---
title: "MML estimation and marginal-fit diagnostics"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{MML estimation and marginal-fit 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 = "#>",
  eval = !is_cran_check
)
```

This vignette explains how `mfrmr` fits `MML` models and how to interpret the
newer strict marginal diagnostics.

## Why the MML calculations are shared

Earlier versions computed closely related quantities multiple times in separate
paths:

- marginal log-likelihood evaluation
- optimization-time gradient calculation
- posterior weights for EAP summaries
- strict marginal expected counts used in diagnostics

The current implementation reuses the same latent-integrated quantities across
estimation and diagnostics. This keeps EAP summaries, gradients, and strict
marginal expected counts aligned.

## Mathematical Core

For a response vector \(\mathbf{x}_n\) and parameter vector \(\beta\), the
current `MML` path targets the marginal likelihood

\[
L(\beta) = \prod_{n=1}^{N} \int p(\mathbf{x}_n \mid \theta, \beta) g(\theta) \, d\theta
\approx
\prod_{n=1}^{N} \sum_{q=1}^{Q} w_q \, p(\mathbf{x}_n \mid \theta_q, \beta),
\]

where \((\theta_q, w_q)\) are Gauss-Hermite nodes and weights. In `mfrmr`, the
integral is approximated with Gauss-Hermite quadrature, the marginal
log-likelihood is optimized from the same shared kernel, and person summaries
are computed post hoc from the posterior bundle. When a latent-regression
population model is active, the package uses person-specific transformed nodes
derived from the same quadrature basis rather than one unconditional fixed
grid.

The posterior weight for person \(n\) at node \(q\) is

\[
\omega_{nq} =
\frac{w_q \, p(\mathbf{x}_n \mid \theta_q, \hat{\beta})}
{\sum_{r=1}^{Q} w_r \, p(\mathbf{x}_n \mid \theta_r, \hat{\beta})}.
\]

Expected a posteriori (EAP) scoring then uses

\[
\hat{\theta}_n^{\mathrm{EAP}} = \sum_{q=1}^{Q} \theta_q \, \omega_{nq}.
\]

This is the kernel that now feeds `logLik`, the gradient, EAP summaries, and
strict marginal expected values.

## Current MML scope

For the `RSM` / `PCM` MML branch:

- the person distribution is integrated with Gauss-Hermite quadrature
- `mml_engine = "direct"` uses gradient-based direct optimization of the
  marginal log-likelihood
- `mml_engine = "em"` and `mml_engine = "hybrid"` are also available for
  `RSM` / `PCM`; bounded `GPCM` uses the direct engine regardless of that
  option
- person summaries are reported post-hoc from the integrated posterior

This is the implemented MML-engine scope.

## Numerical readiness and bounded polishing

An optimizer return code of zero does not by itself establish a stationary
solution. `mfrmr` applies a common terminal-gradient review to direct, hybrid,
and EM fits. For direct and hybrid fitting, a code-zero solution with a larger
terminal gradient triggers a bounded sequence of warm-started polishing stages
when the requested setting is at least as strict as the public default
(`reltol <= 1e-9`). The package retains the best non-worsening candidate under
the recorded selection rule and records every attempt in
`fit$opt$optimizer_polish$Stages`, including the method, portable tolerance
setting, objective, terminal gradient, parameter change, and evaluation
counts. For L-BFGS-B, the stage table also records the actual `factr` and
`pgtol` controls; `EffectiveReltol` is not itself a native L-BFGS-B argument.
EM retains its relative log-likelihood stopping result but must also pass the
same terminal-gradient gate; use the direct engine for bounded gradient
polishing when an EM fit remains under numerical review.

Read `summary(fit)$readiness` as separate gates. `InferenceReady` and the
Numerical row describe numerical optimization, not the design, stability,
diagnostic, or reporting decision. A small gradient cannot repair a
disconnected measurement graph or a boundary-separated facet level.

### Choosing the iteration ceiling

`maxit` limits computation; it does not define convergence. Use the default
`maxit = 400` as the initial analysis ceiling unless a prespecified protocol
uses another value. A fit that stops at `ConvergenceStatus = "iteration_limit"`
is review-only regardless of whether its estimates look plausible. Keep the
data, model, method, anchors, optimizer, tolerance, and quadrature rule fixed,
then use the next ceiling from a prespecified sequence. Accept a result only
after `Converged`, `InferenceReady`, and the Numerical readiness row all pass.
Do not select a run because its coefficients, fit statistics, significance, or
agreement with an expected result are more favorable. Material differences
between separately ready runs are evidence of numerical instability, not a
choice among equally acceptable answers.

## Strict Marginal Diagnostic Target

The strict marginal branch is not based on plugging \(\hat{\theta}_n^{EAP}\)
back into the response model. Instead, it works with posterior-integrated
expectations. For a grouped summary \(g\) and category \(c\),

\[
\mathbb{E}_{\hat{\beta}}(N_{gc}) =
\sum_{n=1}^{N} \sum_{q=1}^{Q}
\omega_{nq} \, I(n \in g) \, P(X_n = c \mid \theta_q, \hat{\beta}).
\]

The corresponding residual compares the observed count to that
latent-integrated expectation rather than to an `EAP` plug-in prediction.

For pairwise local-dependence follow-up, the package keeps the same posterior
weights but replaces the one-category event with agreement or adjacency events
for the relevant pair of facet levels. That is why `top_marginal_cells` and
`top_marginal_pairs` are conceptually related but not numerically comparable.

## Diagnostic Basis In The Package

`diagnose_mfrm()` now keeps two evidence paths explicit:

- `legacy`: residual/EAP-oriented diagnostics inherited from the earlier stack
- `marginal_fit`: strict latent-integrated first-order and pairwise screens
- `both`: returns both without collapsing them into one decision rule

The object returned by `summary(diag)` exposes `diagnostic_basis` so the two
paths can be interpreted separately.

## Literature Positioning

The current design is deliberately aligned with five strands of the IRT fit
literature.

1. Limited-information item-fit logic.
   Orlando and Thissen (2000, 2003) show why grouped or score-conditioned
   comparisons can be more stable than full-information contingency-table
   statistics in realistic IRT settings. The current package borrows that
   limited-information logic, but it does not implement `S-X2` or `S-G2`
   literally. Instead, it applies posterior-integrated grouped residual screens
   to many-facet cells and levels.

2. Generalized residual logic.
   Haberman and Sinharay (2013) define a generalized residual for a summary
   statistic \(T\) as

\[
r = \frac{T - \hat{\mathbb{E}}(T)}{\hat{s}_D},
\]

   where \(\hat{\mathbb{E}}(T)\) and \(\hat{s}_D\) are computed under the
   fitted model. This is the clearest template for thinking about the current
   `marginal_fit` outputs. The current pairwise local-dependence summaries are
   informed by the same observed-versus-expected logic, but they should still
   be read as exploratory agreement screens rather than as formal Haberman-
   Sinharay generalized residual tests.

3. Multi-method fit assessment and practical significance.
   Sinharay and Monroe (2025) review limited-information statistics,
   generalized residuals, posterior predictive checking, and practical
   significance, and recommend prioritizing fit procedures by intended use
   rather than treating one index as universally decisive.

4. Posterior predictive follow-up.
   Sinharay et al. (2006) treat posterior predictive checking as a separate
   model-checking family built around replicated datasets and discrepancy
   measures. mfrmr does not implement posterior-predictive checks; use a
   model-specific external workflow when this corroborating analysis is
   required.

5. Many-facet reporting context.
   Linacre's FACETS framework and applied MFRM studies such as Eckes (2005)
   remain the primary references for severity/leniency, mean-square fit,
   separation, and inter-rater agreement. mfrmr's strict marginal diagnostics are
   designed to sit alongside that many-facet toolkit, not to replace it.

## Interpretation Boundaries

The strict marginal branch is currently a screening layer, not a fully
calibrated inferential test battery.

- well-specified simulation rows are interpreted as Type I proxies
- misspecified rows are interpreted as sensitivity proxies
- posterior-predictive checks remain a follow-up path rather than a completed
  default computation

This package therefore treats strict marginal diagnostics as structured
evidence about possible misfit, not as a single definitive accept/reject rule.
That design choice follows the broader review logic in Sinharay and Monroe
(2025): use several complementary diagnostics, match them to the intended use
of the scores, and examine practical significance before making strong claims.

### Assumption: independent-Bernoulli variance for grouped counts

The `marginal_fit` grid sums per-observation posterior-integrated
variances as `VarianceCount = sum_i w_i^2 * p_i * (1 - p_i)`, which
treats observations within a cell as independent Bernoulli draws
given the fitted parameters. This is the same independence assumption
that underlies conditional independence in the MFRM specification
(Linacre, 1989). When the rating design violates it - e.g. multiple
ratings by the same rater on the same person-criterion combination -
cell-level posterior variances can be underestimated, which in turn
makes the reported standard errors and screening t-statistics
slightly optimistic. The documented follow-up is
`diagnose_mfrm(..., diagnostic_mode = "both")` combined with
`strict_pairwise_local_dependence`, which surfaces evidence of
dependence at the pair level. See Haberman and Sinharay (2013) for a
generalized-residual framework that models such dependence
explicitly; that path is not included in the documented diagnostic scope.

For many-facet reporting, one additional boundary matters. Facet-level
separation/reliability and inter-rater agreement answer different questions.
High rater separation reliability can coexist with weak observed agreement, and
strong observed agreement does not imply that raters are interchangeable on the
latent severity scale. That is why `mfrmr` reports `diagnostics$reliability`
and `diagnostics$interrater` as separate objects.

## Documented simulation-check scope

The package's documented simulation checks cover:

- well-specified baselines
- local dependence misspecification
- latent distribution misspecification
- step-structure misspecification

These checks target `RSM` and `PCM`. `GPCM` is now supported only within a
bounded core route: fitting, slope summaries, posterior scoring, information
curves, direct curve/category reports, exploratory residual-based follow-up,
direct recovery checks, and the slope-aware element-conditional
`fair_average_table()` and `estimate_bias()`. Historical fair-average SE
columns remain scaled facet-measure SEs rather than delta-method SEs of the
fair-average value; `fair_average_table(fair_se = TRUE)` adds distinct
structural delta-method fair-average SEs for non-person rows when the MML
observed-information Hessian is available. Bias SE / `t` / `Prob.` columns are
conditional plug-in screening quantities, and bounded-GPCM rows also carry
profile-likelihood follow-up columns. Summary-table appendix export is
available for supported direct outputs. The APA writer, fit-based
report/export bundles, package-native scorefile export, QC pass/fail
pipelines, linking synthesis, role-based design forecasting, and
diagnostic/signal-detection design screening are available only as caveated
bounded-`GPCM` surfaces with explicit boundary output. Full FACETS-style
score-side contract review, posterior predictive checks, and MCMC estimation
are not available for bounded `GPCM`. See
`gpcm_capability_matrix()` for the status and recommended alternative for each
helper group.

## Why bounded GPCM is the current limit

`GPCM` is the current upper supported scope for three reasons.

1. The bounded slope model uses the documented `MML` probability framework
   under the stated restriction.
2. Direct verification checks are available for that model.
3. Score-side and reporting helpers that rely on Rasch-family semantics remain
   unavailable or carry explicit caveats.

This is a narrower but more defensible claim than saying the whole package is
uniformly generalized to free-discrimination many-facet work.

## Equal weighting as a model-choice principle

Robitzsch and Steinfeld (2018) are helpful because they separate two arguments
that are often conflated in applied many-facet work.

1. A generalized many-facet model with discrimination parameters will often fit
   empirical data better than an equal-weighting `RSM`/`PCM` fit.
2. That fit advantage does not, by itself, settle the operational scoring
   question.

If the intended score interpretation requires equal contributions of items and
raters, then the Rasch-family route remains substantively attractive even when
a slope-aware model fits better. `mfrmr` therefore treats `RSM` / `PCM` as the
equal-weighting reference models and bounded `GPCM` as a supported alternative
for users who explicitly want to inspect or allow discrimination-based
reweighting.

This is also why full FACETS output-contract score-side review is not provided
for bounded `GPCM`: its published form is a Rasch-family
score transformation, and the slope-aware analogue that would replace it in a
free-discrimination context requires careful score-side uncertainty handling.
Package-native scorefile export, manuscript-draft APA text, and fit-based
report/export bundles are available only as caveated sensitivity-reporting
surfaces, not as FACETS-equivalent or operational score transformations.
`fair_average_table()` and `estimate_bias()` themselves are now available under
bounded `GPCM` via the slope-aware element-conditional kernel. For fair averages,
`fair_average_table(fair_se = TRUE)` adds structural delta-method SEs for
non-person rows when the MML Hessian is available; the historical `SE` columns
remain measure-level SEs.

One additional distinction matters for implementation. The `weight` argument in
`fit_mfrm()` is an observation-weight column. It changes how rating events
enter estimation and summaries, but it is not the same thing as the
equal-weighting versus discrimination-weighting question discussed above.

## Practical Reading Order

For users deciding among `RSM`, `PCM`, and bounded `GPCM`, use this reading
order:

1. Start with the score claim. If category thresholds should be common, begin
   with `RSM`; if thresholds may vary by a designated step facet, begin with
   `PCM`.
2. Fit the Rasch-family reference model with `method = "MML"` and read
   `summary(fit)` plus `summary(diagnose_mfrm(fit, diagnostic_mode = "both"))`.
3. Fit bounded `GPCM` only when discrimination-based reweighting is a meaningful
   sensitivity question, not as a routine replacement for the equal-weighting
   model.
4. If bounded `GPCM` fits better, report what changed: slopes, information
   redistribution, bias-screening rows, fair averages, or conclusions. Do not
   let fit improvement alone decide the operational model.

After fitting candidates, `build_model_choice_review()` places the reported
step/slope coordinate counts, identified free-parameter counts, and each fit's
stored readiness decision in `review$model_roles`. Read those fields before
the information criteria: a more flexible fit that is not inference-ready
cannot become the selected operational model through AIC or BIC alone.

This sequence keeps the interpretation aligned with the validation boundary:
`RSM`/`PCM` support the full manuscript/reporting route, while bounded `GPCM`
supports the documented direct and caveated routes.

## Analyses not provided by mfrmr

Posterior-predictive checks and `MCMC` estimation are not provided by mfrmr.
Use external Bayesian software when those analyses are required. They are not
needed for the quadrature-based `MML` route or for the bounded `GPCM` workflows
described here.

## Recommended Expert Reading Of Package Output

A defensible interpretation sequence is:

1. Read `summary(fit)` for estimation status and precision basis.
2. Read `summary(diag)` with `diagnostic_mode = "both"` to keep legacy and
   strict evidence separate.
3. Treat `marginal_fit` and `marginal_pairwise` as screening layers for
   first-order and local-dependence follow-up.
4. Use plots and tables to judge magnitude and practical importance, not only
   presence/absence of a flag.
5. If a use case demands stronger confirmation, treat posterior predictive
   checking as the next methodological step rather than over-reading the
   current screening statistics.

## Key References

- Andrich, D. (1978). *A rating formulation for ordered response categories*.
  Psychometrika, 43, 561-573.
- Bock, R. D., & Aitkin, M. (1981). *Marginal maximum likelihood estimation of
  item parameters: Application of an EM algorithm*. Psychometrika, 46, 443-459.
- Haberman, S. J., & Sinharay, S. (2013). *Generalized residuals for general
  models for contingency tables with application to item response theory*.
  Journal of the American Statistical Association, 108, 1435-1444.
- Eckes, T. (2005). *Examining rater effects in TestDaF writing and speaking
  performance assessments: A many-facet Rasch analysis*. Language Assessment
  Quarterly, 2, 197-221.
- Linacre, J. M. (1989). *Many-facet Rasch measurement*. MESA Press.
- Masters, G. N. (1982). *A Rasch model for partial credit scoring*.
  Psychometrika, 47, 149-174.
- Orlando, M., & Thissen, D. (2000). *Likelihood-based item-fit indices for
  dichotomous item response theory models*. Applied Psychological Measurement,
  24, 50-64.
- Orlando, M., & Thissen, D. (2003). *Further investigation of the performance
  of S-X2: An item fit index for use with dichotomous item response theory
  models*. Applied Psychological Measurement, 27, 289-298.
- Robitzsch, A., & Steinfeld, J. (2018). *Item response models for human
  ratings: Overview, estimation methods, and implementation in R*.
  Psychological Test and Assessment Modeling, 60(1), 101-139.
- Sinharay, S., & Monroe, S. (2025). *Assessment of fit of item response
  theory models: A critical review of the status quo and some future
  directions*. British Journal of Mathematical and Statistical Psychology, 78,
  711-733.
- Sinharay, S., Johnson, M. S., & Stern, H. S. (2006). *Posterior predictive
  assessment of item response theory models*. Applied Psychological
  Measurement, 30, 298-321.
