If extracted_posts is NULL then posts object is used to first extract the incidence draws from posterior (note this will take longer)

hom_plot_incidence_by_location(
  extracted_posts = NULL,
  posts = NULL,
  outbreak_cases = NULL,
  end_time = 60,
  location_labels = NULL,
  sort = TRUE
)

Arguments

extracted_posts

object returned by hom_extract_posterior_draws

posts

Object after calling extract of stan model object of hierarchical model

outbreak_cases

matrix of outbreak case data

end_time

time in days to plot up until

location_labels

tibble with columns `site` and `location`. Will be used to relabel numeric location to values in `site` column

sort

TRUE/FALSE. If TRUE (default), locations will be ordered by mean R0

Value

list containing: * plot - ggplot object * table - tibble object of results

Note

Naming convention throughout is snake case with prefix "hom_" to denote Hierarcical Outbreak Model

Examples

if (FALSE) { mod # RSTAN fit object outbreak_cases <- matrix(c(0,0,1,2,3,0,0,2,4,5),ncol=2) # data of outbreaks in matrix form posts <- rstan::extract(mod) # extract posterior from model object extracted_posts <- hom_extract_posterior_draws(posts) # get object of incidence and r0 result <- hom_plot_incidence_by_location(extracted_posts=extracted_posts, outbreak_cases=outbreak_cases) # plot results show(result$plot) }