mut_model_LL: Mutation rate and Ne from spectrum

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

mut_model_LL(data, mu, Ne, gen_time = 6, neg = FALSE,
  acc = accuracy_stringent)

Arguments

data	The data frame containing iSNV calls. It must have the following columns: freq.var,DPI-days post infection, and only contain 1 allele/ site. Sites not present will be assumed to not have a variant present.
mu	The mutation rate per nucleotide per cellular infectious cycle
Ne	The effective population size
gen_time	The generation time in hours. Default to 6
neg	Boolean return the negative log likelihood not. Default =FALSE
acc	An accuracy data frame

Details

g(f,t) = \frac{2 μ N_e}{f} e^{- \frac{2N_ef}{t}}

This model makes some assumptions. 1) Every infection began with every potential loci with a mutation at frequency 0 - we only model minor alleles 2) The population develops under neutral processes 3) Because we intrate numerically we assume anything present at less than 0.001 (0.1 is essentially at 0. 4) There are 13133 sites that can contain mutations - the number of nucleotides in our concatenated 2014-2015 sample

Value

The log likihood for the data given the parameters and the model

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