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Link stool specimens to AFP cases with the days to laboratory receipt

Source: R/afp_quality.R
afp_specimen_receipt.Rd

Returns one row per stool specimen of the supplied AFP cases, with the days from collection to receipt in the laboratory and the case's administrative unit. A specimen without a collection date is dropped. A receipt dated before collection is treated as an entry error and its interval set to NA. Each specimen takes the administrative unit of the first case row with its EPID.

Usage

afp_specimen_receipt(
  specimens,
  cases,
  level = "adm0",
  from = NULL,
  to = NULL,
  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: "adm0" (country, the default), "adm1" (province) or "adm2" (district). Cases with no identifier at that level are left out.

from, to

First and last onset date of the reporting window, or NULL for no bound.

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 epid, collected, received, days, collection_month, level, guid and name.

See also

afp_specimen_rung() for the laboratory stage each specimen has reached.

Examples

cases <- tibble::tibble(
  epid = c("E1", "E2"),
  adm0_guid = "G0",
  adm0 = "Country",
  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", NA)),
  date_stool_received_in_lab = as.Date(c("2025-03-09", NA, NA))
)
afp_specimen_receipt(specimens, cases)
#> # A tibble: 2 × 8
#>   epid  collected  received    days guid  name    collection_month level
#>   <chr> <date>     <date>     <int> <chr> <chr>   <date>           <chr>
#> 1 E1    2025-03-02 2025-03-09     7 G0    Country 2025-03-01       adm0 
#> 2 E1    2025-03-03 NA            NA G0    Country 2025-03-01       adm0