Compare two data cuts of a clinical dataset

compare_cut() performs a deterministic, key-based comparison of two versions of the same clinical dataset (for example ADSL at two data cuts). It reports observations added, removed and modified, and separately reports schema-level changes (variables added/removed, type and label changes).

Usage

compare_cut(
  old,
  new,
  by,
  compare_labels = TRUE,
  compare_types = TRUE,
  tolerance = 1e-09,
  ignore_vars = NULL,
  name_old = "old",
  name_new = "new",
  dataset = NULL,
  subject_var = NULL,
  backend = c("trialdiff", "waldo", "diffdf"),
  ...
)

Arguments

old, new

Data frames (or tibbles) representing the earlier and later data cut. new is compared against old.

by

Character vector of key variables that uniquely identify an observation within each dataset. Common clinical keys include c("USUBJID", "PARAMCD", "AVISIT") for ADLB or c("USUBJID", "VISIT") for ADVS. Must be present in both datasets.

compare_labels

Logical. If TRUE (default) variable label changes are recorded in the schema comparison.

compare_types

Logical. If TRUE (default) variable type changes are recorded in the schema comparison.

tolerance

Numeric tolerance used when comparing numeric values. Set to 0 for exact comparison.

ignore_vars

Character vector of variables to exclude from the value comparison (for example technical or audit columns).

name_old, name_new

Character labels used in reports.

dataset

Optional dataset name (for example "ADSL"). Inferred from the old/new expressions when not supplied.

subject_var

Optional subject identifier variable. When NULL the function looks for USUBJID, then falls back to the first key.

backend

Low-level comparison backend. "trialdiff" uses the built-in engine; "waldo" additionally uses waldo for whole-column equality short-circuiting when it is installed; "diffdf" delegates value comparison to diffdf and translates its output into a tdiff object (schema comparison remains built in). The "diffdf" backend requires the diffdf package.

...

Reserved for future extensions.

Value

An object of class tdiff: a list with elements meta, added, removed, modified, schema, summary and register. See tdiff-object for details.

Details

The function is deliberately a low-level comparison engine. Clinical meaning is added by classify_changes(), lineage by define_lineage() and impact by assess_impact().

Examples

old <- data.frame(
  USUBJID = c("S1", "S2", "S3"),
  TRT01P = c("Placebo", "Drug A", "Placebo"),
  AGE = c(54, 61, 47),
  stringsAsFactors = FALSE
)
new <- old
new$TRT01P[1] <- "Drug A"
new$AGE[2] <- 62
diff <- compare_cut(old, new, by = "USUBJID", dataset = "ADSL")
diff
#> 
#> ── trialdiff comparison ────────────────────────────────────────────────────────
#> ADSL: old → new
#> Keys: "USUBJID"
#> Observations: 3 → 3 (3 matched)
#> Added: 0 Removed: 0 Modified cells: 2
#> Schema changes: 0