---
title: "Interpreting MAIHDA Plots and Diagnostics"
author: "Hamid Bulut"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Interpreting MAIHDA Plots and Diagnostics}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 4.5
)
```

## Overview

`plot()` on a fitted MAIHDA model gives you several views of the same model, each
answering a different question. This vignette explains, for every plot type, what
it shows, how to read it, and what not to conclude from it. Calling `plot()`
with no specified `type` draws them all.

Lets start with fitting the model.

```{r model}
library(MAIHDA)
data("maihda_health_data")

health_complete <- maihda_health_data[complete.cases(
  maihda_health_data[, c("BMI", "Age", "Gender", "Race", "Education")]
), ]

model <- maihda(
  BMI ~ Age + Gender + Race + Education + (1 | Gender:Race:Education),
  data = health_complete
)
# or equivalently with the helper:
# model <- fit_maihda(
#   BMI ~ Age + Gender + Race + Education + (1 | Gender:Race:Education),
#   data = health_complete
# )
```

## `vpc` -- variance partition

The VPC plot shows how the total unexplained variance splits into a
between-stratum component (the numerator of the VPC/ICC), any other random-effect
components, and the within-stratum residual.

```{r vpc}
plot(model, type = "vpc")
```

**How to read it.** The between-stratum slice is the share of unexplained
variation that lies between intersectional groups. For non-Gaussian models this split is on the latent
scale.

## `predicted` -- stratum predictions with intervals

```{r predicted}
plot(model, type = "predicted")
```

**How to read it.** Each point is a stratum's model-based prediction with a 95%
interval, ordered so you can see which intersections sit above or below the
average. The estimates are shrunken toward the overall mean. For a binomial model the axis is the
predicted probability instead of the outcome mean.

## `obs_vs_shrunken` -- shrinkage made visible

```{r obs-shrunken}
plot(model, type = "obs_vs_shrunken")
```

**How to read it.** This contrasts the raw observed stratum means with the model's
shrunken estimates. Points far from the diagonal are strata whose raw mean was
pulled substantially toward the centre, typically the smallest, noisiest cells.
It is a sanity check on how much the multilevel model is regularising.


## `effect_decomp` -- additive vs. intersection-specific

```{r effect-decomp}
plot(model, type = "effect_decomp")
```

**How to read it.** This separates, for each stratum, the part of its deviation
from the grand mean that is explained by the additive main effects from the
intersection-specific part (the stratum random effect, what is left over after
the additive effects). Large intersection-specific bars are the candidate
"more/less than the sum of the parts" intersections, but treat them as
hypotheses to probe, not as confirmed interactions, since they also absorb sample
composition and estimation noise.

## `ternary` -- relative signal diagnostic

The ternary plot needs the optional `ggtern` package, so it is only drawn here
when that package is installed.

```{r ternary, eval = requireNamespace("ggtern", quietly = TRUE), warning = FALSE, message = FALSE}
plot(model, type = "ternary")
```

**How to read it.** For each stratum the plot normalises three magnitudes to sum
to 1: the additive signal (how far the fixed-effect-only prediction sits from
the grand mean), the intersection-specific signal (the size of the stratum
random effect), and the uncertainty in that estimate. A stratum near the
"uncertainty" corner is dominated by noise; one near the "intersection" corner
carries signal beyond the additive main effects.

## `prediction_deviation` -- the deviation dashboard

```{r prediction-deviation}
plot(model, type = "prediction_deviation")
```

**How to read it.** This two-panel dashboard highlights the
most notable cases or strata. What counts as "notable" depends on the model:
the largest deviation from the mean prediction (Gaussian/Poisson), the largest
absolute deviance residual (binomial), or the most surprising observation
(ordinal).

## Group-comparison plots

When you fit across a higher-level grouping variable with
`compare_maihda_groups()` (or `maihda(group = ...)`), extra plot types become
available -- `group_vpc`, `group_components`, `group_between_variance`, and
`group_pcv` (also reachable as `type = "vpc"`, `"components"`, `"between_variance"`,
and `"pcv"` on the comparison object). Those are covered in the
[group comparison vignette](group_comparison.html).

## Customizing the appearance

Every `plot()` call with a single `type` returns a plain **ggplot** object, so
you are never locked into the package's styling -- restyle it with the usual
ggplot2 grammar by adding a theme, overriding the labels, or dropping in another
layer. Themes, `labs()`, and added layers compose cleanly:

```{r customize-theme}
library(ggplot2)

plot(model, type = "vpc") +
  theme_classic(base_size = 13) +
  labs(title = "Variance partition, restyled")
```

The views that map a fill or colour (`vpc`, `context_vpc`, `effect_decomp`) also
accept a replacement palette. ggplot2 prints a harmless "Scale for fill is
already present ... which will replace the existing scale" message as it swaps
the built-in palette out (suppressed here):

```{r customize-palette, message = FALSE}
plot(model, type = "vpc") +
  scale_fill_brewer(palette = "Set2")
```

A few plot types return something other than a single ggplot, so they restyle
slightly differently:

* **`prediction_deviation`** is a two-panel [patchwork](https://patchwork.data-imaginist.com/).
  `+ theme_*()` styles only the active panel; use `&` to apply a theme to
  *both* panels at once:

  ```{r customize-patchwork, warning = FALSE}
  plot(model, type = "prediction_deviation") & theme_minimal()
  ```

* **`type = "all"`** returns a named list of ggplot objects (it prints them as
  a side effect), so pick one out to restyle it:

  ```{r customize-all, eval = FALSE}
  plots <- plot(model)          # list: vpc, predicted, effect_decomp, ...
  plots$predicted + theme_bw()
  ```

* **`ternary`** is a `ggtern` object with its own coordinate system -- reach for
  the `ggtern::theme_*()` family rather than the standard ggplot2 themes.

## See also

- [Introduction to MAIHDA](introduction.html) -- the end-to-end workflow.
- [MAIHDA for binary outcomes](binary_outcomes.html) -- how these plots adapt to
  logistic models.
