---
title: "Regulatory Authority Profiles"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Regulatory Authority Profiles}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

Different regulatory authorities weight the four R4SUB evidence pillars
(quality, trace, risk, usability) differently. The `r4subprofile` package
encodes these authority-specific requirements so that the SCI can be
calibrated accordingly.

```{r load}
library(r4subprofile)
```

## Supported authorities

```{r authorities}
list_authorities()
```

## Submission types per authority

```{r sub-types-fda}
list_submission_types("FDA")
list_submission_types("EMA")
```

## Creating a submission profile

`submission_profile()` returns a profile with authority-specific pillar
weights, decision bands, and required indicators:

```{r fda-nda}
fda_nda <- submission_profile("FDA", "NDA")
fda_nda$pillar_weights
fda_nda$minimum_coverage
```

```{r ema-maa}
ema_maa <- submission_profile("EMA", "MAA", study_phase = "Phase3")
ema_maa$pillar_weights
```

## Comparing authority weights

FDA NDA vs EMA MAA pillar weights:

```{r compare}
weights_df <- data.frame(
  pillar    = c("quality", "trace", "risk", "usability"),
  FDA_NDA   = unname(fda_nda$pillar_weights),
  EMA_MAA   = unname(ema_maa$pillar_weights)
)
weights_df
```

## Profile summary

`profile_summary()` returns a tidy tibble summarising the profile:

```{r profile-summary}
profile_summary(fda_nda)
```

## Validating evidence against a profile

`validate_against_profile()` checks an evidence table against the
profile's required indicators and asset types:

```{r validate}
ev <- data.frame(
  run_id           = "run-001",
  study_id         = "STUDY01",
  asset_type       = c("dataset", "define", "program", "spec"),
  asset_id         = c("ADSL", "define.xml", "prod_adsl.R", "ADSL"),
  source_name      = "r4subcore",
  source_version   = "0.1.2",
  indicator_id     = c("Q-001", "Q-002", "R-001", "U-001"),
  indicator_name   = c("Quality Check", "Define Check",
                       "Program Validation", "Label Quality"),
  indicator_domain = c("quality", "quality", "risk", "usability"),
  severity         = "info",
  result           = "pass",
  metric_value     = 1,
  metric_unit      = "score",
  message          = "Check passed",
  location         = c("ADSL", "define.xml", "prod_adsl.R", "ADSL"),
  evidence_payload = "{}",
  created_at       = Sys.time(),
  stringsAsFactors = FALSE
)

val <- validate_against_profile(ev, fda_nda)
val$is_compliant
val$coverage
val$missing_indicators
```

The `details` tibble shows per-requirement status:

```{r details}
head(val$details)
```

## Study phase

Some authorities adjust requirements based on study phase. Pass
`study_phase` to reflect phase-specific requirements:

```{r phase}
pmda_nda_p3 <- submission_profile("PMDA", "NDA_JP", study_phase = "Phase3")
pmda_nda_p3$pillar_weights
```