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.
getDistanceMatrix       Build a distance matrix from a tree (time tree
                        or substitution tree)
plotPairs               Plot a set of sampled pairs onto a tree
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)
