setup_infection_histories_old: Propose initial infection histories - OLD VERSION

In seroanalytics/serosolver: Inference Framework for Serological Data

Propose initial infection histories - OLD VERSION

Description

Given a matrix of titre data, proposes plausible initial infection histories from which to begin MCMC sampling. NOTE - MIGHT NEED TO UPDATE THIS FOR GROUPS

Usage

setup_infection_histories_old(
  titre_dat,
  strain_isolation_times,
  sample_prob,
  titre_cutoff = 3
)

Arguments

titre_dat	the matrix of titres data with columns for individual, sample, and titre
strain_isolation_times	vector of real times for all strains
sample_prob	given an infection seems likely based on titre, suggest infection with 1 minus this probability
titre_cutoff	specifies how high the titre must be to imply an infection

Value

an nxm matrix of infection histories containing 1s and 0s, where n is the number of individuals and m is the number of potential infecting strains

See Also

Other setup_infection_histories: setup_infection_histories_titre(), setup_infection_histories_total(), setup_infection_histories()

Examples

data(example_titre_dat)
data(example_antigenic_map)
start_inf <- setup_infection_histories_old(example_titre_dat, example_antigenic_map$inf_times, 0.2, 3)

seroanalytics/serosolver documentation built on April 24, 2023, 9:52 a.m.