---
title: "mfrmr Visual Diagnostics"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{mfrmr Visual Diagnostics}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
is_cran_check <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false")))
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 5,
  eval = !is_cran_check
)
```

This vignette is a compact map of the main base-R diagnostics in `mfrmr`.
It is organized around four practical questions:

- How well do persons, facet levels, and categories target each other?
- Which observations or levels look locally unstable?
- Is the design linked well enough across subsets or forms?
- Where do residual structure and interaction screens point next?

All examples use packaged data and `preset = "publication"` so the same code
is suitable for manuscript-oriented graphics.

If you are selecting figures for a report, use `reporting_checklist()` before
or alongside this vignette. Its `"Visual Displays"` rows now mirror the
public plotting family shown here.

## Minimal setup

```{r setup}
library(mfrmr)

toy <- load_mfrmr_data("example_operational")

fit <- fit_mfrm(
  toy,
  person = "Person",
  facets = c("Rater", "Criterion"),
  score = "Score",
  method = "MML",
  model = "RSM"
)

diag <- diagnose_mfrm(fit, residual_pca = "none")
checklist <- reporting_checklist(fit, diagnostics = diag)
subset(
  checklist$checklist,
  Section == "Visual Displays",
  c("Item", "Available", "NextAction")
)
```

## 1. Targeting and scale structure

Use the Wright map first when you want one shared logit view of persons,
facet levels, and step thresholds.

```{r wright}
plot(fit, type = "wright", preset = "publication", show_ci = TRUE)
```

Interpretation:

- Compare person density on the left to facet and step locations on the right.
- Large gaps suggest weaker targeting in that logit region.
- Wide overlap in marginal confidence whiskers suggests imprecision; estimate
  the relevant pairwise contrast directly before claiming that two levels are
  separated or indistinguishable.

The native view above remains the recommended analytic figure because it keeps
facet uncertainty and fitted step locations visible. For a closer FACETS-facing handoff, switch the
renderer and leave `show_ci` at its default `FALSE`. The fitted coordinates do
not change.

Every retained native facet level is labelled. Only label coordinates are
displaced for collision avoidance, with leader lines back to the fitted
points. Step thresholds form one vertical ladder and their labels include the
fitted transition logits.

```{r wright-facets-style}
plot(
  fit,
  type = "wright",
  renderer = "facets",
  category_labels = c(
    `1` = "Beginning", `2` = "Developing", `3` = "Secure", `4` = "Advanced"
  )
)
```

This renderer uses one common logit ruler, a `*` person-frequency column,
signed facet headers, every facet level, and short labeled score-transition
lines. It is FACETS-style visual correspondence, not a claim that `mfrmr` and FACETS
produce numerically identical estimates. A numerical comparison requires output
from a documented FACETS version and aligned estimator, identification, score,
and orientation settings. Set `show_ci = TRUE` only when
you deliberately want a hybrid FACETS-style ruler with the mfrmr uncertainty
extension. Use `draw = FALSE` and inspect the `facets_style` tables when
rebuilding the display with ggplot2 or another graphics system.

Next, use the pathway map when you want to see how expected scores progress
across theta.

```{r pathway}
plot(fit, type = "pathway", preset = "publication")
```

Interpretation:

- Steeper rises indicate stronger score progression.
- Dominant-category strips show where each category is most likely to govern the score.
- Flat or compressed regions suggest weaker category separation.

The expected-score pathway is not a fit pathway. To review measure against
Infit, place Infit on the horizontal axis and include person rows explicitly:

```{r fit-pathway}
plot(
  fit,
  type = "fit_pathway",
  diagnostics = diag,
  fit_stat = "Infit",
  fit_scale = "mnsq",
  include_person = TRUE,
  show_ci = TRUE,
  preset = "publication"
)
```

Interpretation:

- The vertical axis remains the fitted measure in logits.
- The horizontal axis is Infit MnSq; the 1.0 line is the model-expectation reference.
- Vertical whiskers show measure uncertainty; person and non-person rows have distinct uncertainty bases, recorded in the draw-free payload metadata.
- Treat displaced or flagged rows as review prompts, not automatic exclusions.

## 2. Local response and level issues

Unexpected-response screening is useful for case-level review.

```{r unexpected}
plot_unexpected(
  fit,
  diagnostics = diag,
  abs_z_min = 1.5,
  prob_max = 0.4,
  plot_type = "scatter",
  preset = "publication"
)
```

Interpretation:

- Upper corners combine large residual mismatch with low model probability.
- Repeated appearances of the same persons or levels are more informative than a single extreme point.

Displacement focuses on level movement rather than individual responses.

```{r displacement}
plot_displacement(
  fit,
  diagnostics = diag,
  anchored_only = FALSE,
  plot_type = "lollipop",
  preset = "publication"
)
```

Interpretation:

- Large absolute displacement indicates stronger tension between observed data and current calibration.
- For anchored runs, this is especially useful as an anchor-robustness screen.

### Strict marginal follow-up

When you need the package's latent-integrated follow-up path, switch to `MML`
and request `diagnostic_mode = "both"` so the legacy and strict branches stay
visible side by side. The chunk below uses compact quadrature for optional
local execution; final reporting should be refit with the package default or a
higher quadrature setting.

```{r strict-marginal}
fit_strict <- fit_mfrm(
  toy,
  person = "Person",
  facets = c("Rater", "Criterion"),
  score = "Score",
  method = "MML",
  model = "RSM",
  quad_points = 7,
  maxit = 40
)

diag_strict <- diagnose_mfrm(
  fit_strict,
  residual_pca = "none",
  diagnostic_mode = "both"
)

strict_checklist <- reporting_checklist(fit_strict, diagnostics = diag_strict)
subset(
  strict_checklist$checklist,
  Section == "Visual Displays" &
    Item %in% c("QC / facet dashboard", "Strict marginal visuals"),
  c("Item", "Available", "NextAction")
)

plot_marginal_fit(
  diag_strict,
  top_n = 12,
  preset = "publication"
)
```

Interpretation:

- Treat strict marginal plots as exploratory corroboration screens, not as standalone inferential tests.
- Use the checklist rows to confirm that the current run actually supports the strict branch before routing figures into a report.
- When pairwise follow-up is needed, continue with `plot_marginal_pairwise(diag_strict, preset = "publication")`.

## 3. Linking and coverage

When the design may be incomplete or spread across subsets, inspect the
coverage matrix before interpreting cross-subset contrasts.

```{r linking}
sc <- subset_connectivity_report(fit, diagnostics = diag)
plot(sc, type = "design_matrix", preset = "publication")
```

Interpretation:

- Sparse rows or columns indicate weak subset coverage.
- Facets with low overlap are weaker anchors for cross-subset comparisons.

If you are working across administrations, follow up with anchor-drift plots:

```{r eval = FALSE}
drift <- detect_anchor_drift(current_fit, baseline = baseline_anchors)
plot_anchor_drift(drift, type = "heatmap", preset = "publication")
```

## 4. Residual structure and interaction screens

Residual PCA is a follow-up layer after the main fit screen.

```{r residual-pca}
diag_pca <- diagnose_mfrm(fit, residual_pca = "both", pca_max_factors = 4)
pca <- analyze_residual_pca(diag_pca, mode = "both")
plot_residual_pca(pca, mode = "overall", plot_type = "scree", preset = "publication")
```

Interpretation:

- Early components with noticeably larger eigenvalues deserve follow-up.
- Scree review should usually be paired with loading review for the component of interest.

For interaction screening, use the packaged bias example.

```{r bias}
bias_df <- load_mfrmr_data("example_bias")

fit_bias <- fit_mfrm(
  bias_df,
  person = "Person",
  facets = c("Rater", "Criterion"),
  score = "Score",
  method = "MML",
  model = "RSM",
  quad_points = 7
)

diag_bias <- diagnose_mfrm(fit_bias, residual_pca = "none")
bias <- estimate_bias(fit_bias, diag_bias, facet_a = "Rater", facet_b = "Criterion")

plot_bias_interaction(
  bias,
  plot = "facet_profile",
  preset = "publication"
)
```

Interpretation:

- Facet profiles are useful for seeing whether a small number of levels drives most flagged interaction cells.
- Treat these plots as screening evidence; confirm with the corresponding tables and narrative reports.

## 5. Custom figures without losing the evidence boundary

The built-in plots are intended as safe defaults. Use
`preset = "monochrome"` when a journal, accessibility review, or print workflow
needs grayscale output. For journal figures, teaching material, dashboards, or
lab-specific styles, use `draw = FALSE` and the plot-data accessors instead of
editing screenshots.

```{r custom-plot-data}
plot(fit, type = "wright", preset = "monochrome")

wright_payload <- plot(fit, type = "wright", draw = FALSE, preset = "publication")
plot_data_components(wright_payload)

locations <- plot_data(wright_payload, component = "locations")
head(locations)

pathway_long <- plot_data(
  fit,
  type = "pathway",
  component = "pathway_long",
  preset = "publication"
)
head(pathway_long[, c("Layer", "CurveGroup", "Theta", "Value")])
```

When you build a custom figure, keep the helper's guidance tables with the
plot data:

```{r custom-guidance}
names(wright_payload$data)
wright_payload$data$reference_lines
```

Those metadata are the guardrails for captions and interpretation. They let
you change colors, labels, panels, or rendering technology while preserving the
same measurement scale, reference lines, caveats, and reporting role used by
the package-native plot.

## 6. Secondary visual layer

The package ships a complementary visual layer for teaching and
diagnostic follow-up. These helpers are not default reporting figures;
use them after the main screens above.

- `plot_guttman_scalogram(fit, diagnostics)` renders a person x
  facet-level response matrix with an unexpected-response overlay, for
  teaching-oriented scalogram intuition and local triage.
- `plot_residual_qq(fit, diagnostics)` plots a Normal Q-Q of
  person-level standardized residual aggregates as exploratory
  follow-up on residual tail behavior.
- `plot_rater_trajectory(list(T1 = fit_a, T2 = fit_b))` tracks rater
  severity across named waves. The helper does not perform linking;
  supply waves that have already been placed on a common anchored
  scale (see `vignette("mfrmr-linking-and-dff")`) before interpreting
  movement as rater drift.
- `plot_rater_agreement_heatmap(fit, diagnostics)` renders a
  compact pairwise rater x rater agreement matrix; pass
  `metric = "correlation"` to colour by the Pearson-style `Corr`
  column instead of exact agreement.
- `response_time_review(data, person, facets, time)` summarizes
  response-time metadata by person, facet, and score category. Pair it with
  `plot_response_time_review()` for distribution and grouped timing plots.
  This is a descriptive QC layer, not a joint speed-accuracy model.
- `plot_shrinkage_funnel(fit_eb, show_ci = TRUE)` draws raw and
  empirical-Bayes shrunken facet estimates on the same row, with
  optional confidence whiskers for both estimates. Use this only after
  `apply_empirical_bayes_shrinkage()` or `fit_mfrm(..., facet_shrinkage =
  "empirical_bayes")`.

### Response-time QC context

If your rating-event data include response times, review them separately from
the MFRM likelihood. Rapid and slow response-time flags are descriptive
quality-control prompts; they do not change measures and should not be treated
as proof of disengagement, cheating, or speededness.

```{r response-time-review}
toy_rt <- toy
toy_rt$ResponseTime <- 12 + (seq_len(nrow(toy_rt)) %% 7) +
  as.numeric(toy_rt$Score)
toy_rt$ResponseTime[1] <- 2
toy_rt$ResponseTime[2] <- 38

rt <- response_time_review(
  toy_rt,
  person = "Person",
  facets = c("Rater", "Criterion"),
  score = "Score",
  time = "ResponseTime",
  rapid_quantile = 0.10,
  slow_quantile = 0.90
)

summary(rt)
plot_response_time_review(rt, type = "distribution", preset = "publication")
plot_response_time_review(rt, type = "person", preset = "publication")
```

Interpretation:

- Start with the distribution plot to see whether the rapid/slow thresholds are sensible for this administration.
- Inspect person and facet summaries for concentrated rapid or slow rates rather than isolated events.
- Keep timing flags separate from fit, bias, and validity claims unless the study design explicitly supports stronger speed-accuracy modeling.

### Small-N shrinkage with uncertainty

When a non-person facet has few levels or sparse observations, a large raw
severity estimate can be a noisy estimate rather than a stable facet signal.
The shrinkage funnel shows how far empirical-Bayes pooling moved each level
toward the facet mean and whether the uncertainty remains wide after pooling.

```{r shrinkage-funnel}
fit_eb <- apply_empirical_bayes_shrinkage(fit)

shrink <- plot_shrinkage_funnel(
  fit_eb,
  show_ci = TRUE,
  ci_level = 0.95,
  preset = "publication",
  draw = FALSE
)

head(shrink$data$table[, c(
  "Facet", "Level", "RawEstimate", "RawCI_Lower", "RawCI_Upper",
  "ShrunkEstimate", "ShrunkCI_Lower", "ShrunkCI_Upper",
  "ShrinkageFactor"
)])

plot_shrinkage_funnel(
  fit_eb,
  show_ci = TRUE,
  ci_level = 0.95,
  preset = "publication"
)
```

Interpretation:

- Long raw-to-shrunken segments identify levels most affected by the partial-pooling prior.
- Wide raw whiskers that narrow after pooling indicate estimation instability, not automatic rater-quality failure.
- Report the shrinkage method and keep this display separate from bias, fit, or validity claims.

## Recommended sequence

For a compact visual workflow:

1. `reporting_checklist()` when you want the package to route which figures are already supported.
2. `plot_qc_dashboard()` for one-page triage.
3. `plot_unexpected()`, `plot_displacement()`, `plot_marginal_fit()`, and `plot_interrater_agreement()` for local follow-up.
4. `plot(fit, type = "wright")` and `plot(fit, type = "pathway")` for targeting and scale interpretation.
5. `plot_residual_pca()`, `plot_bias_interaction()`, and `plot_information()` for deeper structural review.
6. `response_time_review()` and `plot_response_time_review()` when response-time metadata are available.
7. `plot_shrinkage_funnel(show_ci = TRUE)` when empirical-Bayes shrinkage was applied.
8. `plot_guttman_scalogram()`, `plot_residual_qq()`,
   `plot_rater_trajectory()`, and `plot_rater_agreement_heatmap()` as
   the teaching / drift / agreement-heatmap follow-up layer.

## Related help

- `help("mfrmr_visual_diagnostics", package = "mfrmr")`
- `help("mfrmr_workflow_methods", package = "mfrmr")`
- `mfrmr_interval_guide("shrinkage")`
