Add Brant test (resolves: https://github.com/jasp-stats/jasp-issues/issues/3295)

[rphars]

Implements the Brant test, which tests the proportional odds (also called parallel lines) assumption in ordered logit models. This resolves: jasp-stats/jasp-issues#3295

The test is described in
Brant, R. (1990). Assessing proportionality in the proportional odds model for ordinal logistic regression. Biometrics, 46(4), 1171–1178. https://doi.org/10.2307/2532457

This is a new implementation, different from earlier implementations in brant::brant and gofcat::brant.test. Several reasons for this:

• brant::brant is not compatible with VGAM
• gofcat::brant.test is compatible, but dependency-heavy.
• It was a nice opportunity to learn more about the underlying logic of the test

The code adds a new menu option when ordinal logit models are selected:

Outputs are tested against:
-STATA's brant (implemented by Long & Freese)
-prior R implementations from brant::brant and gofcat::brant.test.

The code outputs the same results as in STATA's brant:

with every dataset I've tried. Screenshot shows data from: https://stats.oarc.ucla.edu/r/dae/ordinal-logistic-regression/

There is one small implementation difference compared to brant::brant and gofcat::brant.test, which both omit a transpose in one specific place indicated in the code. This leads to minor numerical differences in small samples. The current implementation is consistent with STATA's brant and Brant's paper.

Note: this is my first contribution, so apologies in advance if I missed anything.

[github-actions]

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[JohnnyDoorn]

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[github-actions]

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[JohnnyDoorn]

Really nice, especially as a first contribution! Just some minor suggestions:

• Please add a note in news.md so that your change gets included in the next release notes
• on line 1257 you have a footnote with whitespaces and indentations, which does not work for translations and the like. Please just make this one continuous string
  i.e., gettext("Negative \u03A7\u00B2 statistics are computational artifacts. They indicate the estimated covariance matrix is not positive semi-definite or is ill-conditioned, often due to small samples or sparse data. Test results might be misleading."
• 1:numThresholds / 1:numPredictors → seq_len(...) (safe here given the guards, but it's the style-guide convention).
• the qml logic can be smoothened out so that it works correctly on a JASP restart:

1. GlmInputComponent.qml — make the property a binding (line 25):
   // before
   property bool isOrdinalModel: false
   // after
   property bool isOrdinalModel: family.currentValue === "other" && otherGlmModel.currentValue === "ordinalLogistic"
2. GlmInputComponent.qml — delete both imperative assignments now that the binding does the work.

In the family DropDown's handler, drop just the one line (keep the rest of the handler):

	onCurrentValueChanged:
	{
		isOrdinalModel = (family.currentValue === "other") && (otherGlmModel.currentValue === "ordinalLogistic");   // ← delete this line
		if (!familyMap[currentValue].includes(link.value))
		...

In the otherGlmModel DropDown, remove the entire onCurrentValueChanged block (it exists only to set the property):

		{ label: qsTr("Firth Logistic Regression"),				value: "firthLogistic"}
		]
		onCurrentValueChanged:          // ← delete these
			{                            //    four
				isOrdinalModel = ...     //    lines
			}                            //    entirely
	}

3. GeneralizedLinearModel.qml — tab-indent the new Group (it's a sibling of the just-closed Output group, so 2 tabs / 3 / 4), and drop the stray ; after visible:

    Group
    {
    	title:   qsTr("Assumption Checks")
    	visible: input.isOrdinalModel
   
    	CheckBox
    	{
    		name:  "brantTest"
    		label: qsTr("Brant test of proportional odds")
    	}
    }
   

[JohnnyDoorn]

maybe also add family, link, interceptTerm to the dependencies to ensure it's updated when relevant

[rphars]

Thanks for the extensive review/comments. I'll implement them as soon as time allows!