adjustRate {pedmut} | R Documentation |
Adjust the overall mutation rate of a model
Description
Adjusts the overall mutation rate of a model by scaling the off-diagonal matrix entries.
Usage
adjustRate(mutmat, newrate, afreq = NULL, rate = NULL)
Arguments
mutmat |
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.
Value
A new mutation matrix with the adjusted rate.
See Also
Examples
m = mutationMatrix("equal", afreq = c(a=0.2, b=0.3, c=0.5), rate = 0.2)
m
adjustRate(m, 0.4)
[Package pedmut version 0.9.0 Index]