---
title: "Prediction, Calibration, and Scoring"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Prediction, Calibration, and Scoring}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

The prediction API distinguishes conditional expected responses from new
posterior predictive outcomes. This distinction is retained in the returned
`gp3bayes_prediction` object and in downstream calibration and scoring tools.

```{r}
library(gp3bayes)

binary_prediction_scores(
  c(0.05, 0.20, 0.75, 0.90),
  c(0, 0, 1, 1)
)

binary_threshold_metrics(
  c(0.05, 0.20, 0.75, 0.90),
  c(0, 0, 1, 1),
  thresholds = c(0.3, 0.5, 0.7)
)

duration_prediction_scores(
  c(900, 1100, 1300),
  c(950, 1050, 1400)
)
```

## Fitted predictions

```{r, eval=FALSE}
grid <- create_prediction_grid(
  fit,
  at = list(condition = c("control", "treatment"))
)

support <- audit_prediction_support(fit, grid)

expected <- predict_model(
  fit,
  newdata = grid,
  type = "expected",
  include_group_effects = FALSE
)

predictive <- predict_model(
  fit,
  newdata = grid,
  type = "predictive",
  include_group_effects = FALSE,
  ndraws = 1000
)

prediction_table(expected)
plot_prediction_intervals(expected)
plot_prediction_support(support)
```

For binary fits, expected predictions are event probabilities and can be used
for calibration and threshold summaries. For duration fits, the API separately
exposes the arithmetic expected response, conditional median, and new-outcome
posterior predictive distribution.

```{r, eval=FALSE}
p_binary <- predict_binary_probability(binary_fit)
calibration <- binary_calibration_table(p_binary)
plot_binary_calibration(calibration)

p_duration <- predict_duration(duration_fit, type = "predictive")
duration_quantile_calibration(p_duration)
duration_pit_table(p_duration)
predictive_coverage_table(p_duration)
```

All reported metrics are descriptive. The package does not choose a threshold
or certify predictive adequacy automatically.