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-4.5-noble)convevol_2.2.1.tar.gz(r-4.4-noble)
convevol_2.2.1.tgz(r-4.4-emscripten)convevol_2.2.1.tgz(r-4.3-emscripten)
convevol.pdf |convevol.html✨
convevol/json (API)

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

Peer review:

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

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

3.78 score 30 scripts 375 downloads 16 mentions 22 exports 44 dependencies

Last updated 4 months agofrom:8e05ddcdf4. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-linuxOKDec 01 2024

Exports:allmaxdistancestrallineagescalcchangescalcConvcalcConvCtcalcCscalcCsCtconvnumconvnumsigconvratconvratsigconvSigconvSigCtfindanclabelstonumbersmaxdistmultiancplot2DplotCtplotellipsepullNodeSeqpwCheck

Dependencies:apecliclusterclusterGenerationcodacodetoolscolorspacecombinatcpp11curlDEoptimdeSolvedigestdoParallelexpmfastmatchforeachgeigergenericsglueigraphiteratorslatticelifecyclemagickmagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dsubplexvctrs

R packages: Static PDF and HTML vignettes

Rendered fromTM_Tutorial_v5.pdf.asisusingR.rsp::asison Dec 01 2024.

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

Readme and manuals

Help Manual

Help pageTopics
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 eventsconvnum
Assess the significance of convergent evolution using simulations and the convnum metricconvnumsig
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 distanceconvratsig
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 phylogenyfindanc
Converts taxon names to tip/edge numberslabelstonumbers
Calculates the maximum phenotypic distance between the lineages leading to a pair of taxa.maxdist
Reconstructs ancestral states for multiple charactersmultianc
Sample phylogeny for use in convevol examples and tutorialphy
Plots calcConv or convSig output as a two-dimensional time series.plot2D
Plots calcConv or convSig output.plotCt
Plots an ellipseplotellipse
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 tutorialtrait