setup_infection_histories_titre: Propose initial infection histories based on titres - use...

In seroanalytics/serosolver: Inference Framework for Serological Data

Propose initial infection histories based on titres - use this!

Description

Very similar to setup_infection_histories, but is not restricted to placing starting infections against viruses to which an individual has a titre. Given a matrix of titre data, proposes plausible initial infection histories from which to begin MCMC sampling. The idea is to move along time in the context of antigenic drift and look at an individual's titre against each strain. Where titres are raised, we suggest an infection. However, to avoid suggesting multiple infections for regions of high antigenic similarity, we place a necessary gap (defined by 'space') between proposed infection times.

Usage

setup_infection_histories_titre(
  titre_dat,
  strain_isolation_times,
  space = 5,
  titre_cutoff = 2,
  sample_prob = 0.9
)

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
space	how many epochs must separate proposed infections
titre_cutoff	specifies how high the titre must be to imply an infection
sample_prob	if titre suggests an infection, then add an infection with 1 minus this probability

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_old(), setup_infection_histories_total(), setup_infection_histories()

Examples

data(example_titre_dat)
data(example_antigenic_map)
start_inf <- setup_infection_histories_titre(example_titre_dat, example_antigenic_map$inf_times)

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