---
title: "Validating an FDA study-data package"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Validating an FDA study-data package}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
```

# What this package is

`openstudyval` is an independent R validator for a study-data folder prepared
for an FDA submission. It covers:

- SAS v5 transport constraints from the FDA Study Data Technical Conformance Guide
  (8-character names, 40-character labels, 200-character values)
- eCTD technical-rejection criteria 1734, 1735, 1736, and 1738 where they can
  be evaluated from the study folder
- structural SDTM, SEND, and ADaM checks, plus a CSV rule catalog you can extend

It is not Pinnacle 21, and a clean report is not an FDA certification.

# Run the bundled example

```{r}
library(openstudyval)
report <- validate_submission(example_study("sdtm"), standard = "SDTM")
summary(report)
```

Write the HTML report next to your study:

```{r, eval = FALSE}
write_validation_report(report, "validation-report.html")
```

# Add a study-specific rule

```{r}
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
```

Full MedDRA and WHODrug dictionaries are licensed and are not bundled. Pass
permitted terms in `ct` or as the right-hand side of a `codelist` rule.