# NOT RUN {
# 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)
}
# }
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