Plot MCMC trace for infections per individual

Source: R/plots.R

Plot MCMC trace for infections per individual

plot_infection_history_chains_indiv(
  inf_chain,
  burnin = 0,
  indivs = NULL,
  pad_chain = TRUE
)

Arguments

inf_chain

the data table with infection history samples from serosolver
burnin

optionally remove all samp_no < burnin from the chain
indivs

vector of integers, if not NULL, only plots a subset of individuals (where 1 is the first individual)
pad_chain

if TRUE, pads the infection history MCMC chain to have entries for non-infection events

Value

a list of two ggplot objects - the MCMC trace and MCMC densities

See also

plot_infection_history_chains_indiv

Other infection_history_plots: calculate_infection_history_statistics(), generate_cumulative_inf_plots(), plot_data(), plot_infection_histories(), plot_infection_history_chains_time(), plot_number_infections(), plot_posteriors_infhist(), plot_total_number_infections()

Examples

if (FALSE) {
data(example_inf_chain)
plot_infection_history_chains_indiv(example_inf_chain, 0, 1:10, FALSE)
}