trans_fit: Fit the transmission model

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

Description

This is wrapper around math_fit that fits the presence absence model to each pair present in the data set.

Usage

trans_fit(data, Nb_max, model, threshold, acc, ...)

Arguments

data	a data frame or tibble it will be split by chr pos and pair_id
Nb_max	The maximum bottleneck size to test
model	PA or BetaBin will fit lambda of a zero truncated Poisson. PA-straight, BetaBin-straight will fit 1 Nb.
threshold	limit of variant calling detection
acc	a data frame with accuracy metrics
...	other columns to group by in final output.

Value

a tibble with columns pair_id,lambda,LL (log likelihood), and pair_id if desired.

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