Plot MCMC trace for infections per individual — plot_infection_history_chains_indiv • serosolver

Plots the MCMC trace and posterior density of the inferred total number of infections for selected individuals.

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

Arguments

inf_chain: the infection-history chain returned by load_mcmc_chains, in long format
burnin: if not already discarded, discards rows with `samp_no <= burnin`
indivs: optional vector of individual IDs, as recorded in `inf_chain$i`, to plot
pad_chain: if TRUE, adds zero-valued entries for infection events that are absent from the sparse chain

Value

A list containing the MCMC trace plot and posterior density plot.

See also

plot_infection_history_chains_indiv

Other infection_history_plots: calculate_infection_history_statistics(), plot_antibody_data(), plot_antibody_predictions(), plot_cumulative_infection_histories(), plot_estimated_antibody_model(), plot_individual_number_infections(), plot_infection_history_chains_time(), plot_infection_history_posteriors(), plot_model_fits(), plot_total_number_infections()

Examples

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