From ddacd8c714c189b70a344b3444d0aafadfe97ddc Mon Sep 17 00:00:00 2001 From: will king Date: Thu, 23 Mar 2023 09:47:29 -0700 Subject: [PATCH] added some work in turing --- .../Logistic_WorkingParamRecovery.jl | 410 ++-- Julia-turing models/PlutoModel.jl | 1807 +++++++++++++++++ README.md | 28 + 3 files changed, 2055 insertions(+), 190 deletions(-) create mode 100644 Julia-turing models/PlutoModel.jl diff --git a/Julia-turing models/Logistic_WorkingParamRecovery.jl b/Julia-turing models/Logistic_WorkingParamRecovery.jl index a5e8d51..7c997c6 100644 --- a/Julia-turing models/Logistic_WorkingParamRecovery.jl +++ b/Julia-turing models/Logistic_WorkingParamRecovery.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.12 +# v0.19.19 using Markdown using InteractiveUtils @@ -22,12 +22,12 @@ begin #creating synthetic data #n = 100_000 #successfully tested with n=100_000. It recovered the values quite well. n = 1000 β = [1 2 -3] + α = 0 k=length(β) ϵ = randn(n) X = rand(Uniform(0,1),(n,k)) - #normalize X? - B = (X*β') + B = α .+ (X*β') lB=logistic.(B) y = rand.(Bernoulli.(lB)) end @@ -43,7 +43,7 @@ plot(lB,y,seriestype=:scatter,legend=nothing) # ╔═╡ 0696416b-72ba-46a0-ac54-0f8afbba554b @model function Logit(y,X) - #dims = n,k = size(X) + n,k = size(X) β ~ MvNormal(zeros(k),1) σ ~ Exponential(1) α ~ Normal(0,1) @@ -55,10 +55,16 @@ plot(lB,y,seriestype=:scatter,legend=nothing) end # ╔═╡ a2632230-b891-48b3-ba05-d34dc6076101 +# ╠═╡ disabled = true +#=╠═╡ MvNormal(zeros(k),1) + ╠═╡ =# # ╔═╡ af054878-09ed-4c67-8655-5ff0bd0d1193 +# ╠═╡ disabled = true +#=╠═╡ BernoulliLogit + ╠═╡ =# # ╔═╡ 3f4aa70d-ffce-44fe-8520-831a5a94fe47 testmodel = Logit(y,X) @@ -91,9 +97,9 @@ Turing = "~0.22.0" PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.8.0" +julia_version = "1.8.5" manifest_format = "2.0" -project_hash = "e0a6c795afd95256fbf971b740b22cd9b13e1fc5" +project_hash = "a808c35d6378600ae05d4769016c237f2e50c952" [[deps.AbstractFFTs]] deps = ["ChainRulesCore", "LinearAlgebra"] @@ -103,26 +109,26 @@ version = "1.2.1" [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] -git-tree-sha1 = "5c26c7759412ffcaf0dd6e3172e55d783dd7610b" +git-tree-sha1 = "b4d13c741b2bbe0e1af305a92d2f105a7caa47af" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "4.1.3" +version = "4.2.0" [[deps.AbstractPPL]] -deps = ["AbstractMCMC", "DensityInterface", "Setfield", "SparseArrays"] -git-tree-sha1 = "6320752437e9fbf49639a410017d862ad64415a5" +deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] +git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.5.2" +version = "0.5.4" [[deps.AbstractTrees]] -git-tree-sha1 = "52b3b436f8f73133d7bc3a6c71ee7ed6ab2ab754" +git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.3" +version = "0.4.4" [[deps.Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "cc37d689f599e8df4f464b2fa3870ff7db7492ef" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.4.0" +version = "3.6.1" [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "Setfield", "Statistics", "StatsBase", "StatsFuns", "UnPack"] @@ -169,17 +175,11 @@ git-tree-sha1 = "5ba6c757e8feccf03a1554dfaf3e26b3cfc7fd5e" uuid = "68821587-b530-5797-8361-c406ea357684" version = "3.5.1+1" -[[deps.ArrayInterfaceCore]] -deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c46fb7dd1d8ca1d213ba25848a5ec4e47a1a1b08" -uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.26" - -[[deps.ArrayInterfaceStaticArraysCore]] -deps = ["Adapt", "ArrayInterfaceCore", "LinearAlgebra", "StaticArraysCore"] -git-tree-sha1 = "93c8ba53d8d26e124a5a8d4ec914c3a16e6a0970" -uuid = "dd5226c6-a4d4-4bc7-8575-46859f9c95b9" -version = "0.1.3" +[[deps.ArrayInterface]] +deps = ["Adapt", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "ec9c36854b569323551a6faf2f31fda15e3459a7" +uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" +version = "7.2.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -212,14 +212,14 @@ 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 = "a3704b8e5170f9339dff4e6cb286ad49464d3646" +git-tree-sha1 = "4f8d8df1f690c44e46464266ec928aaa5aabb299" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.10.6" +version = "0.10.7" [[deps.BitFlags]] -git-tree-sha1 = "629c6e4a7be8f427d268cebef2a5e3de6c50d462" +git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.6" +version = "0.1.7" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -228,7 +228,7 @@ uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+0" [[deps.Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.16.1+1" @@ -241,21 +241,21 @@ version = "0.5.1" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "0c8c8887763f42583e1206ee35413a43c91e2623" +git-tree-sha1 = "7d20c2fb8ab838e41069398685e7b6b5f89ed85b" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.45.0" +version = "1.48.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" +git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.6" +version = "1.15.7" [[deps.ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8" +git-tree-sha1 = "485193efd2176b88e6622a39a246f8c5b600e74e" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.4" +version = "0.1.6" [[deps.Clustering]] deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "Random", "SparseArrays", "Statistics", "StatsBase"] @@ -265,15 +265,15 @@ version = "0.14.3" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" +git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.0" +version = "0.7.1" [[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random"] -git-tree-sha1 = "1fd869cc3875b57347f7027521f561cf46d1fcd8" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] +git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.19.0" +version = "3.20.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -283,15 +283,15 @@ version = "0.11.4" [[deps.ColorVectorSpace]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] -git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322" +git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.9.9" +version = "0.9.10" [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" +git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.8" +version = "0.12.10" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -311,14 +311,14 @@ version = "0.3.0" [[deps.Compat]] deps = ["Dates", "LinearAlgebra", "UUIDs"] -git-tree-sha1 = "3ca828fe1b75fa84b021a7860bd039eaea84d2f2" +git-tree-sha1 = "61fdd77467a5c3ad071ef8277ac6bd6af7dd4c04" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.3.0" +version = "4.6.0" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.5.2+0" +version = "1.0.1+0" [[deps.CompositionsBase]] git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" @@ -333,9 +333,9 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95" +git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.4.1" +version = "1.5.1" [[deps.Contour]] git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" @@ -348,9 +348,9 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "e08915633fcb3ea83bf9d6126292e5bc5c739922" +git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.13.0" +version = "1.14.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -396,9 +396,9 @@ version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494" +git-tree-sha1 = "a4ad7ef19d2cdc2eff57abbbe68032b1cd0bd8f8" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.12.2" +version = "1.13.0" [[deps.Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] @@ -412,9 +412,9 @@ 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 = "bee795cdeabc7601776abbd6b9aac2ca62429966" +git-tree-sha1 = "fb372fc76a20edda014dfc2cdb33f23ef80feda6" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.77" +version = "0.25.85" [[deps.DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "DiffRules", "Distributions", "FillArrays", "LinearAlgebra", "NaNMath", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsBase", "StatsFuns", "ZygoteRules"] @@ -424,9 +424,9 @@ version = "0.6.43" [[deps.DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "c36550cb29cbe373e95b3f40486b9a4148f89ffd" +git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.2" +version = "0.9.3" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -441,20 +441,20 @@ version = "0.6.8" [[deps.DynamicPPL]] deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "9a795bb2fe860e2b0a19136429a173de9f8c2774" +git-tree-sha1 = "4b610b80737a35a163833a6cd7c11d6142baaac4" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.21.3" +version = "0.21.4" [[deps.EllipticalSliceSampling]] -deps = ["AbstractMCMC", "ArrayInterfaceCore", "Distributions", "Random", "Statistics"] -git-tree-sha1 = "4cda4527e990c0cc201286e0a0bfbbce00abcfc2" +deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] +git-tree-sha1 = "973b4927d112559dc737f55d6bf06503a5b3fc14" uuid = "cad2338a-1db2-11e9-3401-43bc07c9ede2" -version = "1.0.0" +version = "1.1.0" [[deps.EnumX]] -git-tree-sha1 = "e5333cd1e1c713ee21d07b6ed8b0d8853fabe650" +git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" -version = "1.0.3" +version = "1.0.4" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -496,9 +496,9 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "802bfc139833d2ba893dd9e62ba1767c88d708ae" +git-tree-sha1 = "d3ba08ab64bdfd27234d3f61956c966266757fe6" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.5" +version = "0.13.7" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -520,9 +520,9 @@ version = "0.4.2" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "10fa12fe96e4d76acfa738f4df2126589a67374f" +git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.33" +version = "0.10.35" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -543,9 +543,9 @@ version = "1.1.3" [[deps.FunctionWrappersWrappers]] deps = ["FunctionWrappers"] -git-tree-sha1 = "a5e6e7f12607e90d71b09e6ce2c965e41b337968" +git-tree-sha1 = "b104d487b34566608f8b4e1c39fb0b10aa279ff8" uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf" -version = "0.1.1" +version = "0.1.3" [[deps.Functors]] deps = ["LinearAlgebra"] @@ -565,21 +565,21 @@ version = "3.3.8+0" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "6872f5ec8fd1a38880f027a26739d42dcda6691f" +git-tree-sha1 = "1cd7f0af1aa58abc02ea1d872953a97359cb87fa" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.2" +version = "0.1.4" [[deps.GR]] -deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "00a9d4abadc05b9476e937a5557fcce476b9e547" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"] +git-tree-sha1 = "660b2ea2ec2b010bb02823c6d0ff6afd9bdc5c16" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.69.5" +version = "0.71.7" [[deps.GR_jll]] -deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" +deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "d5e1fd17ac7f3aa4c5287a61ee28d4f8b8e98873" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.69.1+0" +version = "0.71.7+0" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -589,9 +589,9 @@ version = "0.21.0+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "fb83fbe02fe57f2c068013aa94bcdf6760d3a7a7" +git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+1" +version = "2.74.0+2" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -606,9 +606,9 @@ version = "1.0.2" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "0c0e8d05fdd5e9792b31b7c7841f11a2ff8ad633" +git-tree-sha1 = "37e4657cd56b11abe3d10cd4a1ec5fbdb4180263" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.5.4" +version = "1.7.4" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -650,15 +650,15 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.Interpolations]] deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "842dd89a6cb75e02e85fdd75c760cdc43f5d6863" +git-tree-sha1 = "721ec2cf720536ad005cb38f50dbba7b02419a15" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.14.6" +version = "0.14.7" [[deps.IntervalSets]] deps = ["Dates", "Random", "Statistics"] -git-tree-sha1 = "3f91cd3f56ea48d4d2a75c2a65455c5fc74fa347" +git-tree-sha1 = "16c0cc91853084cb5f58a78bd209513900206ce6" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.3" +version = "0.7.4" [[deps.InverseFunctions]] deps = ["Test"] @@ -667,9 +667,9 @@ uuid = "3587e190-3f89-42d0-90ee-14403ec27112" version = "0.1.8" [[deps.InvertedIndices]] -git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" +git-tree-sha1 = "82aec7a3dd64f4d9584659dc0b62ef7db2ef3e19" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.1.0" +version = "1.2.0" [[deps.IrrationalConstants]] git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" @@ -705,10 +705,10 @@ uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.3" [[deps.JpegTurbo_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.2+0" +version = "2.1.91+0" [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] @@ -746,9 +746,15 @@ version = "1.3.0" [[deps.Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] -git-tree-sha1 = "ab9aa169d2160129beb241cb2750ca499b4e90e9" +git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.17" +version = "0.15.18" + +[[deps.Lazy]] +deps = ["MacroTools"] +git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" +uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" +version = "0.15.1" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -796,9 +802,9 @@ version = "1.8.7+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "7739f837d6447403596a75d19ed01fd08d6f56bf" +git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.3.0+3" +version = "1.6.0+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -808,9 +814,9 @@ version = "1.42.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "42b62845d70a619f063a7da093d995ec8e15e778" +git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+1" +version = "1.16.1+2" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -842,15 +848,15 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LogDensityProblems]] deps = ["ArgCheck", "DocStringExtensions", "Random", "Requires", "UnPack"] -git-tree-sha1 = "408a29d70f8032b50b22155e6d7776715144b761" +git-tree-sha1 = "c3e1189191e4528b605070972d7d4e9cd91dd96b" uuid = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" -version = "1.0.2" +version = "1.0.3" [[deps.LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "94d9c52ca447e23eac0c0f074effbcd38830deb5" +git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.18" +version = "0.3.23" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -862,16 +868,16 @@ uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" 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 = "f5f347b828fd95ece7398f412c81569789361697" +deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Serialization", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] +git-tree-sha1 = "c659f7508035a7bdd5102aef2de028ab035f289a" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "5.5.0" +version = "5.7.1" [[deps.MCMCDiagnosticTools]] -deps = ["AbstractFFTs", "DataAPI", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "dab8e9e9cd714fd3adc2344a97504e7e64e78546" +deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] +git-tree-sha1 = "8b862779314f9299cbf7bdbf2413bcbd9c8e77b2" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.1.5" +version = "0.2.6" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] @@ -881,9 +887,9 @@ version = "2022.2.0+0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "4040c0da2bd05130687cc258c1318acd32bace90" +git-tree-sha1 = "c8b7e632d6754a5e36c0d94a4b466a5ba3a30128" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.7.1" +version = "1.8.0" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -924,9 +930,9 @@ version = "0.1.3" [[deps.Missings]] deps = ["DataAPI"] -git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" +git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.2" +version = "1.1.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -937,21 +943,21 @@ version = "2022.2.1" [[deps.MultivariateStats]] deps = ["Arpack", "LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI", "StatsBase"] -git-tree-sha1 = "efe9c8ecab7a6311d4b91568bd6c88897822fabe" +git-tree-sha1 = "91a48569383df24f0fd2baf789df2aade3d0ad80" uuid = "6f286f6a-111f-5878-ab1e-185364afe411" -version = "0.10.0" +version = "0.10.1" [[deps.NNlib]] -deps = ["Adapt", "ChainRulesCore", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "00bcfcea7b2063807fdcab2e0ce86ef00b8b8000" +deps = ["Adapt", "ChainRulesCore", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] +git-tree-sha1 = "33ad5a19dc6730d592d8ce91c14354d758e53b0e" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.8.10" +version = "0.8.19" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" +git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.1" +version = "1.0.2" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] @@ -966,9 +972,9 @@ version = "1.0.0" [[deps.NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "440165bf08bc500b8fe4a7be2dc83271a00c0716" +git-tree-sha1 = "2c3726ceb3388917602169bed973dbc97f1b51a8" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.12" +version = "0.4.13" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" @@ -981,9 +987,9 @@ version = "0.5.4" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "f71d8950b724e9ff6110fc948dff5a329f901d64" +git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.8" +version = "1.12.9" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1003,15 +1009,15 @@ version = "0.8.1+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "5628f092c6186a80484bfefdf89ff64efdaec552" +git-tree-sha1 = "6503b77492fd7fcb9379bf73cd31035670e3c509" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.3.1" +version = "1.3.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" +git-tree-sha1 = "9ff31d101d987eb9d66bd8b176ac7c277beccd09" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.19+0" +version = "1.1.20+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1021,9 +1027,9 @@ version = "0.5.5+0" [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "8a9102cb805df46fc3d6effdc2917f09b0215c0b" +git-tree-sha1 = "e5a1825d3d53aa4ad4fb42bd4927011ad4a78c3d" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.2.10" +version = "0.2.15" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1043,15 +1049,15 @@ version = "10.40.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "cf494dca75a69712a72b80bc48f59dcf3dea63ec" +git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.16" +version = "0.11.17" [[deps.Parsers]] deps = ["Dates", "SnoopPrecompile"] -git-tree-sha1 = "cceb0257b662528ecdf0b4b4302eb00e767b38e7" +git-tree-sha1 = "6f4fbcd1ad45905a5dee3f4256fabb49aa2110c6" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.5.0" +version = "2.5.7" [[deps.Pipe]] git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" @@ -1077,15 +1083,15 @@ version = "3.1.0" [[deps.PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] -git-tree-sha1 = "21303256d239f6b484977314674aef4bb1fe4420" +git-tree-sha1 = "c95373e73290cf50a8a22c3375e4625ded5c5280" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.1" +version = "1.3.4" [[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "47e70b391ff314cc36e7c2400f7d2c5455dc9496" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] +git-tree-sha1 = "da1d3fb7183e38603fcdd2061c47979d91202c97" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.36.1" +version = "1.38.6" [[deps.Preferences]] deps = ["TOML"] @@ -1095,9 +1101,9 @@ version = "1.3.0" [[deps.PrettyTables]] deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "d8ed354439950b34ab04ff8f3dfd49e11bc6c94b" +git-tree-sha1 = "96f6db03ab535bdb901300f88335257b0018689d" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.2.1" +version = "2.2.2" [[deps.Printf]] deps = ["Unicode"] @@ -1123,9 +1129,9 @@ version = "5.15.3+2" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "97aa253e65b784fd13e83774cadc95b38011d734" +git-tree-sha1 = "786efa36b7eff813723c4849c90456609cf06661" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.6.0" +version = "2.8.1" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1154,21 +1160,21 @@ version = "0.1.0" [[deps.RecipesBase]] deps = ["SnoopPrecompile"] -git-tree-sha1 = "d12e612bba40d189cead6ff857ddb67bd2e6a387" +git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.3.1" +version = "1.3.3" [[deps.RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] -git-tree-sha1 = "a030182cccc5c461386c6f055c36ab8449ef1340" +git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.6.10" +version = "0.6.11" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "Tables", "ZygoteRules"] -git-tree-sha1 = "fe25988dce8dd3b763cf39d0ca39b09db3571ff7" +deps = ["Adapt", "ArrayInterface", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "ZygoteRules"] +git-tree-sha1 = "3dcb2a98436389c0aac964428a5fa099118944de" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.32.1" +version = "2.38.0" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1189,21 +1195,21 @@ version = "1.3.0" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.0" +version = "0.7.1" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" +git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.3.0+0" +version = "0.4.0+0" [[deps.Roots]] deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "a3db467ce768343235032a1ca0830fc64158dadf" +git-tree-sha1 = "9c2f5d3768804ed465f0c51540c6074ae9f63900" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.8" +version = "2.0.9" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] @@ -1216,10 +1222,16 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[deps.SciMLBase]] -deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "RuntimeGeneratedFunctions", "StaticArraysCore", "Statistics", "Tables"] -git-tree-sha1 = "5686a5c9660c5fb571e3a8be63ff1848de82bdbd" +deps = ["ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SnoopPrecompile", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces"] +git-tree-sha1 = "fe55d9f9d73fec26f64881ba8d120607c22a54b0" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.71.0" +version = "1.88.0" + +[[deps.SciMLOperators]] +deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"] +git-tree-sha1 = "8419114acbba861ac49e1ab2750bae5c5eda35c4" +uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" +version = "0.1.22" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -1234,18 +1246,18 @@ version = "1.1.1" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "efd23b378ea5f2db53a55ae53d3133de4e080aa9" +git-tree-sha1 = "77d3c4726515dca71f6d80fbb5e251088defe305" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.3.16" +version = "1.3.18" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" [[deps.Setfield]] -deps = ["ConstructionBase", "Future", "MacroTools", "Requires"] -git-tree-sha1 = "38d88503f695eb0301479bc9b0d4320b378bafe5" +deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] +git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" -version = "0.8.2" +version = "1.1.1" [[deps.SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] @@ -1263,9 +1275,10 @@ uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" version = "1.1.0" [[deps.SnoopPrecompile]] -git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85" +deps = ["Preferences"] +git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" -version = "1.0.1" +version = "1.0.3" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1282,9 +1295,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" +git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.1.7" +version = "2.2.0" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -1294,9 +1307,9 @@ version = "0.1.15" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "f86b3a049e5d05227b10e15dbb315c5b90f14988" +git-tree-sha1 = "2d7d9e1ddadc8407ffd460e24218e37ef52dd9a3" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.9" +version = "1.5.16" [[deps.StaticArraysCore]] git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" @@ -1343,15 +1356,21 @@ uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" version = "0.3.0" [[deps.StructArrays]] -deps = ["Adapt", "DataAPI", "StaticArraysCore", "Tables"] -git-tree-sha1 = "13237798b407150a6d2e2bce5d793d7d9576e99e" +deps = ["Adapt", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"] +git-tree-sha1 = "b03a3b745aa49b566f128977a7dd1be8711c5e71" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.13" +version = "0.6.14" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" +[[deps.SymbolicIndexingInterface]] +deps = ["DocStringExtensions"] +git-tree-sha1 = "f8ab052bfcbdb9b48fad2c80c873aa0d0344dfe5" +uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" +version = "0.2.2" + [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" @@ -1378,7 +1397,7 @@ version = "1.10.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.0" +version = "1.10.1" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1398,21 +1417,32 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "d963aad627fd7af56fbbfee67703c2f7bfee9dd7" +git-tree-sha1 = "77817887c4b414b9c6914c61273910e3234eb21c" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.22" +version = "0.2.23" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "8a75929dcd3c38611db2f8d08546decb514fcadf" +git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.9" +version = "0.9.11" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "77fea79baa5b22aeda896a8d9c6445a74500a2c2" +git-tree-sha1 = "c42fa452a60f022e9e087823b47e5a5f8adc53d5" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.74" +version = "0.4.75" + +[[deps.Tricks]] +git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" +uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" +version = "0.1.6" + +[[deps.TruncatedStacktraces]] +deps = ["InteractiveUtils"] +git-tree-sha1 = "7cdbe45f0018b7f681a6b63ad1250ee6f2297a87" +uuid = "781d530d-4396-4725-bb49-402e4bee1e77" +version = "1.0.0" [[deps.Turing]] 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", "Setfield", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker"] @@ -1421,9 +1451,9 @@ uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" version = "0.22.0" [[deps.URIs]] -git-tree-sha1 = "e59ecc5a41b000fa94423a578d29290c7266fc10" +git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.4.0" +version = "1.4.2" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -1450,9 +1480,9 @@ version = "0.2.0" [[deps.Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" +git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.19.0+0" +version = "1.21.0+0" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1474,9 +1504,9 @@ version = "0.5.5" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "58443b63fb7e465a8a7210828c91c08b92132dff" +git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.9.14+0" +version = "2.10.3+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -1616,10 +1646,10 @@ uuid = "83775a58-1f1d-513f-b197-d71354ab007a" version = "1.2.12+3" [[deps.Zstd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c6edfe154ad7b313c01aceca188c05c835c67360" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.2+0" +version = "1.5.4+0" [[deps.ZygoteRules]] deps = ["MacroTools"] diff --git a/Julia-turing models/PlutoModel.jl b/Julia-turing models/PlutoModel.jl new file mode 100644 index 0000000..ebdc478 --- /dev/null +++ b/Julia-turing models/PlutoModel.jl @@ -0,0 +1,1807 @@ +### A Pluto.jl notebook ### +# v0.19.19 + +using Markdown +using InteractiveUtils + +# ╔═╡ c3854198-646b-11ed-1d90-077419a6a860 +using Turing,StatsFuns,Distributions,StatsPlots,FillArrays + +# ╔═╡ 54680695-4d31-4dd9-8b3c-c0af5153abef +using LinearAlgebra + +# ╔═╡ f6fc4578-43c5-4fb7-a24c-2567aa5b33c1 +using Random + +# ╔═╡ 735ae519-019e-48c6-8b73-7982fa60501a +md""" +So it seems like I am having issues where I can't get the herarcheal parameters to work. +""" + +# ╔═╡ bd9391b7-5240-46ca-be26-357292ffaddb +begin #creating synthetic data + #successfully tested with n=100_000. It recovered the values quite well. + n = 1000 + + #####################Independent Data Draws ############## + #= Elapsed time + How long the trial actually takes + It should occur over a range of roughly [0,5], mostly clustered around 1 + =# + elapsed_time = rand(Gamma(8,0.125),n) + + #= Enrollment success + How many of the initially planned group they have enrolled. + =# + enrollment_pctg = rand(Gamma(4,0.12),n) + + #= Competing brands for compound + The number of other brands selling that compound. + =# + compound_count = rand(Poisson(2),n) + + #= Indication Category + Ignore for now + =# + indication_category_index = rand(1:6,n) + indication_category_dummies = zeros(n,6) + for (row,col) in enumerate(indication_category_index) + indication_category_dummies[row,col] = 1 + end + #= Indication Population rate + measured in per 10_000, across 6 national develoment measures + =# + population_rate_raw = rand(MvNormal([50, 60,100, 70,65,40],5*I),n) + population_rate = population_rate_raw[indication_category_index] + + #= Current State + One of 3 options + - Recruiting + - Not yet recruiting + - Active, not recruiting + - Suspended + =# + current_state_prob = Categorical([0.5,0.05,0.4,0.05]) + current_state_index = rand(current_state_prob,n) + current_state_dummies = zeros(n,4) + for (row,col) in enumerate(current_state_index) + current_state_dummies[row,col] = 1 + end + Z = hcat(indication_category_dummies,current_state_dummies) + X = hcat(enrollment_pctg,compound_count,population_rate) +end + +# ╔═╡ 75c5e5a8-0fe5-4739-99a3-4cc17487dc91 +begin + ################# DEPENDENT VARIABLE CREATION ############### + #HyperParameters for conclusion_status + + #draws of hyperparameters for impact of indication category + alpha_indication_category = [1,-0.4,0.7,2,0.1,-1] + + #hyperparameters for impact of current state + alpha_current_state = [1,0.8,1.2,-1.2] + + + #### Parameters for conclusion_status + #get β for enrollment + M_enrollment = Z * vcat(alpha_indication_category,alpha_current_state) + S_enrollment = 0.7 + + β_enrollment = M_enrollment .+ S_enrollment .* randn(n) + + k_x = size(X,2) + β_everything_else = rand(MvNormal([0.5,0.4,0.3],I),n) + + B = sum(X .* β_everything_else',dims=2) .+ β_enrollment .* enrollment_pctg + p = logistic.(B) + y = rand.(Bernoulli.(p)) +end + +# ╔═╡ 322c7879-faf6-4f03-af2c-61e9c2cd76e3 +sum(y) + +# ╔═╡ 8b94ef35-4ec0-420a-9e2b-7aecf1497e97 +histogram(p,bins = [-0.10,0.01,0.25,0.5,0.75,0.99,1.1]) + +# ╔═╡ ea4df00b-72e2-4de6-afb1-f0b1d7e15e9c +histogram(β_enrollment) + +# ╔═╡ 0696416b-72ba-46a0-ac54-0f8afbba554b +@model function Logit(y,X,Z,enrollment_pctg) + n,k_x = size(X) + k_z = size(Z,2) + + α ~ MvNormal(zeros(10),I) + M = Z * α + #σ_β ~ Exponential(0.5) + #β_enrollment .~ Normal.(M,σ_β) + + σ_everything_else ~ Exponential(0.5) + β_everything_else ~ MvNormal(zeros(k_x),σ_everything_else*I) + + μ = X * β_everything_else .+ enrollment_pctg .* M + + p = logistic.(μ) + y .~ Bernoulli.(p) + +end + +# ╔═╡ 3f4aa70d-ffce-44fe-8520-831a5a94fe47 +testmodel = Logit(y,X,Z,enrollment_pctg); + +# ╔═╡ 989b69de-e187-48f2-8454-8d86b232d895 +chain = sample(testmodel,NUTS(),MCMCThreads(),2000,2) + +# ╔═╡ 8da7994b-ac63-4583-a360-d49cc8b04d35 +plot(chain) + +# ╔═╡ 00000000-0000-0000-0000-000000000001 +PLUTO_PROJECT_TOML_CONTENTS = """ +[deps] +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c" +StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" +Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" + +[compat] +Distributions = "~0.25.77" +FillArrays = "~0.13.5" +StatsFuns = "~1.0.1" +StatsPlots = "~0.15.4" +Turing = "~0.22.0" +""" + +# ╔═╡ 00000000-0000-0000-0000-000000000002 +PLUTO_MANIFEST_TOML_CONTENTS = """ +# This file is machine-generated - editing it directly is not advised + 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╠═735ae519-019e-48c6-8b73-7982fa60501a +# ╠═f6fc4578-43c5-4fb7-a24c-2567aa5b33c1 +# ╠═bd9391b7-5240-46ca-be26-357292ffaddb +# ╠═75c5e5a8-0fe5-4739-99a3-4cc17487dc91 +# ╠═322c7879-faf6-4f03-af2c-61e9c2cd76e3 +# ╠═8b94ef35-4ec0-420a-9e2b-7aecf1497e97 +# ╠═ea4df00b-72e2-4de6-afb1-f0b1d7e15e9c +# ╠═0696416b-72ba-46a0-ac54-0f8afbba554b +# ╠═3f4aa70d-ffce-44fe-8520-831a5a94fe47 +# ╠═989b69de-e187-48f2-8454-8d86b232d895 +# ╠═8da7994b-ac63-4583-a360-d49cc8b04d35 +# ╟─00000000-0000-0000-0000-000000000001 +# ╟─00000000-0000-0000-0000-000000000002 diff --git a/README.md b/README.md index 6b98fc8..8a2c717 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,30 @@ # ClinicalTrialsEstimation + +The model I am going to fit + +Terminated .~ Bernoulli.(prob) +duration .~ Gamma(shape,scale) + +#terminated +prob .~ logistic.(M_duration) +M_duration = X * beta_duration +beta_duration .~ MvNormal(N_duration,S_duration) + +N_duration = Z * eta_duration +eta_duration .~ MvNormal + +S_duration = sigma_duration * I +sigma_duration .~ Exponential(0.5) + +#duration +shape .~ lognormal(mu_shape,sigma_shape) +scale .~ lognormal(mu_scale,sigma_scale) + +mu_shape = +sigma_shape = + +mu_scale = +sigma_scale = + +