int.states.sim: Simulation of internal node states on a phylogenetic tree.

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

Description

Samples internal node states on a phylogeny conditional on the observed tip states.

Usage

int.states.sim(tree, rate.mat, root.dist, scale = FALSE,
               states = c("a","c","g","t"), tip.data, N)

Arguments

tree	A tree object of class "phylo" (ape format).
rate.mat	A continuous-time Markov chain (CTMC) rate matrix.
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").
tip.data	A character or integer vector of observed tip states. These tip states must be contained in the vector states.
N	An integer specifying the number of samples to draw.

Details

This simulation function follows the procedure outlined in Nielsen (2002).

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

Value

A character or integer matrix with dimensions c(2*length(tree$tip.label)-1, N), where each column contains an independent sample of internal node states along with the observed tip states.

References

Nielsen R (2002) “Mapping mutations on phylogenies”, Systematic Biology, 51(5):729-739.

See Also

tips.sim, phylojumps.sim

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