fill_DTMCmats: Compute the uniformized matrix (R) of Q and its...

In jsigao/prioritree: A utility for improving phylodynamic analyses in BEAST

Compute the uniformized matrix (R) of Q and its exponentiations (R^2, R^3, ..., R^n) Here the vector of uniformized matrices in stored globally so we check if the provided n (number of events) exceeds the maximum exponent minus 1 (as the first element is an identity matrix) and only append the additional exponentiation(s) when it exceeds

Description

Compute the uniformized matrix (R) of Q and its exponentiations (R^2, R^3, ..., R^n) Here the vector of uniformized matrices in stored globally so we check if the provided n (number of events) exceeds the maximum exponent minus 1 (as the first element is an identity matrix) and only append the additional exponentiation(s) when it exceeds

Usage

fill_DTMCmats(Q, n, indices = NULL)

Arguments

Q	An instantaneous-rate matrix (or a list of matrices for a piecewise constant geographic model) characterizes the CTMC
n	Number of events (which is also the largest exponent to compute in this step)
indices	Which interval we need to update (if not provided then update all)

jsigao/prioritree documentation built on Jan. 9, 2023, 5:35 a.m.