Description Usage Arguments Details
This function determines the Ne and mutation rate assuming all infections begin as a clone and then mutations are built upon this base. The probability of a site going from 0 to x given mu, Ne, and t generations given in Rouzine 2001 JVI as
1 |
x |
The measured frequency - must be between 0 and 1 |
mu |
The mutation rate per nucleotide per cellular infectious cycle |
Ne |
The effective population size |
t |
Generations |
gc_ul |
titer default to NULL use if interested in adjusting for sensitivity |
acc |
sensitivity data frame default is NULL use if interested in adjusting for sensitivity |
g(f,t) = \frac{2 μ N_e}{f} e^{- \frac{2N_ef}{t}}
The output is adjusted to account for the sensitivity. This isn't important in fitting, but it is nice in testing to know the prob of being found+ prob of not being found =1
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