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Support ordinal (argument mode for emmeans backend - #669

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strengejacke merged 4 commits into
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support_emmeans_ordinal
Oct 1, 2026
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Support ordinal (argument mode for emmeans backend#669
strengejacke merged 4 commits into
mainfrom
support_emmeans_ordinal

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@strengejacke

@strengejacke strengejacke commented Sep 30, 2026 •
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@jmgirard is there something I am missing, or is this the expected output? For polr::MASS, the result is the same. Not sure I'm missing a combination of mode and type arguments, or how are ordinal models handled?

data(housing, package = "MASS")
m <- glmmTMB::glmmTMB(Sat ~ Infl + Type + Cont, data = housing, family = glmmTMB::ordinal())

emmeans::emmeans(m, "Type", mode = "prob")
#>  Type       prob SE  df asymp.LCL asymp.UCL
#>  Tower     0.333  0 Inf     0.333     0.333
#>  Apartment 0.333  0 Inf     0.333     0.333
#>  Atrium    0.333  0 Inf     0.333     0.333
#>  Terrace   0.333  0 Inf     0.333     0.333
#> 
#> Results are averaged over the levels of: Sat, Infl, Cont 
#> Confidence level used: 0.95

Created on 2026-09-30 with reprex v2.1.1

@jmgirard

jmgirard commented Sep 30, 2026

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The 0.333 values are expected emmeans behavior. With mode = "prob", emmeans adds the response (Sat) to the reference grid as a pseudo-factor, and emmeans(m, "Type", mode = "prob") averages over it. The three category probabilities sum to 1, so each average is 1/3. emmeans(m, ~ Type | Sat, mode = "prob") gives the per-category probabilities, and these match estimate_means(m, "Type") with the marginaleffects backend (difference below 1e-15 for polr and clm). The cum.prob, exc.prob, and linear.predictor modes add a cut pseudo-factor in the same way, so get_emmeans() needs to add that pseudo-factor to specs. Separately, on main the emmeans backend returns latent-scale values labeled "Probability" for polr, because emmeans ignores type = "response" for these models. I will open a PR into this branch with a fix.

@jmgirard jmgirard mentioned this pull request Sep 30, 2026
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jmgirard and others added 2 commits September 30, 2026 23:43
@jmgirard
Return per-category and per-threshold estimates for ordinal models wi…
ff69ccb 
…th the emmeans backend (#670)

* Add tests for ordinal modes with the emmeans backend (failing)

* Return per-category and per-threshold estimates for ordinal models with the emmeans backend

* Update NEWS entry for ordinal models with the emmeans backend

* Fix ordinal emmeans output for transformed responses, plot names, and docs

- Name the response pseudo-factor after the formula's left-hand side, so
  that models with e.g. factor(y) as response no longer fail.
- Add Latent, Linear_predictor, and Mean_class to the known estimate names.
- Document the ordinal modes and the "prob" default for estimate_means().
- Check the number of matched rows in the glmmTMB test.
@strengejacke @github-actions
Update R/get_emmeans.R
41a49b3 
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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strengejacke requested a lite review from Copilot October 1, 2026 10:38
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Copilot review overview

🟡 Changes recommended

Resolve ordinal mode handling, preserve non-ordinal behavior, correct inherited documentation, and ensure tests run independently.

Review effort: Lite
Findings: 1 Medium severity

Open (1)
What changed in this PR

Adds ordinal-model support for the emmeans backend in estimate_means(), with updated output handling, tests, documentation, NEWS, and version metadata.

Changes:

  • Routes ordinal predictions through emmeans modes.
  • Normalizes ordinal output columns.
  • Adds ordinal backend tests and documentation updates.
File Summary
tests/​testthat/​test-ordinal.R Adds ordinal backend coverage.
R/​utils.R Adds ordinal estimate column names.
R/​get_emmeans.R Implements ordinal mode handling and formatting.
R/​estimate_means.R Documents ordinal prediction modes.
NEWS.md Records the new functionality.
man/​get_emmeans.Rd Updates generated documentation.
man/​estimate_slopes.Rd Updates inherited documentation.
man/​estimate_means.Rd Updates generated documentation.
man/​estimate_contrasts.Rd Updates inherited documentation.
DESCRIPTION Increments the package version.
Files not reviewed (4)
  • man/estimate_contrasts.Rd: Generated file
  • man/estimate_means.Rd: Generated file
  • man/estimate_slopes.Rd: Generated file
  • man/get_emmeans.Rd: Generated file

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Comment thread R/get_emmeans.R
@strengejacke
strengejacke merged commit e6e1f18 into main Oct 1, 2026
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@strengejacke
strengejacke deleted the support_emmeans_ordinal branch October 1, 2026 11:00
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@strengejacke @jmgirard