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July 25, 2022 23:03
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GLM.jl issue with lrtest
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### 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] | |
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" | |
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" | |
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[compat] | |
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""" | |
# ╔═╡ 00000000-0000-0000-0000-000000000002 | |
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uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" | |
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deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] | |
git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" | |
uuid = "276daf66-3868-5448-9aa4-cd146d93841b" | |
version = "2.1.7" | |
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git-tree-sha1 = "2c11d7290036fe7aac9038ff312d3b3a2a5bf89e" | |
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git-tree-sha1 = "472d044a1c8df2b062b23f222573ad6837a615ba" | |
uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" | |
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git-tree-sha1 = "5783b877201a82fc0014cbf381e7e6eb130473a4" | |
uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" | |
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git-tree-sha1 = "4352d5badd1bc8bf0a8c825e886fa1eda4f0f967" | |
uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" | |
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uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" | |
[[deps.TOML]] | |
deps = ["Dates"] | |
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" | |
[[deps.TableTraits]] | |
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git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" | |
uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" | |
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uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" | |
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uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" | |
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uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" | |
[[deps.TranscodingStreams]] | |
deps = ["Random", "Test"] | |
git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" | |
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" | |
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deps = ["Random", "SHA"] | |
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" | |
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uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" | |
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deps = ["DataAPI", "InlineStrings", "Parsers"] | |
git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" | |
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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 |
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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 | |
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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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