R: Analysing Convergent Evolution using the Wheatsheaf Index

# Analysing Convergent Evolution using the Wheatsheaf Index

## Documentation for package ‘windex’ version 2.1.0

- DESCRIPTION file

## Help Pages

backLog | Backtransforms coefficient estimates from logistic regression
error.bars | Plots error bars on a barplot
LRbarplot | Plots a barplot from logistic regression parameter estimates
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 and/or retrieving 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)