setup_infection_histories_new_2: Propose initial infection histories 2 - use this!

Description Usage Arguments Value See Also

Description

Very similar to setup_infection_histories_new, 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

1
2
setup_infection_histories_new_2(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


adamkucharski/serosolver documentation built on May 15, 2019, 10:36 p.m.