Useful plot for looking at simulated data

Plots measured titres and known infection histories for all individuals, facetted by sample time (multi-strain panel) or virus variable (longitidunal single strain)

plot_data(
  titre_dat,
  infection_histories,
  strain_isolation_times,
  n_indivs,
  start_inf = NULL,
  study_design = "multi-strain"
)

Arguments

titre_dat	the data frame of titre data
infection_histories	the infection history matrix
strain_isolation_times	the vector of times at which individuals could be infected
n_indivs	how many individuals to plot
start_inf	if not NULL, plots the infection history matrix used as the starting point in the MCMC chain
study_design	default "multi-strain" facets by sample time. "single-strain" gives sample time on the x-axis and colours by virus

Value

a ggplot object

See also

Other infection_history_plots: calculate_infection_history_statistics(), generate_cumulative_inf_plots(), 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_titre_dat)
data(example_inf_hist)
data(example_antigenic_map)
strain_isolation_times <- example_antigenic_map$inf_times
plot_data(example_titre_dat, example_inf_hist, strain_isolation_times, 5)
}