postmean.moments.phylojumps: Moments of the posterior mean of labeled substitution counts...

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

Description

This function calculates the mean and variance of the posterior mean of labeled substitution counts over a prespecified set of branches on a phylogeny using a simulation-free dynamic programming algorithm and Monte Carlo sampling.

Usage

postmean.moments.phylojumps(tree, rate.mat, label.mat,
                            edge.set, root.dist,
                            scale = FALSE, N = 100000)

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.set	An integer vector of branch indices specifying the branch set over which the moments will be calculated.
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.
N	An integer specifying the number of Monte Carlo samples to draw.

Details

The mean obtained in this function is computed exactly, while the variance is partially approximated using Monte Carlo simulations.

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 mean and variance of the posterior mean of labeled substitution counts.

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

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

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