---
title: "Finding interaction patterns"
author: "Hamid Bulut"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Finding interaction patterns}
  %\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

A common follow-up question is which strata depart most clearly from the
additive expectation.

For this exploratory diagnostic, `maihda()` can compute the adjusted-model
stratum random effects, intervals, and flags. When you use `interactions = "BH"`,
the flags use the Benjamini-Hochberg adjustment. The diagnostic is stored in the
analysis object and can be reused by the effect-decomposition and
predicted-strata plots.

## Run a standard analysis and choose the multiplicity rule

The default is `adjust = "none"`. This reports each stratum-level interval and
flag without a multiple-testing correction.

If the goal is to scan all strata and highlight a smaller set for follow-up, use
an adjustment such as Benjamini-Hochberg:

```{r model-bh}
library(MAIHDA)
model_bh <- maihda(
  BMI ~ Age + Gender + Race + Education + (1 | Gender:Race:Education),
  data = maihda_health_data,
  interactions = "BH" # Benjamini-Hochberg adjustment
)
```

The printed output reports how many strata were flagged and which adjustment rule
was used. The full table is stored in `model_bh$interactions`.

```{r table}
model_bh$interactions
```

Each row is one stratum. The main columns are:

- `interaction`: the adjusted-model stratum random effect, on the model scale.
- `lower` and `upper`: the interval for that random effect.
- `direction`: whether the stratum is above or below the additive expectation.
- `flagged`: whether the stratum passes the selected screening rule.

For frequentist fits, the table also includes the conditional standard error,
p-value, and adjusted p-value when a correction is requested.

## Highlight flagged strata

The plotting methods can reuse the stored diagnostic. Because `model_bh` was
fitted with `interactions = "BH"`, `highlight_interactions = TRUE` uses the
Benjamini-Hochberg flags. In the effect-decomposition plot, the labels also
follow that same flagged set.

```{r plot-decomp, fig.height = 5}
plot(model_bh, type = "effect_decomp", highlight_interactions = TRUE)
```

The same flags can be reused in the predicted-strata view.

```{r plot-predicted, fig.height = 5}
plot(model_bh, type = "predicted", highlight_interactions = TRUE)
```

If the analysis was fitted without a stored interaction diagnostic, pass the
adjustment rule directly:

```{r plot-bh-shorthand, eval = FALSE}
plot(model, type = "effect_decomp", highlight_interactions = "BH")
```


## See also

- [Introduction to MAIHDA](introduction.html), the main two-model workflow.
- [Interpreting MAIHDA plots and diagnostics](interpreting_plots.html), how to
  read the effect-decomposition and predicted-strata plots.
- [Bayesian MAIHDA for sparse intersections](bayesian_sparse_maihda.html), sparse
  cells and uncertainty in variance components.

## References

- Evans, C. R., Williams, D. R., Onnela, J. P., & Subramanian, S. V. (2018). A
  multilevel approach to modeling health inequalities at the intersection of
  multiple social identities. *Social Science & Medicine*, 203, 64-73.

- Merlo, J. (2018). Multilevel analysis of individual heterogeneity and
  discriminatory accuracy (MAIHDA) within an intersectional framework. *Social
  Science & Medicine*, 203, 74-80.
