Calculate means and HPD intervals of new infections per day from the cumulative infections posterior samples

This function takes the trajectory samples of cumulative infections from an EpiFusion posterior object and performs a row-wise 'diff' to find the mean and HPD interval for new daily infections.

calculate_daily_infections(
  cumulative_infection_samples,
  index_date = NA,
  include_median = FALSE
)

Arguments

cumulative_infection_samples

the samples of cumulative infection trajectories from an Epifusion posterior object (generated using the extract_posterior_epifusion() function with include_samples set to TRUE)

index_date

(optional) date you'd like the time series to count from, as a date object or as a string with format YYYY-MM-DD

include_median

(default FALSE) set to TRUE if you would like the median trajectory to be included in the output table

Value

a table with a column for Time and a column for Mean, Upper and Lower 95%, 88% and 66% HPDs for inferred Infections and Rt