Phylogenetic Pairwise Contrasts

Documentation for package ‘phylowise’ version 0.0.1

getDistanceMatrix	Build a distance matrix from a tree (time tree or substitution tree)
plotPairs	Plot a set of sampled pairs onto a tree
PPC.test	Phylogenetic pairwise contrast test on a series of taxon pairs, using ordinary least squares and Bayesian model averaging (BMA). This method does not do multivariate regression, but it returns the data frame that can be used for it.
readBeastTrees	Read a single summary tree or a posterior distribution of annotated nexus trees generated by the BEAST software suites, and apply burn-in. Built on top of the phylotate::read_annotated function.
sampleTaxonPairs	Sample a set of taxon pairs from the tree. These taxa will have non-overlapping edges between their paths and can this be treated as statistically independent. The algorithm iteratively searches for two random taxa that satisfy sampling requirements until there are no more valid pairs. Each pair must descend from an MRCA with dist.min <= tMRCA <= dist.max. c++ is used to speed up the runtime of this code.
simulateSubstitutions	Simulate a substitution count down each branch of a tree. First, the branch rates are sampled from a correlated, uncorrelated or OU process that can be dependent on traits. Then the number of substitutions along each branch is sampled from a Poisson distribution.
simulateTrait	Simulate a trait down a tree using Brownian motion (BM)