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Calculate days from stool collection to laboratory receipt by month

Source: R/afp_quality.R
calc_afp_specimen_receipt_monthly.Rd

For each month of collection, the number of specimens, the number received and percentiles of the days from collection to receipt among those received. There is no threshold. Specimens not yet received are counted in awaiting, since their intervals can only lengthen the month once they arrive.

Usage

calc_afp_specimen_receipt_monthly(
  specimens,
  cases,
  level = "adm0",
  from = NULL,
  to = NULL,
  as_of = Sys.Date(),
  probs = c(p50 = 0.5, p75 = 0.75, p90 = 0.9),
  tail_prob = 0.9,
  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.

as_of

The reporting date, as a Date or a string that as.Date() reads. Defaults to Sys.Date(). Months are judged provisional against it.

probs

Named percentiles to report (default c(p50 = 0.5, p75 = 0.75, p90 = 0.9)), as quantile type 7.

tail_prob

Percentile whose interval decides when a month is no longer provisional (default 0.9).

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 and collection month: level, guid, name, collection_month, specimens, received, one column per element of probs, awaiting and provisional.

Details

A month is provisional while the overall tail_prob percentile interval (default the 90th, across all months and units) has not yet passed since its last day, as of as_of.

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", "2025-03-04")
  ),
  date_stool_received_in_lab = as.Date(c("2025-03-09", NA, "2025-03-06"))
)
calc_afp_specimen_receipt_monthly(specimens, cases, as_of = "2025-06-30")
#> # A tibble: 1 × 11
#>   level guid  name    collection_month specimens received   p50   p75   p90
#>   <chr> <chr> <chr>   <date>               <int>    <int> <dbl> <dbl> <dbl>
#> 1 adm0  G0    Country 2025-03-01               3        2   4.5  5.75   6.5
#> # ℹ 2 more variables: awaiting <int>, provisional <lgl>