Plot cumulative and per time posterior infection probability densities

For each individual requested, plots the median and 95

generate_cumulative_inf_plots(
  inf_chain,
  burnin = 0,
  indivs,
  real_inf_hist = NULL,
  start_inf = NULL,
  strain_isolation_times,
  nsamp = 100,
  ages = NULL,
  number_col = 1,
  pad_chain = TRUE,
  subset_years = NULL,
  return_data = FALSE
)

Arguments

inf_chain	the infection history chain
burnin	only plot samples where samp_no > burnin
indivs	vector of individual ids to plot
real_inf_hist	if not NULL, adds lines to the plots showing the known true infection times
start_inf	if not NULL, adds lines to show where the MCMC chain started
strain_isolation_times	vector of times at which individuals could have been infected
nsamp	how many samples from the MCMC chain to take?
ages	if not NULL, adds lines to show when an individual was born
number_col	how many columns to use for the cumulative infection history plot
pad_chain	if TRUE, pads the infection history MCMC chain to have entries for non-infection events
subset_years	if not NULL, pass a vector of indices to only take a subset of indices from strain_isolation_times
return_data	if TRUE, returns the infection history posterior densities used to generate the plots

Value

two ggplot objects

See also

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

Examples

if (FALSE) {
data(example_inf_chain)
data(example_antigenic_map)
data(example_inf_hist)
data(example_titre_dat)

ages <- unique(example_titre_dat[,c("individual","DOB")])
times <- example_antigenic_map$inf_times
indivs <- 1:10
generate_cumulative_inf_plots(example_inf_chain, 0, indivs, example_inf_hist, NULL, times,
                              ages=ages, number_col=2,pad_chain=FALSE, return_data=TRUE)
}