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Classify stool adequacy for AFP cases

Source: R/afp_quality.R
afp_stool_adequacy.Rd

Returns one logical value per case: TRUE when the stools are adequate, FALSE when they are not, and NA when the definition cannot assess the case. Three definitions are in use and definition selects one.

Usage

afp_stool_adequacy(
  cases,
  definition = c("polished", "polis_field", "followup"),
  cols = list(),
  first_stool_days = c(0, 13),
  second_stool_days = c(1, 14),
  min_days_apart = 1,
  good_condition = "Good",
  poor_condition = "Poor",
  unknown_condition = "Unknown",
  good_onset_quality = "Good",
  adequate_value = "Yes"
)

Arguments

cases

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

definition

One of "polished", "polis_field" or "followup".

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().

first_stool_days

Earliest and latest day after onset at which stool 1 counts (default c(0, 13)).

second_stool_days

Earliest and latest day after onset at which stool 2 counts (default c(1, 14)).

min_days_apart

Fewest days between stool 1 and stool 2 (default 1).

good_condition, poor_condition, unknown_condition

Condition values for a stool in good condition, in poor condition and of unknown condition (defaults "Good", "Poor", "Unknown").

good_onset_quality

Onset date quality value that lets a case be assessed under "polished" (default "Good"). A missing onset date quality column or value does not exclude the case.

adequate_value

Value of the POLIS field that means adequate under "polis_field" (default "Yes").

Value

A logical vector with one element per row of cases.

Details

  • "polished" (the default) is the rule behind the adq_code that calc_polio_indicators() uses for stool_adequacy_cond_pct. A case is adequate when stool 1 was collected 0 to 13 days after onset, stool 2 was collected 1 to 14 days after onset, the two were at least one day apart, and both were recorded in good condition. A stool outside its window, a missing stool 1 to stool 2 interval, stools less than a day apart or a stool in poor condition makes the case inadequate. A case is not assessed (NA) when either condition is missing or unknown, or when the onset date quality is recorded as anything other than good. TRUE here corresponds to code 1 and FALSE to code 0 of that engine.

  • "polis_field" reads the adequacy POLIS writes itself, in the field adequate_stool_with_condition: a case is adequate when the field equals adequate_value, inadequate when it holds any other value, and NA when it is empty. The rise-afg stool collection page and its SPI code used this definition.

  • "followup" is the rule of the CDC desk review that the rise-afg 60-day follow-up page used. The timing windows are the same as "polished", and a stool outside them or a missing stool makes the case inadequate. A condition counts as good when it matches good_condition (ignoring case) or is blank, so a case is never left unassessed.

Timing uses the interval columns clean_afp() writes (onset_to_stool1, onset_to_stool2, stool1_to_stool2), in days.

Examples

cases <- tibble::tibble(
  onset_to_stool1 = c(2, 2, 20),
  onset_to_stool2 = c(3, 3, 21),
  stool1_to_stool2 = c(1, 1, 1),
  stool1condition = c("Good", NA, "Good"),
  stool2condition = c("Good", "Good", "Good"),
  adequate_stool_with_condition = c("Yes", "Yes", "No")
)
afp_stool_adequacy(cases)
#> [1]  TRUE    NA FALSE
afp_stool_adequacy(cases, definition = "followup")
#> [1]  TRUE  TRUE FALSE
afp_stool_adequacy(cases, definition = "polis_field")
#> [1]  TRUE  TRUE FALSE