expokit_dgpadm_Qmat {rexpokit} | R Documentation |
EXPOKIT dgpadm matrix exponentiation on Q matrix
Description
This function exponentiates a matrix via the EXPOKIT padm
function (designed for small dense matrices) and wrapper
function wrapalldgpadm_
around dmexpv.
Usage
expokit_dgpadm_Qmat(Qmat = NULL, t = 2.1,
transpose_needed = TRUE)
Arguments
Qmat |
an input Q transition matrix |
t |
one or more time values to exponentiate by |
transpose_needed |
If TRUE (default), matrix will be transposed (apparently EXPOKIT needs the input matrix to be transposed compared to normal) |
Details
From EXPOKIT:
* Computes exp(t*H), the matrix exponential of a
general matrix in
* full, using the
irreducible rational Pade approximation to the
* exponential function exp(x) = r(x) = (+/-)( I +
2*(q(x)/p(x)) ),
* combined with
scaling-and-squaring.
If Qmat
is NULL (default), a default matrix is
input.
Value
tmpoutmat
the output matrix. wrapalldmexpv_
produces additional output relating to accuracy of the
output matrix etc.; these can be obtained by a direct
call of wrapalldmexpv_.
Author(s)
Nicholas J. Matzke nickmatzke.ncse@gmail.com and Drew Schmidt schmidt@math.utk.edu
See Also
Examples
# Example:
# Make a square instantaneous rate matrix (Q matrix)
# This matrix is taken from Peter Foster's (2001) "The Idiot's Guide
# to the Zen of Likelihood in a Nutshell in Seven Days for Dummies,
# Unleashed" at:
# \url{http://www.bioinf.org/molsys/data/idiots.pdf}
#
# The Q matrix includes the stationary base freqencies, which Pmat
# converges to as t becomes large.
Qmat = matrix(c(-1.218, 0.504, 0.336, 0.378, 0.126, -0.882, 0.252, 0.504, 0.168,
0.504, -1.05, 0.378, 0.126, 0.672, 0.252, -1.05), nrow=4, byrow=TRUE)
# Make a series of t values
tvals = c(0.001, 0.005, 0.01, 0.05, 0.1, 0.5, 1, 2, 5, 14)
# Exponentiate each with EXPOKIT's dgpadm (good for small dense matrices)
for (t in tvals)
{
Pmat = expokit_dgpadm_Qmat(Qmat=Qmat, t=t, transpose_needed=TRUE)
cat("\n\nTime=", t, "\n", sep="")
print(Pmat)
}