r4subpharma

r4subpharma connects the pharmaverse clinical reporting stack to the R4SUB (Ready for Submission) ecosystem. It turns the metadata and datasets a pharmaverse pipeline already produces into standardized R4SUB evidence, so submission readiness can be scored with r4subscore, without changing your pipeline.

Why

A pharmaverse workflow already generates the signals that describe how ready a deliverable is: whether every variable is documented, whether an ADaM dataset matches its metadata, whether types and labels are in place. Those signals are usually discarded as console warnings. r4subpharma captures them as evidence and feeds them to a single, defensible Submission Confidence Index (SCI).

Installation

# install.packages("pak")
pak::pak("R4SUB/r4subpharma")

The metadata contract

Both adapters work from one small table, one row per dataset variable, that [as_variable_metadata()] builds from either a metacore object or a plain data.frame:

Column	Meaning
`dataset`, `variable`	Identify the variable (required)
`label`, `type`	Documentation attributes
`origin`, `derivation`, `is_derived`	Provenance

Quick start

library(r4subpharma)

meta <- data.frame(
  dataset  = "ADSL",
  variable = c("USUBJID", "AGE", "SEX"),
  label    = c("Unique Subject Identifier", "Age", "Sex"),
  type     = c("text", "integer", "text"),
  origin   = c("Predecessor", "Derived", "Predecessor"),
  derivation = c(NA, "Age at informed consent", NA),
  stringsAsFactors = FALSE
)

adsl <- data.frame(USUBJID = "01-001", AGE = 54, SEX = "M")

ctx <- r4subcore::r4sub_run_context("STUDY01", "PROD")
res <- submission_readiness(list(ADSL = adsl), meta, ctx)

res$sci$SCI    # Submission Confidence Index, 0-100
res$sci$band   # decision band

In a real pipeline the metadata comes from metacore and the datasets from admiral; the call is otherwise identical.

How evidence maps to the SCI pillars

Adapter	Indicators	SCI pillar
`metacore_to_evidence()`	`Q-DEFINE-002`, `Q-DEFINE-003`	quality
`adam_to_evidence()`	`T-ADAM-001`, `T-ADAM-002`	trace
`adam_to_evidence()`	`Q-ADAM-001`	quality
`adam_to_evidence()`	`Q-ADAM-002`	usability

See vignette("r4subpharma") for the full walkthrough.

Part of the R4SUB ecosystem

r4subcore: evidence schema and parsers
r4subscore: Submission Confidence Index
r4sub: meta-package for the ecosystem