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support nested grouping variable #71

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merged 2 commits into from
Nov 13, 2023
+30 −4
Merged

support nested grouping variable #71

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cdcd7ca
support nested grouping variable
palday Nov 7, 2023
9c06cd5
YAS
palday Nov 7, 2023
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4 changes: 2 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "JellyMe4"
uuid = "19ac8677-9a15-4623-9afd-84acc6165ce7"
authors = ["Phillip Alday <[email protected]>"]
version = "1.1.1"
version = "1.2.0"

[deps]
CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
Expand All @@ -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"
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4 changes: 2 additions & 2 deletions src/formula.jl
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Expand Up @@ -7,7 +7,7 @@ import RCall: rcopy,

"""
fulldummy2dummy(lhs, grp, bar="|")

"""
function _fulldummy2dummy(lhs, grp, bar="|")
terms = Vector{String}(undef, length(lhs.terms))
Expand Down Expand Up @@ -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
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26 changes: 26 additions & 0 deletions test/lmerMod.jl
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
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