plot_attack_rates: Plot historical attack rates
In seroanalytics/serosolver: Inference Framework for Serological Data

plot_attack_rates

R Documentation

Plot historical attack rates

Description

Plots inferred historical attack rates from the MCMC output on infection histories

Usage

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
)

Arguments

`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