g_ft: Likelihood of frequency starting at 0

In jtmccr1/HIVEr: Analysis of transmission and intrahost iSNV data taken as part of the HIVE cohort

Description

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

Usage

g_ft(x, mu, Ne, t, gc_ul = NULL, acc = NULL)

Arguments

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

Details

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

jtmccr1/HIVEr documentation built on May 29, 2019, 1:50 a.m.