Plots inferred historical attack rates from the MCMC output on infection histories
plot_attack_rates( infection_histories, titre_dat, strain_isolation_times, n_alive = NULL, pointsize = 1, fatten = 1, pad_chain = TRUE, prior_pars = NULL, plot_den = FALSE, true_ar = NULL, by_group = FALSE, group_subset = NULL, plot_residuals = FALSE, colour_by_taken = TRUE, by_val = 5 )
| infection_histories | the MCMC chain for infection histories |
|---|---|
| titre_dat | the data frame of titre data |
| strain_isolation_times | vector of the epochs of potential circulation |
| n_alive | vector with the number of people alive in each year of circulation. Can be left as NULL, and ages will be used to infer this |
| pointsize | Numeric - how big should each point be? |
| fatten | Numeric - fatten parameter for ggplot pointrange |
| pad_chain | if TRUE, fills the infection history data table with entries for non-infection events (ie. 0s). Can be switched to FALSE for speed to get a rough idea of what the attack rates look like. |
| prior_pars | if not NULL, a list of parameters for the attack rate prior, giving the assumed prior_version along with alpha and beta |
| plot_den | if TRUE, produces a violin plot of attack rates rather than pointrange |
| true_ar | data frame of true attack rates, with first column `year` equal to `strain_isolation_times`, and second column `AR` giving the attack rate. Column names: group, j, AR |
| by_group | if TRUE, facets the plot by group ID |
| group_subset | if not NULL, plots only this subset of groups eg. 1:5 |
| plot_residuals | if TRUE, plots the residuals between inferred and true attack rate |
| colour_by_taken | if TRUE, then colours the attack rates by whether or not titres against the circulating virus at that time were measured |
| by_val | frequency of x-axis labels |
| resolution | divides strain isolation times by this number for x axis labels |
a ggplot2 object with the inferred attack rates for each potential epoch of circulation