---
title: "ML Covariate Screening With Synthetic PK Parameters"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{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 the public `pharmax.ml` workflow using
synthetic data with a known covariate signal.

The example is exploratory decision support only. It is not regulatory
validation and does not use proprietary clinical data.

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

# Synthetic Data

```{r}
set.seed(2026)
n <- 120
demo <- data.frame(
  COV_WT = rnorm(n, 70, 10),
  COV_AGE = rnorm(n, 55, 12),
  COV_ALB = rnorm(n, 4.2, 0.4)
)
demo$ETA_CL <- 0.7 * scale(demo$COV_WT)[, 1] + rnorm(n, sd = 0.3)
demo$ETA_V <- 0.5 * scale(demo$COV_ALB)[, 1] + rnorm(n, sd = 0.4)
```

# Data Quality

```{r}
quality <- px_data_quality(demo)
quality
```

# Covariate Screening

```{r}
screen <- px_covariate(demo, method = "auto", n_top = 3)
screen
```

# Conformal Prediction

```{r}
calibration_truth <- demo$ETA_CL[1:80]
calibration_pred <- calibration_truth + rnorm(80, sd = 0.2)
new_pred <- c(-0.5, 0, 0.5)

px_conformal(calibration_truth, calibration_pred, new_pred, alpha = 0.1)
```

# Interpretation

The known signal in this synthetic example is `COV_WT` for `ETA_CL`. A useful
screening method should rank `COV_WT` highly. This is a functional demonstration,
not proof of real-world clinical validity.