moments.ctmcjumps: Restricted factorial moments of labeled substitution counts...

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

Description

This function calculates the 0th, 1st, and 2nd restricted factorial moment matrices of labeled substitution counts for a reversible continuous-time Markov chain (CTMC) model.

Usage

moments.ctmcjumps(t, rate.mat, label.mat,
                  root.dist = NULL, scale = FALSE)

Arguments

t	A nonnegative numeric vector of CTMC time interval lengths.
rate.mat	A reversible CTMC rate matrix.
label.mat	A 0-1 matrix of the same size as rate.mat. This matrix labels the substitutions of interest.
root.dist	A numeric vector defining the CTMC stationary distribution. This only needs to be specified when scale = TRUE.
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.

Details

The 0th restricted factorial moment matrix of labeled CTMC substitution counts is defined as the CTMC transition probability matrix.

Value

A list with named elements "zeroth", "first", and "second". Each list element is a three-dimensional array with dimensions c(nrow(rate.mat), ncol(rate.mat), length(t)). The "zeroth", "first", and "second" elements of this list contain the 0th, 1st, and 2nd restricted factorial moment matrices of labeled CTMC substitution counts, respectively, for the time interval lengths defined by t.

References

Minin VN and Suchard MA (2008) “Counting labeled transitions in continuous-time Markov models of evolution”, Journal of Mathematical Biology, 56(3):391-412.

See Also

ctmc.sim

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