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use StatsModels.[g]vif #22

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merged 5 commits into from
Sep 13, 2023
Merged

use StatsModels.[g]vif #22

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de83c32
use StatsModels.[g]vif
palday Sep 11, 2023
ca34728
compat
palday Sep 13, 2023
eff372f
julia compat floor
palday Sep 13, 2023
2fb1518
Update src/MixedModelsExtras.jl
palday Sep 13, 2023
d037e20
remove unused file
palday Sep 13, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
version: [1.6, 1]
version: [1.8, 1]
arch: [x64]
os: [ubuntu-20.04] # macos-10.15, windows-2019
steps:
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8 changes: 4 additions & 4 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "MixedModelsExtras"
uuid = "781a26e1-49f4-409a-8f4c-c3159d78c17e"
authors = ["Phillip Alday <[email protected]> and contributors"]
version = "1.1.0"
version = "2.0.0"

[deps]
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Expand All @@ -12,11 +12,11 @@ StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"

[compat]
MixedModels = "3, 4"
MixedModels = "4"
StatsBase = "0.33, 0.34"
StatsModels = "0.6.28, 0.7"
StatsModels = "0.7.3"
Tables = "1"
julia = "1.6"
julia = "1.8"

[extras]
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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8 changes: 5 additions & 3 deletions src/MixedModelsExtras.jl
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Expand Up @@ -7,15 +7,17 @@ using StatsBase
using StatsModels
using Tables

using StatsModels: termnames, vif, gvif
export termnames, gvif, vif

StatsModels.termnames(::RandomEffectsTerm) = String[]

include("icc.jl")
export icc

include("r2.jl")
export r², r2, adjr², adjr2

include("vif.jl")
export termnames, gvif, vif

include("remef.jl")
export partial_fitted

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143 changes: 0 additions & 143 deletions src/vif.jl
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6 changes: 3 additions & 3 deletions test/vif.jl
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Expand Up @@ -18,7 +18,7 @@ progress = false
fm2 = fit(MixedModel, @formula(reaction ~ 1 + days * days^2 + (1 | subj)),
dataset(:sleepstudy); progress)

ae_int = ArgumentError("VIF only defined for models with an intercept term")
ae_int = ArgumentError("VIF is only defined for models with an intercept term")
ae_nterm = ArgumentError("VIF not meaningful for models with only one non-intercept term")
@test_throws ae_int vif(fm0)
@test_throws ae_nterm vif(fm1)
Expand Down Expand Up @@ -46,15 +46,15 @@ end
duncan = rdataset("car", "Duncan")

lm1 = lm(@formula(Prestige ~ 1 + Income + Education), duncan)
@test termnames(lm1) == coefnames(lm1)
@test termnames(lm1)[2] == coefnames(lm1)
vif_lm1 = vif(lm1)

# values here taken from car
@test isapprox(vif_lm1, [2.1049, 2.1049]; atol=1e-5)
@test isapprox(vif_lm1, gvif(lm1))

lm2 = lm(@formula(Prestige ~ 1 + Income + Education + Type), duncan)
@test termnames(lm2) == ["(Intercept)", "Income", "Education", "Type"]
@test termnames(lm2)[2] == ["(Intercept)", "Income", "Education", "Type"]
@test isapprox(gvif(lm2), [2.209178, 5.297584, 5.098592]; atol=1e-5)
@test isapprox(gvif(lm2; scale=true),
[1.486330, 2.301648, 1.502666]; atol=1e-5)
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