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Determine if an admission is proven SARS-CoV-2 PCR positive

Source: R/augment-avoncap.R
derive_covid_status.Rd

SARS-CoV-2 PCR positive only lab confirmed diagnosis.

Usage

derive_covid_status(df, v, ...)

Arguments

df

the dataframe.

v

the value set. usually precomputed by the augment framework the value set can be explicitly supplied with v = get_value_sets(df)

...

ignored

Value

a dataframe

Details

admission.covid_pcr_result:

  • based on fields: c19_adm_swab and covid_19_diagnosis

  • Patient reported, clinical diagnoses are assumed PCR negative (although possible in some cases they may not have been done).

  • Lateral flows done in hospital are counted as PCR negative.

  • negative admission swabs are counted as negative

  • NA signifies test not done.

admission.is_covid:

  • Binary confirmed or no-evidence.

  • PCR results count as confirmed,

  • Lateral flow results count as confirmed,

  • anything else is no evidence (includes negatives and test not done)