use ::Matrix{T} instead of ::T to aid type inference (#773)

* use ::Matrix{T} instead of ::T

* update NEWS.md

* JuliaFormatter run (mostly adding trailing commas).

NEWS.md

@@ -1,3 +1,7 @@
+MixedModels v4.24.1 Release Notes
+==============================
+Add type notations in `pwrss(::LinearMixedModel)` and `logdet(::LinearMixedModel)` to enhance type inference. [#773]
+
 MixedModels v4.24.0 Release Notes
 ==============================
 * Properties for `GeneralizedLinearMixedModel` now default to delegation to the internal weighted `LinearMixedModel` when that property is not explicitly handled by `GeneralizedLinearMixedModel`. Previously, properties were delegated on an explicit basis, which meant that they had to be added manually as use cases were discovered. The downside to the new approach is that it is now possible to access properties whose definition in the LMM case doesn't match the GLMM definition when the GLMM definition hasn't been explicitly been implemented. [#767]
@@ -521,3 +525,4 @@ Package dependencies
 [#755]: https://github.com/JuliaStats/MixedModels.jl/issues/755
 [#756]: https://github.com/JuliaStats/MixedModels.jl/issues/756
 [#767]: https://github.com/JuliaStats/MixedModels.jl/issues/767
+[#773]: https://github.com/JuliaStats/MixedModels.jl/issues/773

src/generalizedlinearmixedmodel.jl

@@ -351,7 +351,7 @@ function GeneralizedLinearMixedModel(
     tbl,
     d::Distribution,
     l::Type;
-    kwargs...
+    kwargs...,
 )
     throw(ArgumentError("Expected a Link instance (`$l()`), got a type (`$l`)."))
 end
@@ -376,7 +376,7 @@ function GeneralizedLinearMixedModel(
     tbl::Tables.ColumnTable,
     d::Normal,
     l::IdentityLink;
-    kwargs...
+    kwargs...,
 )
     return throw(
         ArgumentError("use LinearMixedModel for Normal distribution with IdentityLink")

src/likelihoodratiotest.jl

@@ -219,7 +219,7 @@ function _iscomparable(m::LinearMixedModel...)
     if any(getproperty.(getproperty.(m, :optsum), :REML))
         isconstant(coefnames.(m)) || throw(
             ArgumentError(
-                "Likelihood-ratio tests for REML-fitted models are only valid when the fixed-effects specifications are identical",
+                "Likelihood-ratio tests for REML-fitted models are only valid when the fixed-effects specifications are identical"
             ),
         )
     end

src/linalg/logdet.jl

@@ -25,9 +25,9 @@ lower Cholesky factor.
 """
 function LinearAlgebra.logdet(m::LinearMixedModel{T}) where {T}
     L = m.L
-    @inbounds s = sum(j -> LD(L[kp1choose2(j)]), axes(m.reterms, 1))::T
+    @inbounds s = sum(j -> LD(L[kp1choose2(j)])::T, axes(m.reterms, 1))
     if m.optsum.REML
-        lastL = last(L)
+        lastL = last(L)::Matrix{T}
         s += LD(lastL)        # this includes the log of sqrtpwrss
         s -= log(last(lastL)) # so we need to subtract it from the sum
     end

src/linalg/rankUpdate.jl

@@ -12,7 +12,7 @@ function rankUpdate! end
 
 function rankUpdate!(C::AbstractMatrix, a::AbstractArray, α, β)
     return error(
-        "We haven't implemented a method for $(typeof(C)), $(typeof(a)). Please file an issue on GitHub.",
+        "We haven't implemented a method for $(typeof(C)), $(typeof(a)). Please file an issue on GitHub."
     )
 end
 

src/linearmixedmodel.jl

@@ -895,7 +895,7 @@ end
 
 The penalized, weighted residual sum-of-squares.
 """
-pwrss(m::LinearMixedModel{T}) where {T} = abs2(last(last(m.L)))::T
+pwrss(m::LinearMixedModel{T}) where {T} = abs2(last(last(m.L)::Matrix{T}))
 
 """
     ranef!(v::Vector{Matrix{T}}, m::MixedModel{T}, β, uscale::Bool) where {T}

src/mixedmodel.jl

@@ -80,7 +80,7 @@ function StatsAPI.fit(
     tbl,
     d::Type,
     args...;
-    kwargs...
+    kwargs...,
 )
     throw(ArgumentError("Expected a Distribution instance (`$d()`), got a type (`$d`)."))
 end
@@ -91,7 +91,7 @@ function StatsAPI.fit(
     tbl,
     d::Distribution,
     l::Type;
-    kwargs...
+    kwargs...,
 )
     throw(ArgumentError("Expected a Link instance (`$l()`), got a type (`$l`)."))
 end

src/predict.jl

@@ -115,7 +115,7 @@ function _predict(m::MixedModel{T}, newdata, β; new_re_levels) where {T}
             any(any(ismissing, Tables.getcolumn(newdata, col)) for col in respvars)
             throw(
                 ArgumentError(
-                    "Response column must be initialized to a non-missing numeric value.",
+                    "Response column must be initialized to a non-missing numeric value."
                 ),
             )
         end

src/profile/thetapr.jl

@@ -10,7 +10,7 @@ function optsumj(os::OptSummary, j::Integer)
     return OptSummary(
         deleteat!(copy(os.final), j),
         deleteat!(copy(os.lowerbd), j),
-        os.optimizer
+        os.optimizer,
     )
 end
 

src/randomeffectsterm.jl

@@ -174,7 +174,7 @@ function StatsModels.apply_schema(
     if !(typeof(first) <: CategoricalTerm)
         throw(
             ArgumentError(
-                "nesting terms requires categorical grouping term, got $first.  Manually specify $first as `CategoricalTerm` in hints/contrasts",
+                "nesting terms requires categorical grouping term, got $first.  Manually specify $first as `CategoricalTerm` in hints/contrasts"
             ),
         )
     end

src/remat.jl

@@ -586,7 +586,7 @@ end
 function copyscaleinflate!(
     Ljj::UniformBlockDiagonal{T},
     Ajj::UniformBlockDiagonal{T},
-    Λj::ReMat{T,S}
+    Λj::ReMat{T,S},
 ) where {T,S}
     λ = Λj.λ
     dind = diagind(S, S)
@@ -604,7 +604,7 @@ end
 function copyscaleinflate!(
     Ljj::Matrix{T},
     Ajj::UniformBlockDiagonal{T},
-    Λj::ReMat{T,S}
+    Λj::ReMat{T,S},
 ) where {T,S}
     copyto!(Ljj, Ajj)
     n = LinearAlgebra.checksquare(Ljj)

src/simulate.jl

@@ -236,7 +236,7 @@ function _simulate!(
         ismissing(σ) ||
         throw(
             ArgumentError(
-                "You must not specify a dispersion parameter for model families without a dispersion parameter",
+                "You must not specify a dispersion parameter for model families without a dispersion parameter"
             ),
         )
 

src/utilities.jl

@@ -136,7 +136,7 @@ function replicate(
 )
     use_threads && Base.depwarn(
         "use_threads is deprecated and will be removed in a future release",
-        :replicate
+        :replicate,
     )
     if !isnothing(hide_progress)
         Base.depwarn(