Import a FHIR R4 Observation as a clinical score

Parses an HL7 FHIR R4 Observation (as produced by toFHIRObservation) back into a ClinicalScore, the import counterpart of the to*/write* exporters. The instrument_id and each subscale name are recovered from the bundled LOINC map (reverse code lookup, then display, then the verbatim text); the total and subscale values come from valueQuantity (a dataAbsentReason becomes NA); the subject id strips a leading "Patient/"; and the timestamp comes from effectiveDateTime.

Usage

fromFHIR(observation)

Arguments

observation

A FHIR Observation as a list (a toFHIRObservation result or a parsed jsonlite object), a JSON string, or a path to a .json file.

Value

A ClinicalScore.

Details

The round-trip is lossy for three slots that toFHIRObservation does not serialize: items_used and missing_handling cannot be recovered, and stratum is re-derived from the total only when the instrument is registered (via getInstrument), otherwise NA.

See also

toFHIRObservation, writeFHIRBundle

Examples

sc <- scoreInstrument("katz_adl",
  stats::setNames(rep(1, 6), getInstrument("katz_adl")@items),
  subject_id = "P01")
fromFHIR(toFHIRObservation(sc))@total
#> [1] 6