## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
has_pkgs <- all(vapply(
  c("metacore", "pharmaverseadam", "r4subscore"),
  requireNamespace, logical(1), quietly = TRUE
))
knitr::opts_chunk$set(eval = has_pkgs)

## ----eval = TRUE, echo = FALSE, results = "asis"------------------------------
if (!has_pkgs) {
  cat("> The packages needed to run this case study (metacore,",
      "pharmaverseadam, r4subscore) are not installed, so the code below is",
      "shown but not evaluated.\n")
}

## ----setup--------------------------------------------------------------------
library(r4subpharma)

# The CDISC pilot ADaM specification (covers ADSL, ADAE, ADLBC, ADADAS, ADTTE)
e <- new.env()
load(metacore::metacore_example("pilot_ADaM.rda"), envir = e)
spec <- e$metacore

# One of the admiral-built datasets
adsl <- pharmaverseadam::adsl
dim(adsl)

## ----score-adsl---------------------------------------------------------------
ctx <- r4subcore::r4sub_run_context("CDISCPILOT01", "PROD")
spec_adsl <- metacore::select_dataset(spec, "ADSL", verbose = "silent")

res <- submission_readiness(list(ADSL = adsl), spec_adsl, ctx)
res

## ----pillars------------------------------------------------------------------
as.data.frame(res$sci$pillar_scores)

## ----gaps---------------------------------------------------------------------
ev <- res$evidence
missing <- ev[ev$indicator_id == "T-ADAM-001" & ev$result == "fail", ]
nrow(missing)
sub(".*: ", "", missing$message)

## ----types--------------------------------------------------------------------
ev[ev$indicator_id == "Q-ADAM-001" & ev$result == "warn",
   c("location", "message")]

## ----package------------------------------------------------------------------
res_pkg <- submission_readiness(
  list(ADSL = pharmaverseadam::adsl, ADAE = pharmaverseadam::adae),
  spec,
  ctx
)
res_pkg$sci$SCI
as.data.frame(res_pkg$sci$pillar_scores)