phylojumps.sim: Simulation of substitution counts on a phylogenetic tree.

Description Usage Arguments Details Value References See Also

Description

Simulates the number of substitutions on a phylogeny conditional on the observed tip states.

Usage

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phylojumps.sim(tree, rate.mat, root.dist, scale = FALSE,
               states = c("a","c","g","t"), seq.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").

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.

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

An integer matrix with dimensions c(N, ncol(seq.data)), where the i'th column contains N independent samples of substitution counts for the i'th site in seq.data.

References

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

See Also

int.states.sim, tips.sim


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