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

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) }