Add a Hospital Activity Feed (Patient-Days)

Raw case counts at a hospital can rise simply because the hospital is busier, not because infection risk has increased. If you can supply weekly patient-days (or admissions, or bed counts) per hospital, EpiSODIC can normalise case counts against activity for a more reliable signal. This feed is entirely optional: without it, detection falls back to raw counts, which is a reasonable default, not a broken one.

Usage

episodic_synthetic_institution_activity(
  institutions = episodic_synthetic_institutions(),
  start_date = end_date - 5 * 365,
  end_date = Sys.Date(),
  seed = 1
)

Arguments

institutions

A data frame (or tibble) of institutions from your own registry, with institution_key, institution_type and n_beds; filtered internally to hospitals only. Defaults to the synthetic registry episodic_synthetic_cases() draws on, so the two feeds line up with no arguments at all.

institution_key must be the same identifier your case feed uses, not the one episodic_db_institutions() returns: EpiSODIC stores a hash of your key rather than the key itself, and both feeds are hashed on load. Handing this function the database's own table produces a feed whose keys are already hashed, and none of it will match.

start_date, end_date

The period to generate weekly rows for. Defaults to the five years up to today, matching episodic_synthetic_cases().

seed

RNG seed, for reproducible demo data.

Value

A data frame with institution_key, period_start, period_end, patient_days, n_beds, source.

Details

This function is a synthetic example showing the expected shape: weekly patient-days per hospital, modelled as bed count times occupancy, with a realistic winter peak. Use it as a template for your own data, which you pass to episodic_run_cron() as institution_activity - normally a data frame or tibble.

Examples

institutions <- data.frame(
  institution_key = "HOSP-1", institution_type = "hospital", n_beds = 320
)
activity <- episodic_synthetic_institution_activity(
  institutions,
  start_date = as.Date("2025-01-01"), end_date = as.Date("2025-03-31")
)
head(activity)
#>   institution_key period_start period_end patient_days n_beds    source
#> 1          HOSP-1   2025-01-01 2025-01-07         1964    320 synthetic
#> 2          HOSP-1   2025-01-08 2025-01-14         1989    320 synthetic
#> 3          HOSP-1   2025-01-15 2025-01-21         2031    320 synthetic
#> 4          HOSP-1   2025-01-22 2025-01-28         2097    320 synthetic
#> 5          HOSP-1   2025-01-29 2025-02-04         1951    320 synthetic
#> 6          HOSP-1   2025-02-05 2025-02-11         2084    320 synthetic