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Build the POLIS virus (positives) dataset from cleaned cases and ES

Source: R/clean_virus.R
clean_virus.Rd

Constructs the combined positives/virus analytic table from the outputs of clean_afp() and clean_es() – it does not read a raw POLIS viruses table. Every poliovirus-positive record (classification matching WPV/VDPV – i.e. WPV, cVDPV, aVDPV, iVDPV or untyped VDPV) becomes one row, harmonised to a shared schema and tagged by source:

  • surveillance_type ("human" / "environmental") and the finer source (the case surveillance_type_name – AFP / Community / Contact – or "Environmental");

  • measurement and classification_all: the analytic virus label in the shared WPV/cVDPV/aVDPV/iVDPV vocabulary both cleaners emit;

  • the case/sample geography (country_iso3code, adm0/adm1/adm2 + GUIDs), latitude/longitude, the event virus_date (paralysis onset for cases, collection for ES) with year_onset/month_onset, and notification_date;

  • report_date: the VDPV classification-change date for VDPV records, the notification date for WPV records;

  • emergence_group, nt_changes, virus_cluster, virus_is_orphan (the orphan-isolate flag, NA for ES rows since POLIS carries it only on cases), and – when a nopv_emergence reference is supplied – the novel-OPV2 flag nopv2.

Usage

clean_virus(
  cases = NULL,
  es = NULL,
  cfg = polis_active_config(),
  nopv_emergence = NULL,
  separate_rows = FALSE,
  verbose = TRUE
)

Arguments

cases

Optional cleaned AFP table (from clean_afp()). Its poliovirus-positive rows become the human positives.

es

Optional cleaned ES table (from clean_es()). Its poliovirus-positive rows become the environmental positives.

cfg

A polis_config() object. Defaults to polis_active_config() – the config most recently built by polis_config() this session – so a no-cfg call inherits the active session settings rather than fresh defaults.

nopv_emergence

Optional reference of novel-OPV2 (nOPV2) emergence-group names: a character vector, or a data frame with an emergence_group column. When supplied, records whose emergence_group matches are flagged nopv2. Default NULL (no nOPV2 flag).

separate_rows

If TRUE, co-detection records (a fused label such as WPV1andcVDPV 2 or VDPV12and3) are split into one row per detected serotype, with measurement/classification_all set to the component label. Default FALSE (one row per positive record, co-detections kept as the fused label).

verbose

Emit cli progress messages. Default TRUE.

Value

A tibble of poliovirus positives, one row per positive case/sample, columns ordered id -> location -> time -> classification -> dates -> other. When neither input has any positives, returns a 0-row, 0-column tibble.

Examples

cases <- clean_afp(data.frame(
  Id = 1, Epid = "A-1", `Last Update Date` = "2024-03-01",
  `Paralysis Onset Date` = "2024-01-02", `Notification Date` = "2024-01-09",
  `Polio Virus Types` = "WILD1", Classification = "Confirmed (wild)",
  `Admin0 Name` = "NIGERIA", check.names = FALSE
), verbose = FALSE)
clean_virus(cases = cases, verbose = FALSE)
#> # A tibble: 1 × 11
#>   epid  month_onset year_onset notification_date vtype classification_all
#>   <chr>       <dbl>      <dbl> <date>            <chr> <chr>             
#> 1 A-1             1       2024 2024-01-09        WPV 1 WPV 1             
#> # ℹ 5 more variables: virus_date <date>, report_date <date>,
#> #   surveillance_type <chr>, measurement <chr>, source <chr>