A mutation matrix with nonzero mutation overall rate.
newrate
The new overall mutation rate.
afreq
The allele frequencies. Extracted from the mutation matrix if
not provided.
rate
The current overall mutation rate. Calculated from the input if
not provided.
Details
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.