Skip to contents

Construct a reliability-characterised biomarker

Source: R/biomarker.R
physioBiomarker-constructor.Rd

Builds a PhysioBiomarker carrying not just the value but the metadata a clinical reader needs: a confidence interval, a published reference range, reliability indices (ICC / SEM / MDC, per COSMIN reporting), and the measurement provenance (assay, band, method, software version). The value prints with its CI and, when a reference range is supplied, its normative percentile; BiocGenerics::as.data.frame() flattens every field for tabular reporting.

Usage

physioBiomarker(
  value,
  name,
  unit = NA_character_,
  ci = NULL,
  reference_range = NULL,
  reliability = list(),
  provenance = list(),
  interpretation = NA_character_
)

Arguments

value

Numeric scalar value.

name

Character biomarker name (e.g. "DAR").

unit

Character measurement unit (default NA).

ci

Numeric length-2 confidence interval, or NULL for none.

reference_range

Numeric length-2 published reference (normal) range, or NULL for none. Interpreted as a 95 percent reference interval when computing the printed normative percentile.

reliability

Named list of reliability indices, typically icc, sem, and mdc (see icc(), sem(), mdc()).

provenance

Named list describing how the value was computed, typically assay, band, method, and software_version.

interpretation

Optional character interpretation label.

Value

A PhysioBiomarker object.

See also

PhysioBiomarker(), normativeLookup(), is.PhysioBiomarker(), icc(), sem(), mdc()

Examples

bm <- physioBiomarker(
  value = 2.35, name = "DAR", unit = "ratio",
  ci = c(1.90, 2.80), reference_range = c(0.5, 1.2),
  reliability = list(icc = 0.82, sem = 0.15, mdc = 0.42),
  provenance = list(assay = "psd", band = "delta/alpha",
                    method = "welch", software_version = "1.0.0")
)
bm
#> <PhysioBiomarker> DAR = 2.35 ratio [1.9, 2.8]
#>   reliability: ICC=0.82, SEM=0.15, MDC=0.42 
#>   normative: 100th percentile (ref 0.5-1.2)
as.data.frame(bm)
#>   name value  unit ci_lower ci_upper ref_lower ref_upper  icc  sem  mdc
#> 1  DAR  2.35 ratio      1.9      2.8       0.5       1.2 0.82 0.15 0.42
#>   prov_assay   prov_band prov_method prov_software_version interpretation
#> 1        psd delta/alpha       welch                 1.0.0           <NA>