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Derive the fused AFP virus type and analytic classification

Source: R/clean_afp.R
clean_afp_classification.Rd

Decodes the specific poliovirus and fuses it with the case classification into one analytic label, using standard WPV (wild poliovirus) nomenclature throughout – not the legacy WILD n strings, which do not match how downstream surveillance code filters (grepl("WPV|cVDPV", ...)).

Usage

clean_afp_classification(data)

Arguments

data

A cleaned AFP data frame carrying at least classification (and ideally polio_virus_types, vdpv_classifications).

Value

data with vtype, vtype_fixed, classification_all, sabin1/sabin2/sabin3 and (when derivable) hot_case added; the raw classification, polio_virus_types and vdpv_classifications columns are left untouched.

Details

Two layers:

  1. vtype / vtype_fixed decode the virus from polio_virus_types + vdpv_classifications. A VDPV always carries an explicit kind prefix – cVDPV (circulating), aVDPV (ambiguous), iVDPV (immune-deficient) – so the three are never merged or silently dropped; an untyped VDPV n only remains when the kind is genuinely unknown. A few historical country corrections patch early records (Congo 2010, Nigeria 2011, pre-2010 wild) where the virus field was not yet populated.

  2. classification_all is the single analysis label: the vtype_fixed virus string for virus-positive cases, otherwise the raw POLIS classification recoded – Discarded -> NPAFP, Compatible -> COMPATIBLE, Not an AFP -> NOT-AFP, Pending -> PENDING (LAB PENDING when the specimen never reached the lab), VAPP -> VAPP, Not Applicable/Others/VDPV -> UNKNOWN. Cases matching none stay none/NA for manual review.

Classification vocabulary (match on these prefixes, not free text)

Wild

WPV 1, WPV 2, WPV 3, WPV1andWPV3 – prefix WPV.

Circulating VDPV

cVDPV 1/2/3 and combinations – prefix cVDPV.

Ambiguous VDPV

aVDPV 1/2/3 – prefix aVDPV. Include/exclude is a deliberate analyst choice; these are labelled, never folded into cVDPV.

Immune-deficient VDPV

iVDPV 1/2/3 – prefix iVDPV. Same explicit choice as aVDPV.

Untyped VDPV

VDPV 1/2/3 – a VDPV whose kind is unknown.

Wild + VDPV co-detection

WPV1and... (e.g. WPV1andcVDPV 2).

Non-virus

NPAFP, COMPATIBLE, NOT-AFP, PENDING, LAB PENDING, VAPP, UNKNOWN.

So "any WPV1" is grepl("^WPV 1|^WPV1and", classification_all), and "any circulating VDPV2" is grepl("cVDPV 2", classification_all).

Also derives the Sabin-detection flags (sabin1/sabin2/sabin3) and, where the paralysis fields are present, a recomputed hot_case (POLIS also ships paralysis_hot_case; this applies the standard asymmetric + onset-fever + rapid-progression definition, which can differ). Every condition is NA-safe: a missing classification/admin/year leaves the prior value intact rather than nulling it.

Examples

clean_afp_classification(data.frame(
  classification = c("Discarded", "Confirmed (wild)"),
  polio_virus_types = c(NA, "WILD1"),
  vdpv_classifications = c(NA, NA)
))
#>     classification polio_virus_types vdpv_classifications vtype vtype_fixed
#> 1        Discarded              <NA>                   NA  <NA>        <NA>
#> 2 Confirmed (wild)             WILD1                   NA WPV 1       WPV 1
#>   classification_all sabin1 sabin2 sabin3
#> 1              NPAFP     NA     NA     NA
#> 2              WPV 1      0      0      0