observed_cases_single: Cases arising on a given day which are reported between two...

In ben18785/incidenceinflation: Estimate R0 Given Case Reporting Delays

Cases arising on a given day which are reported between two subsequent days

Description

The number of cases originating on day_onset which are subsequently reported between day_1 and day_2 is modelled as a binomial distribution:

cases_reported\sim binomial(cases_true-cases_observed, p_detect)

where cases_observed is the number of cases originating on day_onset reported on day_1; p_detect is the probability a case was undetected on day_1 but is detected by day_2.

Usage

observed_cases_single(
  cases_observed,
  cases_true,
  day_2,
  day_1,
  day_onset,
  reporting_parameters
)

Arguments

cases_observed	observed case count for cases originating on day_onset on day_1
cases_true	true case count originating on day_onset
day_2	day of last observation: day_2 > day_1 >= day_onset
day_1	day of first observation: day_1 >= day_onset
day_onset	day when case originates
reporting_parameters	named list of 'mean' and 'sd' of gamma distribution characterising the reporting delay distribution

Value

a count representing number of cases reported between day_1 and day_2

ben18785/incidenceinflation documentation built on Feb. 8, 2024, 2:36 a.m.