---
title: "Benchmarking ML Covariate Screening With Synthetic PK Parameters"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Benchmarking ML Covariate Screening With Synthetic PK Parameters}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

# Purpose

This vignette demonstrates a synthetic benchmark workflow for `pharmax.ml`.
It is exploratory decision support only. It does not establish clinical validity
or regulatory validation.

```{r setup}
library(pharmax.ml)
```

# Generate Synthetic Scenarios

```{r}
known_signal <- px_simulate_covariates(n = 120, scenario = "known_signal", seed = 2026)
missingness <- px_simulate_covariates(n = 120, scenario = "missingness", seed = 2026)

head(known_signal)
sum(is.na(missingness))
```

# Run A Small Benchmark

```{r}
benchmark <- px_benchmark_covariate(
  scenarios = c("known_signal", "no_signal", "correlated", "missingness"),
  replicates = 3,
  n = 100,
  method = "cor",
  seed = 2026
)

benchmark
```

```{r}
plot(benchmark)
```

# Create A Decision-Support Report

```{r}
quality <- px_data_quality(known_signal, impute = "median")
screen <- px_covariate(quality$data, method = "auto", n_top = 3, seed = 2026)
calibration <- px_calibrate_conformal(
  truth = known_signal$ETA_CL[1:40],
  lower = known_signal$ETA_CL[1:40] - 0.5,
  upper = known_signal$ETA_CL[1:40] + 0.5,
  prediction = known_signal$ETA_CL[1:40],
  alpha = 0.1
)

px_ml_report(
  screen,
  quality = quality,
  calibration = calibration,
  benchmark = benchmark,
  context = list(context_of_use = "Synthetic covariate-screening demonstration")
)
```