## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

## -----------------------------------------------------------------------------
library(openstudyval)
report <- validate_submission(example_study("sdtm"), standard = "SDTM")
summary(report)

## ----eval = FALSE-------------------------------------------------------------
# write_validation_report(report, "validation-report.html")

## -----------------------------------------------------------------------------
extra <- data.frame(
  rule_id = "CUST_ARM",
  publisher = "sponsor",
  standard = "SDTM",
  domains = "DM",
  severity = "Error",
  check = "codelist",
  argument = "ARMCD=A|B",
  message = "ARMCD is not in the study arm codelist.",
  guidance = "Protocol section 6",
  stringsAsFactors = FALSE
)
study <- read_study_data(example_study("sdtm"))
custom <- validate_datasets(study, standard = "SDTM", rules = extra)
"CUST_ARM" %in% custom$issues$rule_id