Overwrite a cohort's placeholders with the gold standard

Joins the gold-standard codebook onto a cohort, or onto any frame carrying a card id, and replaces the named columns with the deck's own values. The replaced columns are kept as <col>_original, so the provenance is not lost and the inference that was there before can still be scored against the truth that replaced it.

Usage

sdt_apply_gold_standard(
  cohort,
  gold,
  on = "card",
  replace = c("triage", "age", "sex"),
  keep_original = TRUE
)

Arguments

cohort: A cohort from sdt_cohort(), or any data frame with a card id column.
gold: An sdt_gold_standard from sdt_read_gold_standard().
on: Name of the card id column in cohort. Values may be padded ("07"), unpadded ("7") or numeric; all three join.
replace: Which columns to overwrite: any of "triage", "age" and "sex". Pass character() to join nothing and only stamp triage_source.
keep_original: Keep each replaced column as <col>_original.

Value

cohort with the named columns replaced, the originals kept when asked for, and a triage_source column reading "gold". A cohort comes back a validated cohort; anything else comes back a tibble::tibble(). The gold_applied attribute records what was done.

Details

In the TDSC corpus the three replaceable columns start out as a circular surrogate (triage, the inter-team consensus call), a constant (age) and an inference from the log's gendered wording (sex). After this function they are the card's own values, and triage_source reads "gold" so a downstream result can say which label it routed on. The engine routes on triage, so which label sits there decides which question a simulation answers.

Provenance

triage_source names where the label sitting in triage came from, so it reads "gold" only when triage was among the columns replaced. Ask for a subset that leaves triage alone and any existing source label is left alone with it: a surrogate must never end up wearing the truth's label.

Examples

if (FALSE) { # \dontrun{
gold <- sdt_read_gold_standard("Patienten Codebook.xlsx")
truth <- sdt_apply_gold_standard(pooled, gold)
mean(truth$triage == truth$triage_original)
} # }