plot_attack_rates: Plot historical attack rates

In seroanalytics/serosolver: Inference Framework for Serological Data

Plot historical attack rates

Description

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

Usage

plot_attack_rates(
  infection_histories,
  antibody_data = NULL,
  possible_exposure_times = NULL,
  n_alive = NULL,
  ymax = 1,
  resolution = 1,
  pad_chain = TRUE,
  true_ar = NULL,
  by_group = FALSE,
  group_subset = NULL,
  cumulative = FALSE,
  add_box = FALSE,
  settings = NULL
)

Arguments

infection_histories	the MCMC chain for infection histories
antibody_data	the data frame of antibody data
possible_exposure_times	vector of the epochs of potential infection
n_alive	vector with the number of people alive in each year of possible infection Can be left as NULL, and the 'birth' variable in 'antibody_data' will be used to calculate the number alive
ymax	Numeric. the maximum y value to put on the axis. Default = 1.
resolution	Integer. How many buckets of time is each year split into? ie. 12 for monthly data, 4 for quarterly etc. Default = 1 for annual.
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.
true_ar	data frame of true attack rates, with first column 'time' matching 'possible_exposure_times', and second column 'AR' giving the attack rate. Column names: population_group, time, AR
by_group	if TRUE, facets the plot by population_group ID
group_subset	if not NULL, plots only this subset of groups eg. 1:5
cumulative	if TRUE, plots the cumulative attack rate
settings	if not NULL, list of serosolver settings as returned from the main serosolver function

Value

a ggplot2 object with the inferred attack rates for each potential epoch of circulation

seroanalytics/serosolver documentation built on Dec. 14, 2024, 5:33 a.m.