Package: windex 2.0.8

Kevin Arbuckle

windex: Analysing Convergent Evolution using the Wheatsheaf Index

Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi:10.1111/2041-210X.12195>, and some other unrelated but perhaps useful functions.

Authors:Kevin Arbuckle and Amanda Minter

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windex.pdf |windex.html✨
windex/json (API)

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

Peer review:

Bug tracker:https://github.com/kevinarbuckle/windex/issues

Datasets:

On CRAN:

2.60 score 8 scripts 610 downloads 4 mentions 20 exports 41 dependencies

Last updated 8 months agofrom:f98de9bf74. Checks:OK: 1 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 23 2024
R-4.5-winNOTEDec 23 2024
R-4.5-linuxNOTEDec 23 2024
R-4.4-winNOTEDec 23 2024
R-4.4-macNOTEDec 23 2024
R-4.3-winNOTEDec 23 2024
R-4.3-macNOTEDec 23 2024

Exports:backLogerror.barslrTestmark.distmodSel.fitMkmodSel.geigermodSel.phylolmmodSel.rayDISCmodSelTabnodeDistpirplotTraitprune2datarichYuleInputssetest.windextreechecktreedatacheckwindexwindex.sim.test

Dependencies:apecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdoParallelexpmforeachgeigergenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcppRcppArmadillorlangscatterplot3dsubplexvctrs

Readme and manuals

Help Manual

Help pageTopics
Backtransforms coefficient estimates from logistic regressionbackLog
Plots error bars on a barploterror.bars
Calculates likelihood ratio testlrTest
Summarising distributions of (exam/coursework/etc.) marks for (UK) university teachingmark.dist
Model selection table for categorical trait evolution models fit in the fitMk function in the package phytools, based on information theoretical measures.modSel.fitMk
Model selection table for phenotypic evolution models fit in the package geiger, based on information theoretical measures.modSel.geiger
Model selection table for phylogenetic (logistic) regressions fit in the phylolm and phyloglm functions in the package phylolm, based on information theoretical measures.modSel.phylolm
Model selection table for evolutionary pathway models fit in the package corHMM, based on information theoretical measures.modSel.rayDISC
Model selection table based on information theoretical measures.modSelTab
Plotting and/or retrieving distribution of divergence times of a pair of species from a set of phylogenetic trees.nodeDist
Calculates phylogenetic imbalance ratio (PIR)pir
Provides a visualisation of up to three-dimensional trait space (not accounting for phylogeny) for data explorationplotTrait
Prunes a phylogenetic tree to match a vector (e.g. of species names in a dataset)prune2data
Generates the inputs necessary to run richness.yule.test() in aperichYuleInputs
Sample data for windexsample.data
Phylogenetic tree to accompany sample.datasample.tree
Calculates standard errorse
Tests for particularly strong convergent evolution given topological constraintstest.windex
Checks a set of phylogenetic trees to confirm they are ultrametric and binary.treecheck
Checks a set of phylogenetic trees to confirm they are ultrametric and binary and that tip labels match a list of names.treedatacheck
Calculates Wheatsheaf index with 95% confidence intervalswindex
Tests for presence of convergent evolution (over and above that expected from Brownian motion)windex.sim.test