Calculate days from stool collection to laboratory receipt by area — calc_afp_specimen_receipt_by

For each administrative unit, the number of specimens received and percentiles of the days from collection to receipt. Units with fewer than min_received received specimens are left out. Rows are sorted from the longest interval at the highest percentile in probs, then at the lowest.

Usage

calc_afp_specimen_receipt_by_area(
  specimens,
  cases,
  level = "adm1",
  from = NULL,
  to = NULL,
  probs = c(p50 = 0.5, p75 = 0.75, p90 = 0.9),
  min_received = 20,
  cols = list()
)

Arguments

specimens: Cleaned human specimen table from clean_human_spec(), one row per specimen.
cases: AFP cases whose specimens are wanted. Only specimens whose EPID appears here are kept, so filter cases to the window first or use from and to.
level: Administrative level to group by (default "adm1", province).
from, to: First and last onset date of the reporting window, or NULL for no bound.
probs: Named percentiles to report (default c(p50 = 0.5, p75 = 0.75, p90 = 0.9)), as quantile type 7.
min_received: Fewest received specimens a unit needs to be listed (default 20).
cols: Named list overriding default column names, in the style of calc_polio_indicators(), for example list(cases = list(stool1_condition = "s1_cond")). The defaults are the polished defaults plus the module columns listed under Details of calc_afp_timeliness().

Value

A tibble with one row per unit: level, guid, name, received and one column per element of probs.

Examples

cases <- tibble::tibble(
  epid = c("E1", "E2"),
  adm1_guid = c("P1", "P2"),
  adm1 = c("Prov A", "Prov B"),
  paralysis_onset_date = as.Date("2025-03-01")
)
specimens <- tibble::tibble(
  epid = c("E1", "E1", "E2"),
  date_stool_collected = as.Date(
    c("2025-03-02", "2025-03-03", "2025-03-04")
  ),
  date_stool_received_in_lab = as.Date(c("2025-03-09", NA, "2025-03-06"))
)
calc_afp_specimen_receipt_by_area(specimens, cases, min_received = 1)
#> # A tibble: 2 × 7
#>   level guid  name   received   p50   p75   p90
#>   <chr> <chr> <chr>     <int> <dbl> <dbl> <dbl>
#> 1 adm1  P1    Prov A        1     7     7     7
#> 2 adm1  P2    Prov B        1     2     2     2