joint.post.moments.phylojumps: Joint posterior moments of labeled substitution counts on a...

In dunleavy005/phylomoments: Efficient Computations of Phylogenetic Stochastic Mapping Moments

Description

This function computes the posterior means, variances, and covariance of labeled substitution counts over two prespecified sets of branches on a phylogeny using a simulation-free dynamic programming algorithm.

Usage

joint.post.moments.phylojumps(tree, rate.mat, label.mat,
                              edge.set1 = NULL, edge.set2 = NULL,
                              subtree = NULL, root.dist, scale = FALSE,
                              states = c("a","c","g","t"), seq.data)

Arguments

tree	A tree object of class "phylo" (ape format).
rate.mat	A reversible continuous-time Markov chain (CTMC) rate matrix.
label.mat	A 0-1 matrix of the same size as rate.mat. This matrix labels the substitutions of interest.
edge.set1, edge.set2	Two integer vectors of branch indices specifying the branch sets over which the joint posterior moments will be calculated.
subtree	An integer denoting a node index in the tree. If provided, then edge.set1 will consist of the branches in the subtree beneath the specified node (including the branch above subtree), while edge.set2 will contain the branches in the complementary supertree.
root.dist	A numeric vector defining the root distribution of the evolutionary process on the tree. If this process starts at stationarity (as is commonly assumed), then the root distribution is equal to the CTMC stationary distribution.
scale	A logical indicating whether to scale the time dimension. If TRUE, then time is specified in terms of the expected number of CTMC substitutions per site.
states	A character or integer vector denoting the CTMC state space. Defaults to the set of DNA nucleotides c("a","c","g","t").
seq.data	A character or integer matrix representing the observed sequence alignment with rows (columns) that correspond to the sequences (sites) under study. All elements of seq.data must be contained in the vector states.

Details

More information on phylogenetic tree objects of class "phylo" can be found at http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf.

Value

A numeric vector holding the posterior means, variances, and covariance of labeled substitution counts summed over all sites in seq.data.

References

Dhar A and Minin VN (2017) “Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time”, Journal of Computational Biology, 24(5):377-399.

See Also

joint.prior.moments.phylojumps, joint.postmean.moments.phylojumps, post.moments.phylojumps

dunleavy005/phylomoments documentation built on May 15, 2019, 5:59 p.m.