCt
Plots an ellipse	plotellipse
Extracts a vector of ancestors for a given taxon. Code written by Jonathan S. Mitchell for Zelditch et al. (2017)	pullNodeSeq
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.	pwCheck
Sample data for use in convevol examples and tutorial	trait

Package: convevol 2.2.1

convevol: Analysis of Convergent Evolution

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)