rework likelihoodratio test to be just a pretty-printing wrapper around lrtest

NEWS.md

@@ -10,6 +10,8 @@ MixedModels v5.0.0 Release Notes
 - The `prfit!` convenience function has been removed. [#853]
 - The `dataset` and `datasets` functions have been removed. They are now housed in `MixedModelsDatasets`.[#854]
 - One argument `predict(::GeneralizedLinearMixedModel)`, i.e. prediction on the original data, now supports the `type` keyword argument. [#856]
+- `isnested(A::ReMat, B::ReMat)` is now a method of `StatsModels.isnested`.[#858]
+- [BREAKING ]`likelihoodratiotest` has been reworked to be a thin wrapper around `StatsModels.lrtest`. The historical difference in behavior in terms of nesting checks created some confusion. Users advanced enough to create models with non-obvious nesting are assumed to be advanced enough to manually compute the likelihood ratio test. The function `likelihoodratiotest` and associated `LikelihoodRatioTest` type (now with a type parameter for number of models) has been kept to enable printing of test results with model formulae. Most users should not notice a difference in behavior, but the display has been slightly changed and the internal field structure has changed.[#858]
 
 MixedModels v4.38.0 Release Notes
 ==============================
@@ -671,3 +673,9 @@ Package dependencies
 [#840]: https://github.com/JuliaStats/MixedModels.jl/issues/840
 [#841]: https://github.com/JuliaStats/MixedModels.jl/issues/841
 [#842]: https://github.com/JuliaStats/MixedModels.jl/issues/842
+[#849]: https://github.com/JuliaStats/MixedModels.jl/issues/849
+[#850]: https://github.com/JuliaStats/MixedModels.jl/issues/850
+[#853]: https://github.com/JuliaStats/MixedModels.jl/issues/853
+[#854]: https://github.com/JuliaStats/MixedModels.jl/issues/854
+[#856]: https://github.com/JuliaStats/MixedModels.jl/issues/856
+[#858]: https://github.com/JuliaStats/MixedModels.jl/issues/858

Project.toml

@@ -17,6 +17,7 @@ MixedModelsDatasets = "7e9fb7ac-9f67-43bf-b2c8-96ba0796cbb6"
 NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"
 PooledArrays = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -61,6 +62,7 @@ NLopt = "0.6, 1"
 PRIMA = "0.2"
 PooledArrays = "0.5, 1"
 PrecompileTools = "1"
+Printf = "1"
 ProgressMeter = "1.7"
 Random = "1"
 RegressionFormulae = "0.1.3"

src/MixedModels.jl

@@ -23,6 +23,7 @@ using MixedModelsDatasets: dataset
 using PooledArrays: PooledArrays, PooledArray
 using NLopt: NLopt
 using PrecompileTools: PrecompileTools, @setup_workload, @compile_workload
+using Printf: @sprintf
 using ProgressMeter: ProgressMeter, Progress, finish!, next!
 using Random: Random, AbstractRNG, randn!
 using SparseArrays: SparseArrays, SparseMatrixCSC, SparseVector, dropzeros!, nnz
@@ -36,12 +37,12 @@ using StatsAPI:
     loglikelihood, meanresponse, modelmatrix, nobs, pvalue, predict, r2, residuals
 using StatsAPI: response, responsename, stderror, vcov, weights
 using StatsBase: StatsBase, CoefTable, model_response, summarystats
-using StatsFuns: log2π, normccdf
+using StatsFuns: chisqccdf, log2π, normccdf
 using StatsModels: StatsModels, AbstractContrasts, AbstractTerm, CategoricalTerm
 using StatsModels: ConstantTerm, DummyCoding, EffectsCoding, FormulaTerm, FunctionTerm
 using StatsModels: HelmertCoding, HypothesisCoding, InteractionTerm, InterceptTerm
 using StatsModels: MatrixTerm, SeqDiffCoding, TableRegressionModel
-using StatsModels: apply_schema, drop_term, formula, lrtest, modelcols, @formula
+using StatsModels: apply_schema, drop_term, formula, lrtest, modelcols, isnested, @formula
 using StructTypes: StructTypes
 using Tables: Tables, columntable
 using TypedTables: TypedTables, DictTable, FlexTable, Table