From 47350fc535bd21b15c10159e3f1ec409e590aa35 Mon Sep 17 00:00:00 2001 From: Rob J Goedman Date: Sun, 2 Oct 2022 09:24:21 -0600 Subject: [PATCH] Rel 0.7.2 --- Manifest.toml | 436 ++-- notebooks/Chapters/01 - Introduction.jl | 1802 +++++++++++++++++ ...ssion with multiple predictors backup 1.jl | 223 ++ ...ssion with multiple predictors backup 2.jl | 223 ++ ...ear regression with multiple predictors.jl | 2 +- 5 files changed, 2491 insertions(+), 195 deletions(-) create mode 100644 notebooks/Chapters/10 - Linear regression with multiple predictors backup 1.jl create mode 100644 notebooks/Chapters/10 - Linear regression with multiple predictors backup 2.jl diff --git a/Manifest.toml b/Manifest.toml index 94f40d3..e73fa78 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -29,9 +29,9 @@ uuid = "6e696c72-6542-2067-7265-42206c756150" version = "1.1.4" [[deps.AbstractTrees]] -git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" +git-tree-sha1 = "5c0b629df8a5566a06f5fef5100b53ea56e465a0" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.3.4" +version = "0.4.2" [[deps.Adapt]] deps = ["LinearAlgebra"] @@ -41,9 +41,9 @@ version = "3.4.0" [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "Setfield", "Statistics", "StatsBase", "StatsFuns", "UnPack"] -git-tree-sha1 = "345effa84030f273ee86fcdd706d8484ce9a1a3c" +git-tree-sha1 = "0091e2e4d0a7125da0e3ad8c7dbff9171a921461" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.3.5" +version = "0.3.6" [[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "Random", "Requires"] @@ -86,9 +86,9 @@ version = "0.2.0" [[deps.ArrayInterfaceCore]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "12bebdb8491042f36c8700705f11c28fef284515" +git-tree-sha1 = "5bb0f8292405a516880a3809954cb832ae7a31c5" uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.16" +version = "0.1.20" [[deps.ArrayInterfaceStaticArraysCore]] deps = ["Adapt", "ArrayInterfaceCore", "LinearAlgebra", "StaticArraysCore"] @@ -119,9 +119,9 @@ version = "0.4.6" [[deps.BangBang]] deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] -git-tree-sha1 = "b15a6bc52594f5e4a3b825858d1089618871bf9d" +git-tree-sha1 = "7fe6d92c4f281cf4ca6f2fba0ce7b299742da7ca" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.36" +version = "0.3.37" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -133,9 +133,14 @@ version = "0.1.1" [[deps.Bijectors]] deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "875f3845e1256ee1d9e0c8ca3993e709b32c0ed1" +git-tree-sha1 = "a3704b8e5170f9339dff4e6cb286ad49464d3646" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.10.3" +version = "0.10.6" + +[[deps.BitFlags]] +git-tree-sha1 = "84259bb6172806304b9101094a7cc4bc6f56dbc6" +uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" +version = "0.1.5" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -168,9 +173,9 @@ version = "0.5.1" [[deps.CategoricalArrays]] deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] -git-tree-sha1 = "5f5a975d996026a8dd877c35fe26a7b8179c02ba" +git-tree-sha1 = "5084cc1a28976dd1642c9f337b28a3cb03e0f7d2" uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" -version = "0.10.6" +version = "0.10.7" [[deps.Chain]] git-tree-sha1 = "8c4920235f6c561e401dfe569beb8b924adad003" @@ -178,16 +183,16 @@ uuid = "8be319e6-bccf-4806-a6f7-6fae938471bc" version = "0.5.0" [[deps.ChainRules]] -deps = ["ChainRulesCore", "Compat", "Distributed", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics"] -git-tree-sha1 = "e762b70af7c1d914f677d9588a1d3b32e5f832af" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] +git-tree-sha1 = "a5fd229d3569a6600ae47abe8cd48cbeb972e173" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.39.1" +version = "1.44.6" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "80ca332f6dcb2508adba68f22f551adb2d00a624" +git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.3" +version = "1.15.6" [[deps.ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] @@ -248,10 +253,10 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "9be8be1d8a6f44b96482c8af52238ea7987da3e3" +deps = ["Dates", "LinearAlgebra", "UUIDs"] +git-tree-sha1 = "5856d3031cdb1f3b2b6340dfdc66b6d9a149a374" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.45.0" +version = "4.2.0" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -265,9 +270,9 @@ version = "0.1.1" [[deps.Configurations]] deps = ["ExproniconLite", "OrderedCollections", "TOML"] -git-tree-sha1 = "ab9b7c51e8acdd20c769bccde050b5615921c533" +git-tree-sha1 = "62a7c76dbad02fdfdaa53608104edf760938c4ca" uuid = "5218b696-f38b-4ac9-8b61-a12ec717816d" -version = "0.17.3" +version = "0.17.4" [[deps.ConsoleProgressMonitor]] deps = ["Logging", "ProgressMeter"] @@ -277,9 +282,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "59d00b3139a9de4eb961057eabb65ac6522be954" +git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.4.0" +version = "1.4.1" [[deps.Contour]] git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" @@ -292,15 +297,15 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40" +git-tree-sha1 = "1106fa7e1256b402a86a8e7b15c00c85036fef49" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.10.0" +version = "1.11.0" [[deps.DataFrames]] deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "daa21eb85147f72e41f6352a57fccea377e310a9" +git-tree-sha1 = "db2a9cb664fcea7836da4b414c3278d71dd602d2" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.3.4" +version = "1.3.6" [[deps.DataFramesMeta]] deps = ["Chain", "DataFrames", "MacroTools", "OrderedCollections", "Reexport"] @@ -336,8 +341,9 @@ version = "0.1.2" [[deps.DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "19b1417ff479c07e523fcbf2fd735a3fde3d1ab3" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -version = "1.0.0" +version = "1.9.0" [[deps.DensityInterface]] deps = ["InverseFunctions", "Test"] @@ -346,16 +352,16 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffResults]] -deps = ["StaticArrays"] -git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805" +deps = ["StaticArraysCore"] +git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" -version = "1.0.3" +version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "28d605d9a0ac17118fe2c5e9ce0fbb76c3ceb120" +git-tree-sha1 = "992a23afdb109d0d2f8802a30cf5ae4b1fe7ea68" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.11.0" +version = "1.11.1" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -363,15 +369,15 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "aafa0665e3db0d3d0890cdc8191ea03dc279b042" +git-tree-sha1 = "0d7d213133d948c56e8c2d9f4eab0293491d8e4a" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.66" +version = "0.25.75" [[deps.DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "DiffRules", "Distributions", "FillArrays", "LinearAlgebra", "NaNMath", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsBase", "StatsFuns", "ZygoteRules"] -git-tree-sha1 = "ec811a2688b3504ce5b315fe7bc86464480d5964" +git-tree-sha1 = "0c139e48a8cea06c6ecbbec19d3ebc5dcbd7870d" uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c" -version = "0.6.41" +version = "0.6.43" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -386,9 +392,9 @@ version = "1.6.0" [[deps.DrWatson]] deps = ["Dates", "FileIO", "JLD2", "LibGit2", "MacroTools", "Pkg", "Random", "Requires", "Scratch", "UnPack"] -git-tree-sha1 = "67e9001646db6e45006643bf37716ecd831d37d2" +git-tree-sha1 = "b485075152173ac6c8790b04aac3ecbb5a356f24" uuid = "634d3b9d-ee7a-5ddf-bec9-22491ea816e1" -version = "2.9.1" +version = "2.10.0" [[deps.DualNumbers]] deps = ["Calculus", "NaNMath", "SpecialFunctions"] @@ -397,16 +403,16 @@ uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" version = "0.6.8" [[deps.DynamicPPL]] -deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "Distributions", "LinearAlgebra", "MacroTools", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "c6f574d855670c2906af3f4053e6db10224e5dda" +deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] +git-tree-sha1 = "7bc3920ba1e577ad3d7ebac75602ab42b557e28e" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.19.3" +version = "0.20.2" [[deps.EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3f3a2501fa7236e9b911e0f7a588c657e822bb6d" +git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053" uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.2.3+0" +version = "2.2.4+0" [[deps.EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterfaceCore", "Distributions", "Random", "Statistics"] @@ -426,9 +432,14 @@ uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.8" [[deps.ExproniconLite]] -git-tree-sha1 = "8b08cc88844e4d01db5a2405a08e9178e19e479e" +git-tree-sha1 = "07b85b02d910f90dde6b383484c5ee6c0f169fa3" uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" -version = "0.6.13" +version = "0.7.0" + +[[deps.Extents]] +git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" +uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" +version = "0.1.1" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -437,10 +448,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" version = "0.4.1" [[deps.FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "ccd479984c7838684b3ac204b716c89955c76623" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.2+0" +version = "4.4.2+2" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] @@ -462,24 +473,24 @@ version = "1.15.0" [[deps.FilePathsBase]] deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] -git-tree-sha1 = "129b104185df66e408edd6625d480b7f9e9823a0" +git-tree-sha1 = "e27c4ebe80e8699540f2d6c805cc12203b614f12" uuid = "48062228-2e41-5def-b9a4-89aafe57970f" -version = "0.9.18" +version = "0.9.20" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "246621d23d1f43e3b9c368bf3b72b2331a27c286" +git-tree-sha1 = "87519eb762f85534445f5cda35be12e32759ee14" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.2" +version = "0.13.4" [[deps.FiniteDiff]] -deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "e3af8444c9916abed11f4357c2f59b6801e5b376" +deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] +git-tree-sha1 = "5a2cff9b6b77b33b89f3d97a4d367747adce647e" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.13.1" +version = "2.15.0" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -501,9 +512,9 @@ version = "0.4.2" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "2f18915445b248731ec5db4e4a17e451020bf21e" +git-tree-sha1 = "187198a4ed8ccd7b5d99c41b69c679269ea2b2d4" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.30" +version = "0.10.32" [[deps.FreeType]] deps = ["CEnum", "FreeType2_jll"] @@ -534,10 +545,17 @@ git-tree-sha1 = "241552bc2209f0fa068b6415b1942cc0aa486bcc" uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" version = "1.1.2" +[[deps.FunctionWrappersWrappers]] +deps = ["FunctionWrappers"] +git-tree-sha1 = "a5e6e7f12607e90d71b09e6ce2c965e41b337968" +uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf" +version = "0.1.1" + [[deps.Functors]] -git-tree-sha1 = "223fffa49ca0ff9ce4f875be001ffe173b2b7de4" +deps = ["LinearAlgebra"] +git-tree-sha1 = "a2657dd0f3e8a61dbe70fc7c122038bd33790af5" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.2.8" +version = "0.3.0" [[deps.Future]] deps = ["Random"] @@ -545,9 +563,9 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.FuzzyCompletions]] deps = ["REPL"] -git-tree-sha1 = "efd6c064e15e92fcce436977c825d2117bf8ce76" +git-tree-sha1 = "e16dd964b4dfaebcded16b2af32f05e235b354be" uuid = "fb4132e2-a121-4a70-b8a1-d5b831dcdcc2" -version = "0.5.0" +version = "0.5.1" [[deps.GLFW]] deps = ["GLFW_jll"] @@ -557,9 +575,9 @@ version = "3.4.1" [[deps.GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "51d2dfe8e590fbd74e7a842cf6d13d8a2f45dc01" +git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.6+0" +version = "3.3.8+0" [[deps.GLM]] deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "StatsModels"] @@ -569,21 +587,27 @@ version = "1.8.0" [[deps.GLMakie]] deps = ["ColorTypes", "Colors", "FileIO", "FixedPointNumbers", "FreeTypeAbstraction", "GLFW", "GeometryBasics", "LinearAlgebra", "Makie", "Markdown", "MeshIO", "ModernGL", "Observables", "Printf", "Serialization", "ShaderAbstractions", "StaticArrays"] -git-tree-sha1 = "f851a36de76664c20c2f58e92bbb39c68ce3d583" +git-tree-sha1 = "b0eaead91cb9fd157f7a164f4c07e463a3291535" uuid = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" -version = "0.6.12" +version = "0.6.13" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "d88b17a38322e153c519f5a9ed8d91e9baa03d8f" +git-tree-sha1 = "6872f5ec8fd1a38880f027a26739d42dcda6691f" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.1" +version = "0.1.2" + +[[deps.GeoInterface]] +deps = ["Extents"] +git-tree-sha1 = "fb28b5dc239d0174d7297310ef7b84a11804dfab" +uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" +version = "1.0.1" [[deps.GeometryBasics]] -deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "83ea630384a13fc4f002b77690bc0afeb4255ac9" +deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] +git-tree-sha1 = "12a584db96f1d460421d5fb8860822971cdb8455" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.4.2" +version = "0.4.4" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -592,16 +616,16 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] +git-tree-sha1 = "fb83fbe02fe57f2c068013aa94bcdf6760d3a7a7" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.68.3+2" +version = "2.74.0+1" [[deps.GraphMakie]] deps = ["GeometryBasics", "Graphs", "LinearAlgebra", "Makie", "NetworkLayout", "StaticArrays"] -git-tree-sha1 = "d295b0f36f45856569edffa37d7d959c73ec9c12" +git-tree-sha1 = "16b83061b26bf4e03e27e5232107ec547c5d53b7" uuid = "1ecd5474-83a3-4783-bb4f-06765db800d2" -version = "0.4.0" +version = "0.4.1" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] @@ -617,15 +641,15 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "db5c7e27c0d46fd824d470a3c32a4fc6c935fa96" +git-tree-sha1 = "ba2d094a88b6b287bd25cfa86f301e7693ffae2f" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.7.1" +version = "1.7.4" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] -git-tree-sha1 = "53c7e69a6ffeb26bd594f5a1421b889e7219eeaa" +git-tree-sha1 = "678d136003ed5bceaab05cf64519e3f956ffa4ba" uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" -version = "0.9.0" +version = "0.9.1" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -633,10 +657,10 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "ed47af35905b7cc8f1a522ca684b35a212269bd8" +deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "4abede886fcba15cd5fd041fef776b230d004cee" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.2.0" +version = "1.4.0" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -692,9 +716,9 @@ uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959" version = "1.0.0" [[deps.Inflate]] -git-tree-sha1 = "f5fc07d4e706b84f72d54eedcc1c13d92fb0871c" +git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.2" +version = "0.1.3" [[deps.IniFile]] git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" @@ -729,22 +753,22 @@ deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.Interpolations]] -deps = ["AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "b7bc05649af456efc75d178846f47006c2c4c3c7" +deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] +git-tree-sha1 = "f67b55b6447d36733596aea445a9f119e83498b6" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.13.6" +version = "0.14.5" [[deps.IntervalSets]] deps = ["Dates", "Random", "Statistics"] -git-tree-sha1 = "57af5939800bce15980bddd2426912c4f83012d8" +git-tree-sha1 = "3f91cd3f56ea48d4d2a75c2a65455c5fc74fa347" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.1" +version = "0.7.3" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "b3364212fb5d870f724876ffcd34dd8ec6d98918" +git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.7" +version = "0.1.8" [[deps.InvertedIndices]] git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" @@ -774,9 +798,9 @@ version = "1.0.0" [[deps.JLD2]] deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "81b9477b49402b47fbe7f7ae0b252077f53e4a08" +git-tree-sha1 = "0d0ad913e827d13c5e88a73f9333d7e33c424576" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.22" +version = "0.4.24" [[deps.JLLWrappers]] deps = ["Preferences"] @@ -804,9 +828,9 @@ version = "2.1.2+0" [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] -git-tree-sha1 = "0a7ca818440ce8c70ebb5d42ac4ebf3205675f04" +git-tree-sha1 = "9816b296736292a80b9a3200eb7fbb57aaa3917a" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.4" +version = "0.6.5" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -841,9 +865,9 @@ version = "0.3.1" [[deps.LeftChildRightSiblingTrees]] deps = ["AbstractTrees"] -git-tree-sha1 = "b864cb409e8e445688bc478ef87c0afe4f6d1f8d" +git-tree-sha1 = "fb6803dafae4a5d62ea5cab204b1e657d9737e7f" uuid = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e" -version = "0.1.3" +version = "0.2.0" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -917,19 +941,25 @@ version = "2.36.0+0" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "f27132e551e959b3667d8c93eae90973225032dd" +git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.1.1" +version = "7.2.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[deps.LogDensityProblems]] +deps = ["ArgCheck", "DocStringExtensions", "Random", "Requires", "UnPack"] +git-tree-sha1 = "408a29d70f8032b50b22155e6d7776715144b761" +uuid = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" +version = "1.0.2" + [[deps.LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "361c2b088575b07946508f135ac556751240091c" +git-tree-sha1 = "94d9c52ca447e23eac0c0f074effbcd38830deb5" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.17" +version = "0.3.18" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -942,15 +972,15 @@ version = "0.4.9" [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Compat", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Serialization", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] -git-tree-sha1 = "8cb9b8fb081afd7728f5de25b9025bff97cb5c7a" +git-tree-sha1 = "0995883c615e93187e8365e35af771afcf74da03" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "5.3.1" +version = "5.4.0" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "058d08594e91ba1d98dcc3669f9421a76824aa95" +git-tree-sha1 = "59ac3cc5c08023f58b9cd6a5c447c4407cede6bc" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.1.3" +version = "0.1.4" [[deps.MIMEs]] git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" @@ -959,9 +989,9 @@ version = "0.1.4" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "e595b205efd49508358f7dc670a940c790204629" +git-tree-sha1 = "41d162ae9c868218b1f3fe78cba878aa348c2d26" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2022.0.0+0" +version = "2022.1.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] @@ -977,15 +1007,15 @@ version = "0.5.9" [[deps.Makie]] deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Distributions", "DocStringExtensions", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MakieCore", "Markdown", "Match", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "Printf", "Random", "RelocatableFolders", "Serialization", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "UnicodeFun"] -git-tree-sha1 = "c27ed640732b1e9bd7bb8f40d987873d8f5b4bca" +git-tree-sha1 = "b0323393a7190c9bf5b03af442fc115756df8e59" uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" -version = "0.17.12" +version = "0.17.13" [[deps.MakieCore]] deps = ["Observables"] -git-tree-sha1 = "9bd42b962d5c6182fa0d74b1970edb075fe313e5" +git-tree-sha1 = "fbf705d2bdea8fc93f1ae8ca2965d8e03d4ca98c" uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" -version = "0.3.6" +version = "0.4.0" [[deps.MappedArrays]] git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" @@ -1009,9 +1039,9 @@ version = "0.4.3" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] -git-tree-sha1 = "14cb991ee7ccc6dabda93d310400575c3cae435b" +git-tree-sha1 = "6872f9594ff273da6d13c7c1a1545d5a8c7d0c1c" uuid = "739be429-bea8-5141-9913-cc70e7f3736d" -version = "1.1.2" +version = "1.1.6" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] @@ -1040,16 +1070,16 @@ version = "1.0.2" uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[deps.Mocking]] -deps = ["Compat", "ExprTools"] -git-tree-sha1 = "29714d0a7a8083bba8427a4fbfb00a540c681ce7" +deps = ["ExprTools"] +git-tree-sha1 = "748f6e1e4de814b101911e64cc12d83a6af66782" uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" -version = "0.7.3" +version = "0.7.2" [[deps.ModernGL]] deps = ["Libdl"] -git-tree-sha1 = "344f8896e55541e30d5ccffcbf747c98ad57ca47" +git-tree-sha1 = "713fd24142921db94e5f7d7961f9ee033c6573d5" uuid = "66fc600b-dfda-50eb-8b99-91cfa97b1301" -version = "1.1.4" +version = "1.1.5" [[deps.MosaicViews]] deps = ["MappedArrays", "OffsetArrays", "PaddedViews", "StackViews"] @@ -1080,9 +1110,10 @@ uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" version = "0.8.9" [[deps.NaNMath]] -git-tree-sha1 = "b086b7ea07f8e38cf122f5016af580881ac914fe" +deps = ["OpenLibm_jll"] +git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.7" +version = "1.0.1" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] @@ -1091,9 +1122,9 @@ uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" version = "0.9.6" [[deps.NamedTupleTools]] -git-tree-sha1 = "befc30261949849408ac945a1ebb9fa5ec5e1fd5" +git-tree-sha1 = "17eeb975b00de066fb343aa8d56884f51d4a651c" uuid = "d9ec5142-1e00-5aa0-9d6a-321866360f50" -version = "0.14.0" +version = "0.14.1" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1123,9 +1154,9 @@ uuid = "2bd173c7-0d6d-553b-b6af-13a54713934c" version = "1.3.0" [[deps.Observables]] -git-tree-sha1 = "dfd8d34871bc3ad08cd16026c1828e271d554db9" +git-tree-sha1 = "5a9ea4b9430d511980c01e9f7173739595bbd335" uuid = "510215fc-4207-5dde-b226-833fc4488ee2" -version = "0.5.1" +version = "0.5.2" [[deps.OffsetArrays]] deps = ["Adapt"] @@ -1142,7 +1173,7 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.20+0" +version = "0.3.21+0" [[deps.OpenEXR]] deps = ["Colors", "FileIO", "OpenEXR_jll"] @@ -1161,6 +1192,12 @@ deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" version = "0.8.1+0" +[[deps.OpenSSL]] +deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] +git-tree-sha1 = "02be9f845cb58c2d6029a6d5f67f4e0af3237814" +uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" +version = "1.1.3" + [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "e60321e3f2616584ff98f0a4f18d98ae6f89bbb3" @@ -1175,9 +1212,15 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "7351d1daa3dad1bcf67c79d1ba34dd3f6136c9aa" +git-tree-sha1 = "b9fe76d1a39807fdcf790b991981a922de0c3050" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.1" +version = "1.7.3" + +[[deps.Optimisers]] +deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] +git-tree-sha1 = "1ef34738708e3f31994b52693286dabcb3d29f6b" +uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" +version = "0.2.9" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1190,11 +1233,10 @@ git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.4.1" -[[deps.PCRE_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488" -uuid = "2f80f16e-611a-54ab-bc61-aa92de5b98fc" -version = "8.44.0+0" +[[deps.PCRE2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" +version = "10.40.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -1228,9 +1270,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates"] -git-tree-sha1 = "0044b23da09b5608b4ecacb4e5e6c6332f833a7e" +git-tree-sha1 = "3d5bf43e3e8b412656404ed9466f1dcbf7c50269" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.3.2" +version = "2.4.0" [[deps.Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1245,25 +1287,25 @@ version = "1.8.0" [[deps.PkgVersion]] deps = ["Pkg"] -git-tree-sha1 = "a7a7e1a88853564e551e4eba8650f8c38df79b37" +git-tree-sha1 = "f6cf8e7944e50901594838951729a1861e668cb8" uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" -version = "0.1.1" +version = "0.3.2" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "9888e59493658e476d3073f1ce24348bdc086660" +deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] +git-tree-sha1 = "21303256d239f6b484977314674aef4bb1fe4420" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.0" +version = "1.3.1" [[deps.Pluto]] deps = ["Base64", "Configurations", "Dates", "Distributed", "FileWatching", "FuzzyCompletions", "HTTP", "HypertextLiteral", "InteractiveUtils", "Logging", "MIMEs", "Markdown", "MsgPack", "Pkg", "PrecompileSignatures", "REPL", "RelocatableFolders", "Sockets", "TOML", "Tables", "URIs", "UUIDs"] -git-tree-sha1 = "c189ae928e2cfc3495b13e85d9e90ddedeac0a4d" +git-tree-sha1 = "ec10219bc0b9a2c26c342abdb955ba82ebd90825" uuid = "c3e4b0f8-55cb-11ea-2926-15256bba5781" -version = "0.19.11" +version = "0.19.12" [[deps.PlutoPDF]] deps = ["DefaultApplication", "Distributed", "JSON", "NodeJS", "Pluto"] -git-tree-sha1 = "026e742a46219225316ec40e3d47a02fc9a04b76" +git-tree-sha1 = "a6a2a64212e2942f37830fd2753573949124e6fe" repo-rev = "main" repo-url = "https://github.com/JuliaPluto/PlutoPDF.jl" uuid = "6eb38059-8c05-41f7-8871-5e7e2697ace6" @@ -1271,9 +1313,9 @@ version = "0.1.4" [[deps.PlutoUI]] deps = ["AbstractPlutoDingetjes", "Base64", "ColorTypes", "Dates", "Hyperscript", "HypertextLiteral", "IOCapture", "InteractiveUtils", "JSON", "Logging", "Markdown", "Random", "Reexport", "UUIDs"] -git-tree-sha1 = "8d1f54886b9037091edf146b517989fc4a09efec" +git-tree-sha1 = "2777a5c2c91b3145f5aa75b61bb4c2eb38797136" uuid = "7f904dfe-b85e-4ff6-b463-dae2292396a8" -version = "0.7.39" +version = "0.7.43" [[deps.PolygonOps]] git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6" @@ -1333,9 +1375,9 @@ version = "1.0.0" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "78aadffb3efd2155af139781b8a8df1ef279ea39" +git-tree-sha1 = "3c009334f45dfd546a16a57960a821a1a023d241" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.4.2" +version = "2.5.0" [[deps.RData]] deps = ["CategoricalArrays", "CodecZlib", "DataFrames", "Dates", "FileIO", "Requires", "TimeZones", "Unicode"] @@ -1369,15 +1411,16 @@ uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" version = "0.1.0" [[deps.RecipesBase]] -git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" +deps = ["SnoopPrecompile"] +git-tree-sha1 = "612a4d76ad98e9722c8ba387614539155a59e30c" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.2.1" +version = "1.3.0" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "ZygoteRules"] -git-tree-sha1 = "4ce7584604489e537b2ab84ed92b4107d03377f0" +deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "Tables", "ZygoteRules"] +git-tree-sha1 = "3004608dc42101a944e44c1c68b599fa7c669080" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.31.2" +version = "2.32.0" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1415,10 +1458,10 @@ uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" version = "0.3.0+0" [[deps.Roots]] -deps = ["CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "50f945fb7d7fdece03bbc76ff1ab96170f64a892" +deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] +git-tree-sha1 = "422c880f74967af5a8db5702c6df9a03b465202e" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.2" +version = "2.0.7" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -1436,10 +1479,10 @@ uuid = "7b38b023-a4d7-4c5e-8d43-3f3097f304eb" version = "0.3.3" [[deps.SciMLBase]] -deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "RecipesBase", "RecursiveArrayTools", "StaticArraysCore", "Statistics", "Tables"] -git-tree-sha1 = "7cb46ff55af945a8b68e148bf22f9325f7221d8d" +deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "StaticArraysCore", "Statistics", "Tables"] +git-tree-sha1 = "2c7b9be95f91c971ae4e4a6e3a0556b839874f2b" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.45.0" +version = "1.59.4" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -1454,9 +1497,9 @@ version = "1.1.1" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "db8481cf5d6278a121184809e9eb1628943c7704" +git-tree-sha1 = "c0f56940fc967f3d5efed58ba829747af5f8b586" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.3.13" +version = "1.3.15" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1478,9 +1521,9 @@ deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" [[deps.ShiftedArrays]] -git-tree-sha1 = "22395afdcf37d6709a5a0766cc4a5ca52cb85ea0" +git-tree-sha1 = "503688b59397b3307443af35cd953a13e8005c16" uuid = "1277b4bf-5013-50f5-be3d-901d8477a67a" -version = "1.0.0" +version = "2.0.0" [[deps.Showoff]] deps = ["Dates", "Grisu"] @@ -1511,6 +1554,11 @@ git-tree-sha1 = "8fb59825be681d451c246a795117f317ecbcaa28" uuid = "45858cf5-a6b0-47a3-bbea-62219f50df47" version = "0.1.2" +[[deps.SnoopPrecompile]] +git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85" +uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" +version = "1.0.1" + [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1550,14 +1598,14 @@ version = "0.1.1" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "23368a3313d12a2326ad0035f0db0c0966f438ef" +git-tree-sha1 = "f86b3a049e5d05227b10e15dbb315c5b90f14988" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.2" +version = "1.5.9" [[deps.StaticArraysCore]] -git-tree-sha1 = "66fe9eb253f910fe8cf161953880cfdaef01cdf0" +git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.0.1" +version = "1.4.0" [[deps.StatisticalTraits]] deps = ["ScientificTypesBase"] @@ -1571,15 +1619,15 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "2c11d7290036fe7aac9038ff312d3b3a2a5bf89e" +git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.4.0" +version = "1.5.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "0005d75f43ff23688914536c5e9d5ac94f8077f7" +git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.20" +version = "0.33.21" [[deps.StatsFuns]] deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] @@ -1589,15 +1637,15 @@ version = "1.0.1" [[deps.StatsModels]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "4352d5badd1bc8bf0a8c825e886fa1eda4f0f967" +git-tree-sha1 = "a5e15f27abd2692ccb61a99e0854dfb7d48017db" uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" -version = "0.6.30" +version = "0.6.33" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] -git-tree-sha1 = "ec47fb6069c57f1cee2f67541bf8f23415146de7" +deps = ["Adapt", "DataAPI", "StaticArraysCore", "Tables"] +git-tree-sha1 = "8c6ac65ec9ab781af05b08ff305ddc727c25f680" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.11" +version = "0.6.12" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1621,9 +1669,9 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" +git-tree-sha1 = "2d7164f7b8a066bcfa6224e67736ce0eb54aef5b" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.7.0" +version = "1.9.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -1638,9 +1686,9 @@ version = "0.1.1" [[deps.TerminalLoggers]] deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"] -git-tree-sha1 = "62846a48a6cd70e63aa29944b8c4ef704360d72f" +git-tree-sha1 = "f53e34e784ae771eb9ccde4d72e578aa453d0554" uuid = "5d786b92-1e48-4d6f-9151-6b4477ca9bed" -version = "0.1.5" +version = "0.1.6" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] @@ -1648,9 +1696,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TiffImages]] deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "UUIDs"] -git-tree-sha1 = "fcf41697256f2b759de9380a7e8196d6516f0310" +git-tree-sha1 = "70e6d2da9210371c927176cb7a56d41ef1260db7" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.6.0" +version = "0.6.1" [[deps.TimeZones]] deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Scratch", "Unicode"] @@ -1659,16 +1707,16 @@ uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" version = "1.9.0" [[deps.Tracker]] -deps = ["Adapt", "DiffRules", "ForwardDiff", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "0874c1b5de1b5529b776cfeca3ec0acfada97b1b" +deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] +git-tree-sha1 = "d963aad627fd7af56fbbfee67703c2f7bfee9dd7" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.20" +version = "0.2.22" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" +git-tree-sha1 = "8a75929dcd3c38611db2f8d08546decb514fcadf" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.6" +version = "0.9.9" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] @@ -1682,10 +1730,10 @@ uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" version = "0.1.6" [[deps.Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker", "ZygoteRules"] -git-tree-sha1 = "d5e128d1a8db72ebdd2b76644d19128cf90dda29" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker"] +git-tree-sha1 = "68fb67dab0c11de2bb1d761d7a742b965a9bc875" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.21.9" +version = "0.21.12" [[deps.URIs]] git-tree-sha1 = "e59ecc5a41b000fa94423a578d29290c7266fc10" @@ -1844,7 +1892,7 @@ version = "0.15.1+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.2.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1859,10 +1907,10 @@ uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" version = "1.6.38+0" [[deps.libsixel_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "78736dab31ae7a53540a6b752efc61f77b304c5b" +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] +git-tree-sha1 = "d4f63314c8aa1e48cd22aa0c17ed76cd1ae48c3c" uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" -version = "1.8.6+1" +version = "1.10.3+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] diff --git a/notebooks/Chapters/01 - Introduction.jl b/notebooks/Chapters/01 - Introduction.jl index 93d090a..7e79d62 100644 --- a/notebooks/Chapters/01 - Introduction.jl +++ b/notebooks/Chapters/01 - Introduction.jl @@ -46,6 +46,9 @@ html""" """ +# ╔═╡ 2099b552-d48d-4233-b593-39864c413261 +Base.active_project() + # ╔═╡ 4755dab0-d228-41d3-934a-56f2863a5652 md"###### A typical set of Julia packages to include in notebooks." @@ -704,10 +707,1807 @@ mad.(lnk1_4t) # ╔═╡ b413c2d6-dc44-4437-8123-ee7793863387 mean.(lnk1_4t) +# ╔═╡ 00000000-0000-0000-0000-000000000001 +PLUTO_PROJECT_TOML_CONTENTS = """ +[deps] +AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67" +CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" +GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a" +Logging = "56ddb016-857b-54e1-b83d-db4d58db5568" +Optim = "429524aa-4258-5aef-a3af-852621145aeb" +Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" +RegressionAndOtherStories = "21324389-b050-441a-ba7b-9a837781bda0" +Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" + +[compat] +AlgebraOfGraphics = "~0.6.10" +CairoMakie = "~0.8.13" +GLM = "~1.8.0" +Optim = "~1.7.1" +RegressionAndOtherStories = "~0.7.2" +Turing = "~0.21.9" +""" + +# ╔═╡ 00000000-0000-0000-0000-000000000002 +PLUTO_MANIFEST_TOML_CONTENTS = """ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.9.0-DEV" +manifest_format = "2.0" +project_hash = "5aa0c981b39c13a87e152bf722557e51089f9d5e" + +[[deps.AbstractFFTs]] +deps = ["ChainRulesCore", "LinearAlgebra"] +git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.2.1" + +[[deps.AbstractMCMC]] +deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] +git-tree-sha1 = "5c26c7759412ffcaf0dd6e3172e55d783dd7610b" +uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" +version = "4.1.3" + +[[deps.AbstractPPL]] +deps = ["AbstractMCMC", "DensityInterface", "Setfield", "SparseArrays"] +git-tree-sha1 = "6320752437e9fbf49639a410017d862ad64415a5" +uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" +version = "0.5.2" + 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predictors backup 1.jl @@ -0,0 +1,223 @@ +### A Pluto.jl notebook ### +# v0.19.11 + +using Markdown +using InteractiveUtils + +# ╔═╡ da0eb04e-9930-4f49-809b-3ba5fe16a59c +using Pkg, DrWatson + +# ╔═╡ d7992c39-0617-42b5-b977-f04260d2bd03 +begin + # Specific to this notebook + using GLM + + # Specific to ROSTuringPluto + using Optim + using Logging + using Turing + + # Graphics related + using GLMakie + + # Common data files and functions + using RegressionAndOtherStories + import RegressionAndOtherStories: link + + Logging.disable_logging(Logging.Warn) +end; + +# ╔═╡ f90c8b82-a52d-45a4-86eb-d2c7eb905692 +md"### KidIQ: kidiq.csv" + +# ╔═╡ 2daed834-e53d-4530-98bd-e80b5b99162f +md" ###### Widen the notebook." + +# ╔═╡ d1c76cd1-2537-470e-a9d5-ebaa5b9dec7e +html""" + +""" + + +# ╔═╡ dfe95bfa-507a-4831-b3b5-f26b1d537112 +kidiq = CSV.read(ros_datadir("KidIQ", "kidiq.csv"), DataFrame) + +# ╔═╡ 4a4605a4-084a-4d64-a444-fa0fcf41ef91 +let + f = Figure() + ax = Axis(f[1, 1]; title="KidIQ data: kid_score ~ mom_hs") + scatter!(kidiq[kidiq.mom_hs .== 0, :mom_hs], kidiq[kidiq.mom_hs .== 0, :kid_score]; color=:red, markersize = 3) + scatter!(kidiq[kidiq.mom_hs .== 1, :mom_hs], kidiq[kidiq.mom_hs .== 1, :kid_score]; color=:blue, markersize = 3) + ax = Axis(f[1, 2]; title="KidIQ data: kid_score ~ mom_iq") + scatter!(kidiq[kidiq.mom_hs .== 0, :mom_iq], kidiq[kidiq.mom_hs .== 0, :kid_score]; color=:red, markersize = 3) + scatter!(kidiq[kidiq.mom_hs .== 1, :mom_iq], kidiq[kidiq.mom_hs .== 1, :kid_score]; color=:blue, markersize = 3) + current_figure() +end + +# ╔═╡ d8d8e6b4-6406-43ac-9472-a7afab027aef +stan10_1 = " +data { + int N; + vector[N] mom_hs; + vector[N] kid_score; +} +parameters { + real a; + real b; + real sigma; +} +model { + vector[N] mu; + a ~ normal(100, 10); + b ~ normal(5, 10); + mu = a + b * mom_hs; + kid_score ~ normal(mu, sigma); +} +"; + +# ╔═╡ cf817e35-2098-4acd-a518-4904db52f495 +@model function ppl10_1(x, y) + a ~ Normal(100, 10) + b ~ Normal(5, 10) + σ ~ Exponential(1) + μ = a .+ b .* x + for i in eachindex(y) + y[i] ~ Normal(μ[i], σ) + end +end + +# ╔═╡ a9fcb0f0-5134-48a8-8d93-bfb8203e089e +begin + m10_1t = ppl10_1(kidiq.mom_hs, kidiq.mom_iq) + chns10_1t = sample(m10_1t, NUTS(), MCMCThreads(), 1000, 4) + describe(chns10_1t) +end + +# ╔═╡ 9073f433-fbec-4cf7-8ef0-ba870854eb75 +begin + post10_1t = DataFrame(chns10_1t)[:, 3:5] + ms10_1t = model_summary(post10_1t, [:a, :b, :σ]) +end + +# ╔═╡ b77b121b-38d3-485c-a9a2-c9ae87fe3423 +let + f = Figure() + ax = Axis(f[1, 1]; title="KidIQ data: kid_score ~ mom_hs") + scatter!(kidiq[kidiq.mom_hs .== 0, :mom_hs], kidiq[kidiq.mom_hs .== 0, :kid_score]; color=:red, markersize = 3) + scatter!(kidiq[kidiq.mom_hs .== 1, :mom_hs], kidiq[kidiq.mom_hs .== 1, :kid_score]; color=:blue, markersize = 3) + lines!([0.0, 1.0], [ms10_1t[:a, :median], ms10_1t[:a, :median] + ms10_1t[:b, :median]]) + current_figure() +end + +# ╔═╡ 3e15c7db-6c76-47a9-af3f-66a2eb67a8aa +@model function ppl10_2(x, y) + a ~ Normal(25, 3) + b ~ Normal(1, 2) + σ ~ Exponential(1) + μ = a .+ b .* x + for i in eachindex(y) + y[i] ~ Normal(μ[i], σ) + end +end + +# ╔═╡ 358093fe-3102-4c21-be0a-5d33569c13fd +begin + m10_2t = ppl10_2(kidiq.mom_iq, kidiq.kid_score) + chns10_2t = sample(m10_2t, NUTS(), MCMCThreads(), 1000, 4) + describe(chns10_2t) +end + +# ╔═╡ f4ab1e3d-8f64-4415-a257-63e9d43c60db +begin + post10_2t = DataFrame(chns10_2t)[:, 3:5] + ms10_2t = model_summary(post10_2t, [:a, :b, :sigma]) +end + +# ╔═╡ 90f0236a-2c5b-4ea8-83cf-490037bf8c15 +let + f = Figure() + ax = Axis(f[1, 1]; title="KidIQ data: kid_score ~ mom_iq") + scatter!(kidiq[kidiq.mom_hs .== 0, :mom_iq], kidiq[kidiq.mom_hs .== 0, :kid_score]; color=:red, markersize = 3) + scatter!(kidiq[kidiq.mom_hs .== 1, :mom_iq], kidiq[kidiq.mom_hs .== 1, :kid_score]; color=:blue, markersize = 3) + x = LinRange(70.0, 140.0, 100) + lines!(x, ms10_2t[:a, :median] .+ ms10_2t[:b, :median] .* x) + current_figure() +end + +# ╔═╡ bcf8c679-0e35-42e7-b4dd-91ac8dfb5721 +@model function ppl10_3(x, y, z) + a ~ Normal(25, 2) + b ~ Normal(5, 2) + c ~ Normal(1, 2) + σ ~ Exponential(1) + μ = a .+ b .* x .+ c .* y + for i in eachindex(y) + z[i] ~ Normal(μ[i], σ) + end +end + +# ╔═╡ b1c6c6a5-1784-438a-b930-49ce7aef80ab +begin + m10_3t = ppl10_3(kidiq.mom_hs, kidiq.mom_iq, kidiq.kid_score) + chns10_3t = sample(m10_3t, NUTS(), MCMCThreads(), 1000, 4) + describe(chns10_3t) +end + +# ╔═╡ b6330c4f-8129-4bbd-aa39-3ddd00c062b5 +begin + post10_3t = DataFrame(chns10_3t)[:, 3:6] + ms10_3t = model_summary(post10_3t, [:a, :b, :c, :σ]) +end + +# ╔═╡ 6014b70b-c10d-4b91-94f7-79dc291cc92b +let + momnohs(x) = x == 0 + nohs = findall(momnohs, kidiq.mom_hs) + + momhs(x) = x == 1 + hs = findall(momhs, kidiq.mom_hs) + + f = Figure() + ax = Axis(f[1, 1]; title="KidIQ data: kid_score ~ mom_hs + mom_iq") + sca1 = scatter!(kidiq[kidiq.mom_hs .== 0, :mom_iq], kidiq[kidiq.mom_hs .== 0, :kid_score]; color=:red, markersize = 3) + sca2 = scatter!(kidiq[kidiq.mom_hs .== 1, :mom_iq], kidiq[kidiq.mom_hs .== 1, :kid_score]; color=:blue, markersize = 3) + x = sort(kidiq.mom_iq[nohs]) + lin1 =lines!(x, ms10_3t[:a, :median] .+ ms10_3t[:b, :median] .* kidiq.mom_hs[nohs] .+ ms10_3t[:c, :median] .* x; + color=:darkred) + x = sort(kidiq.mom_iq[hs]) + lin2 =lines!(x, ms10_3t[:a, :median] .+ ms10_3t[:b, :median] .* kidiq.mom_hs[hs] .+ ms10_3t[:c, :median] .* x; + color=:darkblue) + Legend(f[1, 2], + [sca1, sca2, lin1, lin2], + ["No high school", "High school", "No high school", "High School"]) + current_figure() +end + +# ╔═╡ Cell order: +# ╟─f90c8b82-a52d-45a4-86eb-d2c7eb905692 +# ╟─2daed834-e53d-4530-98bd-e80b5b99162f +# ╠═d1c76cd1-2537-470e-a9d5-ebaa5b9dec7e +# ╠═da0eb04e-9930-4f49-809b-3ba5fe16a59c +# ╠═d7992c39-0617-42b5-b977-f04260d2bd03 +# ╠═dfe95bfa-507a-4831-b3b5-f26b1d537112 +# ╠═4a4605a4-084a-4d64-a444-fa0fcf41ef91 +# ╠═d8d8e6b4-6406-43ac-9472-a7afab027aef +# ╠═cf817e35-2098-4acd-a518-4904db52f495 +# ╠═a9fcb0f0-5134-48a8-8d93-bfb8203e089e +# ╠═9073f433-fbec-4cf7-8ef0-ba870854eb75 +# ╠═b77b121b-38d3-485c-a9a2-c9ae87fe3423 +# ╠═3e15c7db-6c76-47a9-af3f-66a2eb67a8aa +# ╠═358093fe-3102-4c21-be0a-5d33569c13fd +# ╠═f4ab1e3d-8f64-4415-a257-63e9d43c60db +# ╠═90f0236a-2c5b-4ea8-83cf-490037bf8c15 +# ╠═bcf8c679-0e35-42e7-b4dd-91ac8dfb5721 +# ╠═b1c6c6a5-1784-438a-b930-49ce7aef80ab +# ╠═b6330c4f-8129-4bbd-aa39-3ddd00c062b5 +# ╠═6014b70b-c10d-4b91-94f7-79dc291cc92b diff --git a/notebooks/Chapters/10 - Linear regression with multiple predictors backup 2.jl b/notebooks/Chapters/10 - Linear regression with multiple predictors backup 2.jl new file mode 100644 index 0000000..b7b5ad9 --- /dev/null +++ b/notebooks/Chapters/10 - Linear regression with multiple predictors backup 2.jl @@ -0,0 +1,223 @@ +### A Pluto.jl notebook ### +# v0.19.11 + +using Markdown +using InteractiveUtils + +# ╔═╡ da0eb04e-9930-4f49-809b-3ba5fe16a59c +using Pkg, DrWatson + +# ╔═╡ d7992c39-0617-42b5-b977-f04260d2bd03 +begin + # Specific to this notebook + using GLM + + # Specific to ROSTuringPluto + using Optim + using Logging + using Turing + + # Graphics related + using GLMakie + + # Common data files and functions + using RegressionAndOtherStories + import RegressionAndOtherStories: link + + Logging.disable_logging(Logging.Warn) +end; + +# ╔═╡ f90c8b82-a52d-45a4-86eb-d2c7eb905692 +md"### KidIQ: kidiq.csv" + +# ╔═╡ 2daed834-e53d-4530-98bd-e80b5b99162f +md" ###### Widen the notebook." + +# ╔═╡ d1c76cd1-2537-470e-a9d5-ebaa5b9dec7e +html""" + +""" + + +# ╔═╡ dfe95bfa-507a-4831-b3b5-f26b1d537112 +kidiq = CSV.read(ros_datadir("KidIQ", "kidiq.csv"), DataFrame) + +# ╔═╡ 4a4605a4-084a-4d64-a444-fa0fcf41ef91 +let + f = Figure() + ax = Axis(f[1, 1]; title="KidIQ data: kid_score ~ mom_hs") + scatter!(kidiq[kidiq.mom_hs .== 0, :mom_hs], kidiq[kidiq.mom_hs .== 0, :kid_score]; color=:red, markersize = 3) + scatter!(kidiq[kidiq.mom_hs .== 1, :mom_hs], kidiq[kidiq.mom_hs .== 1, :kid_score]; color=:blue, markersize = 3) + ax = Axis(f[1, 2]; title="KidIQ data: kid_score ~ mom_iq") + scatter!(kidiq[kidiq.mom_hs .== 0, :mom_iq], kidiq[kidiq.mom_hs .== 0, :kid_score]; color=:red, markersize = 3) + scatter!(kidiq[kidiq.mom_hs .== 1, :mom_iq], kidiq[kidiq.mom_hs .== 1, :kid_score]; color=:blue, markersize = 3) + current_figure() +end + +# ╔═╡ d8d8e6b4-6406-43ac-9472-a7afab027aef +stan10_1 = " +data { + int N; + vector[N] mom_hs; + vector[N] kid_score; +} +parameters { + real a; + real b; + real sigma; +} +model { + vector[N] mu; + a ~ normal(100, 10); + b ~ normal(5, 10); + mu = a + b * mom_hs; + kid_score ~ normal(mu, sigma); +} +"; + +# ╔═╡ cf817e35-2098-4acd-a518-4904db52f495 +@model function ppl10_1(x, y) + a ~ Normal(100, 10) + b ~ Normal(5, 10) + σ ~ Exponential(1) + μ = a .+ b .* x + for i in eachindex(y) + y[i] ~ Normal(μ[i], σ) + end +end + +# ╔═╡ a9fcb0f0-5134-48a8-8d93-bfb8203e089e +begin + m10_1t = ppl10_1(kidiq.mom_hs, kidiq.mom_iq) + chns10_1t = sample(m10_1t, NUTS(), MCMCThreads(), 1000, 4) + describe(chns10_1t) +end + +# ╔═╡ 9073f433-fbec-4cf7-8ef0-ba870854eb75 +begin + post10_1t = DataFrame(chns10_1t)[:, 3:5] + ms10_1t = model_summary(post10_1t, [:a, :b, :σ]) +end + +# ╔═╡ b77b121b-38d3-485c-a9a2-c9ae87fe3423 +let + f = Figure() + ax = Axis(f[1, 1]; title="KidIQ data: kid_score ~ mom_hs") + scatter!(kidiq[kidiq.mom_hs .== 0, :mom_hs], kidiq[kidiq.mom_hs .== 0, :kid_score]; color=:red, markersize = 3) + scatter!(kidiq[kidiq.mom_hs .== 1, :mom_hs], kidiq[kidiq.mom_hs .== 1, :kid_score]; color=:blue, markersize = 3) + lines!([0.0, 1.0], [ms10_1t[:a, :median], ms10_1t[:a, :median] + ms10_1t[:b, :median]]) + current_figure() +end + +# ╔═╡ 3e15c7db-6c76-47a9-af3f-66a2eb67a8aa +@model function ppl10_2(x, y) + a ~ Normal(25, 3) + b ~ Normal(1, 2) + σ ~ Exponential(1) + μ = a .+ b .* x + for i in eachindex(y) + y[i] ~ Normal(μ[i], σ) + end +end + +# ╔═╡ 358093fe-3102-4c21-be0a-5d33569c13fd +begin + m10_2t = ppl10_2(kidiq.mom_iq, kidiq.kid_score) + chns10_2t = sample(m10_2t, NUTS(), MCMCThreads(), 1000, 4) + describe(chns10_2t) +end + +# ╔═╡ f4ab1e3d-8f64-4415-a257-63e9d43c60db +begin + post10_2t = DataFrame(chns10_2t)[:, 3:5] + ms10_2t = model_summary(post10_2t, [:a, :b, :sigma]) +end + +# ╔═╡ 90f0236a-2c5b-4ea8-83cf-490037bf8c15 +let + f = Figure() + ax = Axis(f[1, 1]; title="KidIQ data: kid_score ~ mom_iq") + scatter!(kidiq[kidiq.mom_hs .== 0, :mom_iq], kidiq[kidiq.mom_hs .== 0, :kid_score]; color=:red, markersize = 3) + scatter!(kidiq[kidiq.mom_hs .== 1, :mom_iq], kidiq[kidiq.mom_hs .== 1, :kid_score]; color=:blue, markersize = 3) + x = LinRange(70.0, 140.0, 100) + lines!(x, ms10_2t[:a, :median] .+ ms10_2t[:b, :median] .* x) + current_figure() +end + +# ╔═╡ bcf8c679-0e35-42e7-b4dd-91ac8dfb5721 +@model function ppl10_3(x, y, z) + a ~ Normal(25, 2) + b ~ Normal(5, 2) + c ~ Normal(1, 2) + σ ~ Exponential(1) + μ = a .+ b .* x .+ c .* y + for i in eachindex(y) + z[i] ~ Normal(μ[i], σ) + end +end + +# ╔═╡ b1c6c6a5-1784-438a-b930-49ce7aef80ab +begin + m10_3t = ppl10_3(kidiq.mom_hs, kidiq.mom_iq, kidiq.kid_score) + chns10_3t = sample(m10_3t, NUTS(), MCMCThreads(), 1000, 4) + describe(chns10_3t) +end + +# ╔═╡ b6330c4f-8129-4bbd-aa39-3ddd00c062b5 +begin + post10_3t = DataFrame(chns10_3t)[:, 3:6] + ms10_3t = model_summary(post10_3t, [:a, :b, :c, :σ]) +end + +# ╔═╡ 6014b70b-c10d-4b91-94f7-79dc291cc92b +let + momnohs(x) = x == 0 + nohs = findall(momnohs, kidiq.mom_hs) + + momhs(x) = x == 1 + hs = findall(momhs, kidiq.mom_hs) + + f = Figure() + ax = Axis(f[1, 1]; title="KidIQ data: kid_score ~ mom_hs + mom_iq") + sca1 = scatter!(kidiq[kidiq.mom_hs .== 0, :mom_iq], kidiq[kidiq.mom_hs .== 0, :kid_score]; color=:red, markersize = 3) + sca2 = scatter!(kidiq[kidiq.mom_hs .== 1, :mom_iq], kidiq[kidiq.mom_hs .== 1, :kid_score]; color=:blue, markersize = 3) + x = sort(kidiq.mom_iq[nohs]) + lin1 =lines!(x, ms10_3t[:a, :median] .+ ms10_3t[:b, :median] .* kidiq.mom_hs[nohs] .+ ms10_3t[:c, :median] .* x; + color=:darkred) + x = sort(kidiq.mom_iq[hs]) + lin2 =lines!(x, ms10_3t[:a, :median] .+ ms10_3t[:b, :median] .* kidiq.mom_hs[hs] .+ ms10_3t[:c, :median] .* x; + color=:darkblue) + Legend(f[1, 2], + [sca1, sca2, lin1, lin2], + ["No high school", "High school", "No high school", "High School"]) + current_figure() +end + +# ╔═╡ Cell order: +# ╟─f90c8b82-a52d-45a4-86eb-d2c7eb905692 +# ╟─2daed834-e53d-4530-98bd-e80b5b99162f +# ╠═d1c76cd1-2537-470e-a9d5-ebaa5b9dec7e +# ╠═da0eb04e-9930-4f49-809b-3ba5fe16a59c +# ╠═d7992c39-0617-42b5-b977-f04260d2bd03 +# ╠═dfe95bfa-507a-4831-b3b5-f26b1d537112 +# ╠═4a4605a4-084a-4d64-a444-fa0fcf41ef91 +# ╠═d8d8e6b4-6406-43ac-9472-a7afab027aef +# ╠═cf817e35-2098-4acd-a518-4904db52f495 +# ╠═a9fcb0f0-5134-48a8-8d93-bfb8203e089e +# ╠═9073f433-fbec-4cf7-8ef0-ba870854eb75 +# ╠═b77b121b-38d3-485c-a9a2-c9ae87fe3423 +# ╠═3e15c7db-6c76-47a9-af3f-66a2eb67a8aa +# ╠═358093fe-3102-4c21-be0a-5d33569c13fd +# ╠═f4ab1e3d-8f64-4415-a257-63e9d43c60db +# ╠═90f0236a-2c5b-4ea8-83cf-490037bf8c15 +# ╠═bcf8c679-0e35-42e7-b4dd-91ac8dfb5721 +# ╠═b1c6c6a5-1784-438a-b930-49ce7aef80ab +# ╠═b6330c4f-8129-4bbd-aa39-3ddd00c062b5 +# ╠═6014b70b-c10d-4b91-94f7-79dc291cc92b diff --git a/notebooks/Chapters/10 - Linear regression with multiple predictors.jl b/notebooks/Chapters/10 - Linear regression with multiple predictors.jl index 27bfe7b..b7b5ad9 100644 --- a/notebooks/Chapters/10 - Linear regression with multiple predictors.jl +++ b/notebooks/Chapters/10 - Linear regression with multiple predictors.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.10 +# v0.19.11 using Markdown using InteractiveUtils