Analysing Convergent Evolution using the Wheatsheaf Index

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Documentation for package ‘windex’ version 2.0.4.1

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windex-package windex: Analysing Convergent Evolution using the Wheatsheaf Index
backLog Backtransforms coefficient estimates from logistic regression
error.bars Plots error bars on a barplot
lrTest Calculates likelihood ratio test
mark.dist Summarising distributions of (exam/coursework/etc.) marks for (UK) university teaching
modSel.fitMk Model selection table for categorical trait evolution models fit in the fitMk function in the package phytools, based on information theoretical measures.
modSel.geiger Model selection table for phenotypic evolution models fit in the package geiger, 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.rayDISC Model selection table for evolutionary pathway models fit in the package corHMM, based on information theoretical measures.
modSelTab Model selection table based on information theoretical measures.
nodeDist Plotting distribution of divergence times of a pair of species from a set of phylogenetic trees.
pir Calculates phylogenetic imbalance ratio (PIR)
plotTrait Provides a visualisation of up to three-dimensional trait space (not accounting for phylogeny) for data exploration
prune2data Prunes a phylogenetic tree to match a vector (e.g. of species names in a dataset)
richYuleInputs Generates the inputs necessary to run richness.yule.test() in ape
sample.data Sample data for windex
sample.tree Phylogenetic tree to accompany sample.data
se Calculates standard error
test.windex Tests for particularly strong convergent evolution given topological constraints
treecheck Checks a set of phylogenetic trees to confirm they are ultrametric and binary.
treedatacheck Checks a set of phylogenetic trees to confirm they are ultrametric and binary and that tip labels match a list of names.
windex Calculates Wheatsheaf index with 95% confidence intervals
windex.sim.test Tests for presence of convergent evolution (over and above that expected from Brownian motion)