Skip to contents

Calculate the stool specimen pathway for AFP cases

Source: R/afp_quality.R
calc_afp_specimen_pathway.Rd

The share of AFP cases meeting each stool collection component, in the order the adequacy definition builds it, ending on adequacy itself. The components are those of afp_stool_components().

Usage

calc_afp_specimen_pathway(
  cases,
  level = "adm0",
  from = NULL,
  to = NULL,
  collection_days = 14,
  min_days_apart = 1,
  adequacy = "polis_field",
  adequacy_args = list(),
  cols = list()
)

Arguments

cases

Cleaned AFP cases, one row per case (data.frame or tibble).

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.

collection_days

Latest day after onset at which a stool counts as collected in time (default 14).

min_days_apart

Fewest days between the two collection dates for apart (default 1).

adequacy

Stool adequacy definition passed to afp_stool_adequacy() (default "polis_field", which the rise-afg stool collection page used).

adequacy_args

Named list of further arguments for afp_stool_adequacy(), for example list(adequate_value = "YES").

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 step: level, guid, name, step, met, cases and pct. pct is on a scale of 0 to 100.

Details

  • Steps: first_in_window, both_in_window, apart and adequate.

  • Numerator (met): cases meeting the step.

  • Denominator (cases): every case in the unit and window.

  • Threshold: stools count within collection_days (default 14) of onset.

A case that adequacy cannot assess counts as not adequate here. The default adequacy is the POLIS field, as on the rise-afg page; this differs from stool_adequacy_cond_pct in calc_polio_indicators(), which applies the "polished" rule and leaves unassessed cases out of its denominator.

Examples

cases <- tibble::tibble(
  adm0_guid = "G0",
  adm0 = "Country",
  paralysis_onset_date = as.Date("2025-03-01"),
  stool1collection_date = as.Date("2025-03-03"),
  stool2collection_date = as.Date(c("2025-03-04", NA)),
  adequate_stool_with_condition = c("Yes", "No")
)
calc_afp_specimen_pathway(cases)
#> # A tibble: 4 × 7
#>   level guid  name    step              met cases   pct
#>   <chr> <chr> <chr>   <chr>           <int> <int> <dbl>
#> 1 adm0  G0    Country first_in_window     2     2   100
#> 2 adm0  G0    Country both_in_window      1     2    50
#> 3 adm0  G0    Country apart               1     2    50
#> 4 adm0  G0    Country adequate            1     2    50