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Adjusts the overall mutation rate of a model by scaling the off-diagonal matrix entries.
adjustRate(mutmat, newrate, afreq = NULL, rate = NULL)A new mutation matrix with the adjusted rate.
A mutation matrix with nonzero mutation overall rate.
The new overall mutation rate.
The allele frequencies. Extracted from the mutation matrix if not provided.
The current overall mutation rate. Calculated from the input if not provided.
The adjusted matrix is calculated as a * M + (1-a) * I, where M is the
original matrix, a = newrate/rate, and I is the identity matrix.
The maximum allowed value of newrate (to avoid negative values in the
adjusted matrix) is rate/(1 - m)), where m is the smallest diagonal
element in the original matrix.
mutRate()
m = mutationMatrix("equal", afreq = c(a=0.2, b=0.3, c=0.5), rate = 0.2)
m
adjustRate(m, 0.4)
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