simulations: Simulate probability of transmission based on frequency

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

Description

Simulate probability of transmission based on frequency

Usage

simulations(data, runs, lambda, FUN, threshold = NULL, acc = NULL, ...)

Arguments

data	data frame of transmission data
runs	how many simulations to run
lambda	What is the lamda of the zero truncated Poisson to use
FUN	what function to use to simulate the found column pa_sim or betabin_sim unquoted
threshold	- optional to pass to betabinomial simulator
acc	optional to pass to betabinomial simulation
...	columns to group for simulations. These will get the same bottleneck size within each replication. It should probably only ever be pair_id.(ie each person gets the same bottleneck within a run)

Value

a data frame of simulated logit fits to frequency in donor vs. probability of transmission

Examples

simulations(small_trans,10,3.2,pa_sim)
simulations(small_trans,10,3.2,betabin_sim,0.02,accuracy_stringent)

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