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windex (version 2.1.0)

Analysing Convergent Evolution using the Wheatsheaf Index

Description

Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) , and some other unrelated but perhaps useful functions.

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Version

Install

install.packages('windex')

Monthly Downloads

230

Version

2.1.0

License

GPL-2

Maintainer

Kevin Arbuckle

Last Published

February 6th, 2025

Functions in windex (2.1.0)

backLog

Backtransforms coefficient estimates from logistic regression
modSelTab

Model selection table based on information theoretical measures.
prune2data

Prunes a phylogenetic tree to match a vector (e.g. of species names in a dataset)
plotTrait

Provides a visualisation of up to three-dimensional trait space (not accounting for phylogeny) for data exploration
lrTest

Calculates likelihood ratio test
treecheck

Checks a set of phylogenetic trees to confirm they are ultrametric and binary.
test.windex

Tests for particularly strong convergent evolution given topological constraints
richYuleInputs

Generates the inputs necessary to run richness.yule.test() in ape
sample.data

Sample data for windex
se

Calculates standard error
nodeDist

Plotting and/or retrieving distribution of divergence times of a pair of species from a set of phylogenetic trees.
pir

Calculates phylogenetic imbalance ratio (PIR)
treedatacheck

Checks a set of phylogenetic trees to confirm they are ultrametric and binary and that tip labels match a list of names.
sample.tree

Phylogenetic tree to accompany sample.data
windex.sim.test

Tests for presence of convergent evolution (over and above that expected from Brownian motion)
windex

Calculates Wheatsheaf index with 95% confidence intervals
LRbarplot

Plots a barplot from logistic regression parameter estimates
mark.dist

Summarising distributions of (exam/coursework/etc.) marks for (UK) university teaching
modSel.geiger

Model selection table for phenotypic evolution models fit in the package geiger, based on information theoretical measures.
error.bars

Plots error bars on a barplot
modSel.rayDISC

Model selection table for evolutionary pathway models fit in the package corHMM, based on information theoretical measures.
modSel.phylolm

Model selection table for phylogenetic (logistic) regressions fit in the phylolm and phyloglm functions in the package phylolm, based on information theoretical measures.
modSel.fitMk

Model selection table for categorical trait evolution models fit in the fitMk function in the package phytools, based on information theoretical measures.