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@jerlich
Created July 25, 2022 23:03
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GLM.jl issue with lrtest
### A Pluto.jl notebook ###
# v0.19.9
using Markdown
using InteractiveUtils
# ╔═╡ caea71e0-0c68-11ed-0f9a-913b221ef108
using DataFrames, CSV, GLM
# ╔═╡ c2a89f5b-8126-4a81-9fcb-0e31efd42b1d
fname = "mwe.csv"
# ╔═╡ a28e59bc-cdb2-4e05-a8b0-64715e8a0c85
md"""## Two strange things with GLM.jl
We read in the data and define two models (one nested in the other).
"""
# ╔═╡ c2630318-b2c4-4d82-9547-f6c01ef3b52b
df = CSV.read(fname, DataFrame); md"read in the data"
# ╔═╡ aed40ba6-30e9-4896-acaa-c1bb63069be5
f = @formula(actual_shift ~ pred_shift * infusion)
# ╔═╡ 13254d53-b850-4d54-8424-a539911d8adb
fr = @formula(actual_shift ~ pred_shift)
# ╔═╡ 84a16d14-0205-4367-963d-248110163e1b
m1 = lm(f, df)
# ╔═╡ 2b94f48b-d826-46f6-9c7d-71816444c6d4
m1r = lm(fr, df)
# ╔═╡ 9cc81676-32e8-480f-bdea-403c5911cd56
ft = ftest(m1r.model, m1.model)
# ╔═╡ d48ac01f-b84b-4e62-87a9-f6358752fbff
lt = lrtest(m1r.model, m1.model)
# ╔═╡ 27b7b158-7192-4acc-8913-2ed57ca11934
md"""
Comparing the nested models, `ftest` gives p=$(round(ft.pval[2],digits=4)) but `lrtest` gives $(round(lt.pval[2], digits=4)). In R, `anova` gives the same results as julia `ftest` and other methods all give _p < 0.05_. (e.g. using `drop1` or `lmtest::lrtest`)
"""
# ╔═╡ 4e040ae5-1cc9-46e7-81d0-178751d1a5b5
md"""
### 2nd Strange thing
`lm(f,df)` gives different results from `glm(f,df,Normal())`. Also the coefficients and std. err. are the same, the `glm` has a lower pvalue for the interaction term (maybe because it is using a z-stat instead of a t-stat?)
I checked that in R, lm and glm both give a t-stat with the same value (the same as `lm` in julia)
"""
# ╔═╡ c664bbf3-3290-41cc-b068-d06eba596f26
m2 = glm(f, df, Normal())
# ╔═╡ 00000000-0000-0000-0000-000000000001
PLUTO_PROJECT_TOML_CONTENTS = """
[deps]
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GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
[compat]
CSV = "~0.10.4"
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GLM = "~1.8.0"
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# ╔═╡ 00000000-0000-0000-0000-000000000002
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uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
version = "0.6.30"
[[deps.SuiteSparse]]
deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
[[deps.TableTraits]]
deps = ["IteratorInterfaceExtensions"]
git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
version = "1.0.1"
[[deps.Tables]]
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"]
git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.7.0"
[[deps.Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
[[deps.Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
[[deps.TranscodingStreams]]
deps = ["Random", "Test"]
git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c"
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
version = "0.9.6"
[[deps.UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
[[deps.Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
[[deps.WeakRefStrings]]
deps = ["DataAPI", "InlineStrings", "Parsers"]
git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23"
uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
version = "1.4.2"
[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
"""
# ╔═╡ Cell order:
# ╠═caea71e0-0c68-11ed-0f9a-913b221ef108
# ╠═c2a89f5b-8126-4a81-9fcb-0e31efd42b1d
# ╟─a28e59bc-cdb2-4e05-a8b0-64715e8a0c85
# ╟─c2630318-b2c4-4d82-9547-f6c01ef3b52b
# ╠═aed40ba6-30e9-4896-acaa-c1bb63069be5
# ╠═13254d53-b850-4d54-8424-a539911d8adb
# ╠═84a16d14-0205-4367-963d-248110163e1b
# ╠═2b94f48b-d826-46f6-9c7d-71816444c6d4
# ╠═9cc81676-32e8-480f-bdea-403c5911cd56
# ╠═d48ac01f-b84b-4e62-87a9-f6358752fbff
# ╠═27b7b158-7192-4acc-8913-2ed57ca11934
# ╟─4e040ae5-1cc9-46e7-81d0-178751d1a5b5
# ╠═c664bbf3-3290-41cc-b068-d06eba596f26
# ╟─00000000-0000-0000-0000-000000000001
# ╟─00000000-0000-0000-0000-000000000002
actual_shift pred_shift infusion
0.132756132756133 0.315823146645022 infusion
0.159518348623853 0.284901666666667 sb_change
-0.193181818181818 -0.321694318181818 sb_change
-0.11021685669573 -0.182074753521127 infusion
0.172482552342971 0.305509448529412 sb_change
0.249158249158249 0.313505162037037 infusion
0.0525856044723969 0.26591400462963 sb_change
-0.0689085545722714 -0.0738073045722714 sb_change
0.023342670401494 -0.260771765873016 sb_change
-0.093167701863354 -0.0999712137681159 sb_change
-0.170570039770216 -0.359395188172043 infusion
-0.183423913043478 -0.412505 sb_change
-0.0118644067796611 -0.0456748234463277 sb_change
0.296440129449838 0.386584375 infusion
0.220170454545455 0.208560454545455 sb_change
0.153171390013495 0.393170304487179 sb_change
-0.245055735346998 -0.426677841828479 sb_change
0.206847697756789 0.359088025137741 sb_change
-0.415584415584416 -0.443264564393939 infusion
-0.0904344193817878 -0.278369736842105 sb_change
0.183695652173913 0.31377419384058 sb_change
0.0721003134796238 0.34412904454023 sb_change
0.0832164562879851 0.302948313172043 sb_change
0.0449074074074074 0.195725 infusion
0.0573543015726179 0.161521271135266 sb_change
-0.0174065793676142 -0.0192794176292629 sb_change
-0.0416666666666667 0.124202430555556 sb_change
-0.0411590992986342 -0.12162376984127 sb_change
-0.2 -0.225376041666667 infusion
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