support nested grouping variable (#71)

* support nested grouping variable * YAS
palday · Nov 13, 2023 · e0d753d · e0d753d · palday · Nov 13, 2023
1 parent 7a89cd3
commit e0d753d
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Showing 3 changed files with 30 additions and 4 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "JellyMe4"
 uuid = "19ac8677-9a15-4623-9afd-84acc6165ce7"
 authors = ["Phillip Alday <me@phillipalday.com>"]
-version = "1.1.1"
+version = "1.2.0"
 
 [deps]
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
@@ -22,7 +22,7 @@ CategoricalArrays = "0.10"
 DataFrames = "1"
 Distributions = "0.25"
 GLM = "1.3"
-LinearAlgebra = "1"
+LinearAlgebra = "0, 1"
 MixedModels = "4"
 RCall = "0.13"
 RegressionFormulae = "0.1"

diff --git a/src/formula.jl b/src/formula.jl
@@ -7,7 +7,7 @@ import RCall: rcopy,
 
 """
     fulldummy2dummy(lhs, grp, bar="|")
-    
+
 """
 function _fulldummy2dummy(lhs, grp, bar="|")
     terms = Vector{String}(undef, length(lhs.terms))
@@ -64,7 +64,7 @@ function convert_julia_to_r(f::StatsModels.FormulaTerm)::AbstractString
             end
 
         elseif trm isa MixedModels.RandomEffectsTerm
-            rhs[idx] = _fulldummy2dummy(trm.lhs, trm.rhs.sym)
+            rhs[idx] = _fulldummy2dummy(trm.lhs, string(trm.rhs))
         else
             rhs[idx] = string(trm)
         end

diff --git a/test/lmerMod.jl b/test/lmerMod.jl
@@ -5,6 +5,7 @@ using Tables: columntable
 
 using JellyMe4: _set_lmer, _set_afex_installed
 using MixedModels: dataset
+using DataFrames
 
 const LMM = LinearMixedModel
 const GLMM = GeneralizedLinearMixedModel
@@ -136,6 +137,18 @@ const GLMM = GeneralizedLinearMixedModel
             @test only(rlmm.rePCA) ≈ only(jlmm.rePCA) atol = 0.05
         end
 
+        @testset "nested grouping" begin
+            pastes = DataFrame(dataset(:pastes))
+            @rput pastes
+            jlmm = fit(MixedModel, @formula(strength ~ 1 + (1 | batch / cask)), pastes;
+                       REML=false, progress=false)
+            rlmm = rcopy(R"lme4::lmer(strength ~ 1 + (1 | batch / cask), pastes,REML=FALSE)")
+
+            @test jlmm.θ ≈ rlmm.θ atol = 0.001
+            @test objective(jlmm) ≈ objective(rlmm) atol = 0.001
+            @test fixef(jlmm) ≈ fixef(rlmm) atol = 0.001
+        end
+
         @testset "dummy" begin
             # TODO
         end
@@ -274,6 +287,19 @@ const GLMM = GeneralizedLinearMixedModel
                 end
             end
         end
+
+        @testset "nested grouping" begin
+            pastes = DataFrame(dataset(:pastes))
+            @rput pastes
+            jlmm = fit(MixedModel, @formula(strength ~ 1 + (1 | batch / cask)), pastes;
+                       REML=false, progress=false)
+            rlmm = (jlmm, pastes)
+            @rput rlmm
+
+            @test jlmm.θ ≈ rcopy(R"""getME(rlmm, "theta")""") atol = 0.001
+            @test objective(jlmm) ≈ rcopy(R"deviance(rlmm)") atol = 0.001
+            @test only(fixef(jlmm)) ≈ rcopy(R"fixef(rlmm)") atol = 0.001
+        end
     end
 
     @testset "lmerControl warnings" begin