## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
has_score <- requireNamespace("r4subscore", quietly = TRUE)

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

## ----meta---------------------------------------------------------------------
meta <- data.frame(
  dataset  = "ADSL",
  variable = c("USUBJID", "AGE", "SEX", "TRTSDT"),
  label    = c("Unique Subject Identifier", "Age", "Sex", "Date of First Exposure"),
  type     = c("text", "integer", "text", "integer"),
  origin   = c("Predecessor", "Derived", "Predecessor", "Derived"),
  derivation = c(NA, "Age at informed consent", NA, "First dosing date from EX"),
  stringsAsFactors = FALSE
)

as_variable_metadata(meta)

## ----metacore, eval = FALSE---------------------------------------------------
# mc <- metacore::spec_to_metacore("adam_spec.xlsx")
# meta <- as_variable_metadata(metacore::select_dataset(mc, "ADSL"))

## ----meta-evidence------------------------------------------------------------
ctx <- r4subcore::r4sub_run_context("STUDY01", "PROD")
ev_meta <- metacore_to_evidence(meta, ctx)

ev_meta[, c("indicator_id", "location", "result", "severity")]

## ----adam-evidence------------------------------------------------------------
adsl <- data.frame(
  USUBJID = c("01-001", "01-002"),
  AGE     = c(54, 61),
  TRTSDT  = c(19100, 19112),
  STUDYID = c("STUDY01", "STUDY01"),
  stringsAsFactors = FALSE
)

ev_adam <- adam_to_evidence(adsl, meta, ctx, dataset_name = "ADSL")

ev_adam[, c("indicator_id", "indicator_domain", "location", "result")]

## ----readiness, eval = has_score----------------------------------------------
res <- submission_readiness(list(ADSL = adsl), meta, ctx)
res

## ----sci, eval = has_score----------------------------------------------------
res$sci$SCI
res$sci$band