plot_cumulative_infection_histories: Plot cumulative and per time posterior infection probability...

In adamkucharski/serosolver: Inference Framework for Serological Data

Plot cumulative and per time posterior infection probability densities

Description

For each individual requested, plots the median and 95

Usage

plot_cumulative_infection_histories(
  inf_chain,
  burnin = 0,
  indivs,
  real_inf_hist = NULL,
  start_inf = NULL,
  possible_exposure_times,
  nsamp = 100,
  ages = NULL,
  number_col = 1,
  pad_chain = TRUE,
  subset_times = 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
possible_exposure_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_times	if not NULL, pass a vector of indices to only take a subset of indices from possible_exposure_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_antibody_data(), plot_individual_number_infections(), plot_infection_history_chains_indiv(), plot_infection_history_chains_time(), plot_model_fits(), plot_posteriors_infhist(), plot_total_number_infections()

Examples

## Not run: 
data(example_inf_chain)
data(example_antigenic_map)
data(example_inf_hist)
data(example_antibody_data)

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

## End(Not run)

adamkucharski/serosolver documentation built on April 28, 2024, 6:19 p.m.