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Normalise chemistry and apply the ARA shift for a block of sample rows

Source: R/mspaf.R
dot-mspaf_adjust.Rd

Filters to SSD-eligible analytes, joins SSD params + the reference table, applies the per-analyte chemistry normalisation (BDL → 0), records the ref_source diagnostic, and computes the added-risk-adjusted concentration C_adj = max(C_norm - ref_norm, 0). Operates on one or many samples; the caller is responsible for any per-sample grouping downstream.

Usage

.mspaf_adjust(sample_rows, ref_table, ssd_params, ara_enabled = TRUE)

Arguments

sample_rows

Long-format chemistry rows (one or more samples). Must carry detected.

ref_table

Tibble (analyte, ref_norm).

ssd_params

Tibble from derive_ssd_params().

ara_enabled

Logical; whether the caller supplied a reference.

Value

A list list(tox, dropped) where tox has the eligible, normalisation-resolved rows (with C_norm, ref_norm, ref_source, C_adj) and dropped is a (analyte, reason) tibble of rows dropped for a missing required co-analyte.

Details

ref_source distinguishes:

  • "disabled" — ARA off (no reference supplied to add_mspaf());

  • "matched" — ARA on and a reference value was found for the analyte;

  • "unmatched" — ARA on but no reference match (assessed against raw normalised concentration, i.e. ref_norm = 0).