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b/deps/generate_fake_data_rbc_sv.jl index 27c7b4e..6e12320 100644 --- a/deps/generate_fake_data_rbc_sv.jl +++ b/deps/generate_fake_data_rbc_sv.jl @@ -13,6 +13,8 @@ x0 = rand(MvNormal(mod_perturb.x_ergodic_var)) prob = QuadraticStateSpaceProblem(mod_perturb, x0, (0, T)) sol = solve(prob, DirectIteration()) z_vec = VectorOfArray(sol.z) +u_vec = VectorOfArray(sol.u) W_vec = sol.W CSV.write(joinpath(pkgdir(HMCExamples), "data/rbc_sv_2.csv"), DataFrame(c_obs=z_vec[1, :], i_obs=z_vec[2, :])) +CSV.write(joinpath(pkgdir(HMCExamples), "data/rbc_sv_2_joint_latents.csv"), DataFrame(zlag_obs=u_vec[2, :], ν_obs=u_vec[3, :])) CSV.write(joinpath(pkgdir(HMCExamples), "data/rbc_sv_2_joint_shocks.csv"), DataFrame(epsilon=W_vec[1, :], volshocks = W_vec[2, :])) \ No newline at end of file diff --git a/scripts/Manifest.toml b/scripts/Manifest.toml index f14d86a..76bfe64 100644 --- a/scripts/Manifest.toml +++ b/scripts/Manifest.toml @@ -1,44 +1,88 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.7.1" +julia_version = "1.8.5" manifest_format = "2.0" +project_hash = "12d4c1c4fd464345fccea6b6e17c72a781c1c828" + +[[deps.AbstractAlgebra]] +deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Markdown", "Random", "RandomExtensions", "SparseArrays", "Test"] +git-tree-sha1 = "29e65c331f97db9189ef00a4c7aed8127c2fd2d4" +uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" +version = "0.27.10" [[deps.AbstractFFTs]] deps = ["ChainRulesCore", "LinearAlgebra"] -git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" +git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.2.1" +version = "1.3.1" [[deps.AbstractMCMC]] -deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] -git-tree-sha1 = "5c26c7759412ffcaf0dd6e3172e55d783dd7610b" +deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] +git-tree-sha1 = "323799cab36200a01f5e9da3fecbd58329e2dd27" uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "4.1.3" +version = "4.4.0" + +[[deps.AbstractPPL]] +deps = ["AbstractMCMC", "DensityInterface", "Random", "Setfield", "SparseArrays"] +git-tree-sha1 = "33ea6c6837332395dbf3ba336f273c9f7fcf4db9" +uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" +version = "0.5.4" [[deps.AbstractTrees]] -git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" +git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.3.4" +version = "0.4.4" [[deps.Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "cc37d689f599e8df4f464b2fa3870ff7db7492ef" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.3" +version = "3.6.1" + +[[deps.AdvancedHMC]] +deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Requires", "Setfield", "SimpleUnPack", "Statistics", "StatsBase", "StatsFuns"] +git-tree-sha1 = "25d38b80e29533f5f85af19692a39e4275047a51" +uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" +version = "0.4.5" + +[[deps.AdvancedMH]] +deps = ["AbstractMCMC", "Distributions", "LogDensityProblems", "Random", "Requires"] +git-tree-sha1 = "165af834eee68d0a96c58daa950ddf0b3f45f608" +uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" +version = "0.7.4" + +[[deps.AdvancedPS]] +deps = ["AbstractMCMC", "Distributions", "Libtask", "Random", "Random123", "StatsFuns"] +git-tree-sha1 = "4d73400b3583147b1b639794696c78202a226584" +uuid = "576499cb-2369-40b2-a588-c64705576edc" +version = "0.4.3" + +[[deps.AdvancedVI]] +deps = ["Bijectors", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] +git-tree-sha1 = "67fcc7d46c26250e89fc62798fbe07b5ee264c6f" +uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" +version = "0.1.6" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" version = "2.3.0" +[[deps.ArgParse]] +deps = ["Logging", "TextWrap"] +git-tree-sha1 = "3102bce13da501c9104df33549f511cd25264d7d" +uuid = "c7e460c6-2fb9-53a9-8c5b-16f535851c63" +version = "1.1.4" + [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" [[deps.Arpack]] deps = ["Arpack_jll", "Libdl", "LinearAlgebra", "Logging"] -git-tree-sha1 = "91ca22c4b8437da89b030f08d71db55a379ce958" +git-tree-sha1 = "9b9b347613394885fd1c8c7729bfc60528faa436" uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" -version = "0.5.3" +version = "0.5.4" [[deps.Arpack_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"] @@ -46,21 +90,26 @@ git-tree-sha1 = "5ba6c757e8feccf03a1554dfaf3e26b3cfc7fd5e" uuid = "68821587-b530-5797-8361-c406ea357684" version = "3.5.1+1" +[[deps.ArrayInterface]] +deps = ["Adapt", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "53bb1691fb8560633ed8c0fa11d8b0900aaa805c" +uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" +version = "7.4.2" + [[deps.ArrayInterfaceCore]] -deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "40debc9f72d0511e12d817c7ca06a721b6423ba3" +deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "e5f08b5689b1aad068e01751889f2f615c7db36d" uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.17" - -[[deps.ArrayInterfaceStaticArraysCore]] -deps = ["Adapt", "ArrayInterfaceCore", "LinearAlgebra", "StaticArraysCore"] -git-tree-sha1 = 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"Unicode", "WeakRefStrings", "WorkerUtilities"] +git-tree-sha1 = "c700cce799b51c9045473de751e9319bdd1c6e94" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.4" +version = "0.10.9" [[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" @@ -116,35 +198,47 @@ git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" version = "0.5.1" +[[deps.ChainRules]] +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] +git-tree-sha1 = "7d20c2fb8ab838e41069398685e7b6b5f89ed85b" +uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" +version = "1.48.0" + [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "2dd813e5f2f7eec2d1268c57cf2373d3ee91fcea" +git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.1" +version = "1.15.7" [[deps.ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "1e315e3f4b0b7ce40feded39c73049692126cf53" +git-tree-sha1 = "485193efd2176b88e6622a39a246f8c5b600e74e" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.3" +version = "0.1.6" + +[[deps.CloseOpenIntervals]] +deps = ["Static", "StaticArrayInterface"] +git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" +uuid = 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"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"] @@ -154,25 +248,47 @@ 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 = 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[[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +version = "1.0.1+0" + +[[deps.CompositeTypes]] +git-tree-sha1 = "02d2316b7ffceff992f3096ae48c7829a8aa0638" +uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" +version = "0.1.3" [[deps.CompositionsBase]] git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" @@ -187,14 +303,20 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "59d00b3139a9de4eb961057eabb65ac6522be954" +git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.4.0" +version = "1.5.1" [[deps.Contour]] -git-tree-sha1 = "a599cfb8b1909b0f97c5e1b923ab92e1c0406076" +git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.6.1" +version = "0.6.2" + +[[deps.CpuId]] +deps = ["Markdown"] +git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406" +uuid = 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"Reexport", "SentinelArrays", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "aa51303df86f8626a962fccb878430cdb0a97eee" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.3.4" +version = "1.5.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -248,11 +370,41 @@ git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" +[[deps.DiffEqBase]] +deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "15a24aa2414fad34136724c4a16e556f264ddd11" +uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" +version = "6.122.1" + +[[deps.DiffResults]] +deps = ["StaticArraysCore"] +git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" +uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" +version = "1.1.0" + +[[deps.DiffRules]] +deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "a4ad7ef19d2cdc2eff57abbbe68032b1cd0bd8f8" +uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" +version = "1.13.0" + +[[deps.DifferenceEquations]] +deps = ["ChainRulesCore", "CommonSolve", "DiffEqBase", "Distributions", "LinearAlgebra", "PDMats", "RecursiveArrayTools", "SciMLBase", "UnPack"] +git-tree-sha1 = "314fea53dfb8fd2d222cbcc0392ea578c1bee953" +uuid = "e0ca9c66-1f9e-11ec-127a-1304ce62169c" +version = "0.5.1" + +[[deps.DifferentiableStateSpaceModels]] +deps = ["ChainRulesCore", "DifferenceEquations", "GeneralizedSylvesterSolver", "LaTeXStrings", 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"OpenSSL_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "bab67c0d1c4662d2c4be8c6007751b0b6111de5c" +git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8" uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" -version = "1.12.1+0" +version = "1.12.2+2" + +[[deps.HMCExamples]] +deps = ["AdvancedHMC", "ArgParse", "AxisArrays", "CSV", "DataFrames", "DelimitedFiles", "DifferenceEquations", "DifferentiableStateSpaceModels", "Distributions", "DynamicPPL", "HDF5", "JSON", "LaTeXStrings", "LinearAlgebra", "Logging", "MCMCChains", "MCMCChainsStorage", "MKL", "Plots", "Random", "RecursiveArrayTools", "Serialization", "SymbolicUtils", "Symbolics", "Turing", "Zygote"] +git-tree-sha1 = "8b8e7068526d0f6aeafa5ceaef6a3315fcc8488b" +repo-rev = "main" +repo-url = "https://github.com/HighDimensionalEconLab/HMCExamples.jl" +uuid = "04c4e5f0-d543-11eb-2b99-3f716ccaf3f5" +version = "0.1.0" [[deps.HTTP]] -deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "0fa77022fe4b511826b39c894c90daf5fce3334a" +deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "37e4657cd56b11abe3d10cd4a1ec5fbdb4180263" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.17" +version = "1.7.4" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -439,11 +696,28 @@ git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" version = "2.8.1+1" +[[deps.HostCPUFeatures]] +deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] +git-tree-sha1 = "734fd90dd2f920a2f1921d5388dcebe805b262dc" +uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" +version = "0.1.14" + [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "SpecialFunctions", "Test"] -git-tree-sha1 = "cb7099a0109939f16a4d3b572ba8396b1f6c7c31" +deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "fd77260897e227f9623fcd65d6a3ba6e88f8e947" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.10" +version = "0.3.12" + +[[deps.IRTools]] +deps = ["InteractiveUtils", "MacroTools", "Test"] +git-tree-sha1 = "0ade27f0c49cebd8db2523c4eeccf779407cf12c" +uuid = "7869d1d1-7146-5819-86e3-90919afe41df" +version = "0.4.9" + +[[deps.IfElse]] +git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" +uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" +version = "0.1.1" [[deps.IniFile]] git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" @@ -457,9 +731,20 @@ version = "0.3.1" [[deps.InlineStrings]] deps = ["Parsers"] -git-tree-sha1 = "a8671d5c9670a62cb36b7d44c376bdb09181aa26" +git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.1.3" +version = "1.4.0" + +[[deps.InplaceOps]] +deps = ["LinearAlgebra", "Test"] +git-tree-sha1 = "50b41d59e7164ab6fda65e71049fee9d890731ff" +uuid = "505f98c9-085e-5b2c-8e89-488be7bf1f34" +version = "0.3.0" + +[[deps.IntegerMathUtils]] +git-tree-sha1 = "f366daebdfb079fd1fe4e3d560f99a0c892e15bc" +uuid = "18e54dd8-cb9d-406c-a71d-865a43cbb235" +version = "0.1.0" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -472,32 +757,32 @@ 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 = "721ec2cf720536ad005cb38f50dbba7b02419a15" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.13.6" +version = "0.14.7" [[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" +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.1.0" +version = "1.3.0" [[deps.IrrationalConstants]] -git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.1" +version = "0.2.2" [[deps.IterTools]] git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" @@ -509,6 +794,12 @@ git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" +[[deps.JLFzf]] +deps = ["Pipe", "REPL", "Random", "fzf_jll"] +git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" +uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" +version = "0.1.5" + [[deps.JLLWrappers]] deps = ["Preferences"] git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" @@ -522,16 +813,22 @@ 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"] -git-tree-sha1 = "591e8dc09ad18386189610acafb970032c519707" +git-tree-sha1 = "9816b296736292a80b9a3200eb7fbb57aaa3917a" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" -version = "0.6.3" +version = "0.6.5" + +[[deps.KroneckerTools]] +deps = ["LinearAlgebra", "QuasiTriangular"] +git-tree-sha1 = "4d10b5380330679eeff1e7324309f596db426d9b" +uuid = "7e59e93b-e0cb-42c7-aa95-426cb754d61e" +version = "0.1.1" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -545,6 +842,23 @@ git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" version = "3.0.0+1" +[[deps.LLVM]] +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] +git-tree-sha1 = "f044a2796a9e18e0531b9b3072b0019a61f264bc" +uuid = "929cbde3-209d-540e-8aea-75f648917ca0" +version = "4.17.1" + +[[deps.LLVMExtra_jll]] +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "070e4b5b65827f82c16ae0916376cb47377aa1b5" +uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" +version = "0.0.18+0" + +[[deps.LRUCache]] +git-tree-sha1 = "d862633ef6097461037a00a13f709a62ae4bdfdd" +uuid = "8ac3fa9e-de4c-5943-b1dc-09c6b5f20637" +version = "1.4.0" + [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" @@ -556,11 +870,34 @@ git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" version = "1.3.0" +[[deps.LabelledArrays]] +deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "LinearAlgebra", "MacroTools", "PreallocationTools", "RecursiveArrayTools", "StaticArrays"] +git-tree-sha1 = "cd04158424635efd05ff38d5f55843397b7416a9" +uuid = "2ee39098-c373-598a-b85f-a56591580800" +version = "1.14.0" + +[[deps.LambertW]] +git-tree-sha1 = "c5ffc834de5d61d00d2b0e18c96267cffc21f648" +uuid = "984bce1d-4616-540c-a9ee-88d1112d94c9" +version = "0.4.6" + [[deps.Latexify]] -deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "46a39b9c58749eefb5f2dc1178cb8fab5332b1ab" +deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] +git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.15" +version = "0.15.18" + +[[deps.LayoutPointers]] +deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] +git-tree-sha1 = "88b8f66b604da079a627b6fb2860d3704a6729a1" +uuid = "10f19ff3-798f-405d-979b-55457f8fc047" +version = "0.1.14" + +[[deps.Lazy]] +deps = ["MacroTools"] +git-tree-sha1 = "1370f8202dac30758f3c345f9909b97f53d87d3f" +uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" +version = "0.15.1" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -568,17 +905,19 @@ uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" [[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"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" +version = "0.6.3" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" +version = "7.84.0+0" [[deps.LibGit2]] deps = ["Base64", "NetworkOptions", "Printf", "SHA"] @@ -587,6 +926,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" +version = "1.10.2+0" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" @@ -605,9 +945,9 @@ 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"] @@ -617,9 +957,9 @@ 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"] @@ -627,6 +967,12 @@ git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" version = "2.35.0+0" +[[deps.Libtask]] +deps = ["FunctionWrappers", "LRUCache", "LinearAlgebra", "Statistics"] +git-tree-sha1 = "3e893f18b4326ed392b699a4948b30885125d371" +uuid = "6f1fad26-d15e-5dc8-ae53-837a1d7b8c9f" +version = "0.8.5" + [[deps.Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" @@ -639,36 +985,66 @@ git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" version = "2.36.0+0" +[[deps.LineSearches]] +deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] +git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" +uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" +version = "7.2.0" + [[deps.LinearAlgebra]] deps = ["Libdl", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[deps.LinearMaps]] +deps = ["ChainRulesCore", "LinearAlgebra", "SparseArrays", "Statistics"] +git-tree-sha1 = "4af48c3585177561e9f0d24eb9619ad3abf77cc7" +uuid = "7a12625a-238d-50fd-b39a-03d52299707e" +version = "3.10.0" + +[[deps.LogDensityProblems]] +deps = ["ArgCheck", "DocStringExtensions", "Random"] +git-tree-sha1 = "f9a11237204bc137617194d79d813069838fcf61" +uuid = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" +version = "2.1.1" + +[[deps.LogDensityProblemsAD]] +deps = ["DocStringExtensions", "LogDensityProblems", "Requires", "SimpleUnPack"] +git-tree-sha1 = "79b13f322a23844bb026a0586ae7a649bba7c826" +uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" +version = "1.4.1" + [[deps.LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "09e4b894ce6a976c354a69041a04748180d43637" +git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.15" +version = "0.3.23" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "5d4d2d9904227b8bd66386c1138cf4d5ffa826bf" +git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "0.4.9" +version = "1.0.0" + +[[deps.LoopVectorization]] +deps = ["ArrayInterface", "ArrayInterfaceCore", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "SpecialFunctions", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] +git-tree-sha1 = "a282dbdbc2860134d6809acd951543ce359bcf15" +uuid = "bdcacae8-1622-11e9-2a5c-532679323890" +version = "0.12.155" [[deps.MAT]] deps = ["BufferedStreams", "CodecZlib", "HDF5", "SparseArrays"] -git-tree-sha1 = "971be550166fe3f604d28715302b58a3f7293160" +git-tree-sha1 = "6eff5740c8ab02c90065719579c7aa0eb40c9f69" uuid = "23992714-dd62-5051-b70f-ba57cb901cac" -version = "0.10.3" +version = "0.10.4" [[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" +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 = 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+git-tree-sha1 = "6862738f9796b3edc1c09d0890afce4eca9e7e93" uuid = "510215fc-4207-5dde-b226-833fc4488ee2" -version = "0.5.1" +version = "0.5.4" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "1ea784113a6aa054c5ebd95945fa5e52c2f378e7" +git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.7" +version = "1.12.9" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -782,16 +1231,24 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" +version = "0.3.20+0" [[deps.OpenLibm_jll]] 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 = "6503b77492fd7fcb9379bf73cd31035670e3c509" +uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" +version = "1.3.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9a36165cf84cff35851809a40a928e1103702013" +git-tree-sha1 = "9ff31d101d987eb9d66bd8b176ac7c277beccd09" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.16+0" +version = "1.1.20+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -799,6 +1256,12 @@ git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" +[[deps.Optimisers]] +deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] +git-tree-sha1 = "e5a1825d3d53aa4ad4fb42bd4927011ad4a78c3d" +uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" +version = "0.2.15" + [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" @@ -806,27 +1269,37 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.2+0" [[deps.OrderedCollections]] -git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" +git-tree-sha1 = "d78db6df34313deaca15c5c0b9ff562c704fe1ab" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.4.1" +version = "1.5.0" -[[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"] -git-tree-sha1 = "ca433b9e2f5ca3a0ce6702a032fce95a3b6e1e48" +git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.14" +version = "0.11.17" + +[[deps.Parameters]] +deps = ["OrderedCollections", "UnPack"] +git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" +uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" +version = "0.12.3" [[deps.Parsers]] -deps = ["Dates"] -git-tree-sha1 = "0044b23da09b5608b4ecacb4e5e6c6332f833a7e" +deps = ["Dates", "SnoopPrecompile"] +git-tree-sha1 = "478ac6c952fddd4399e71d4779797c538d0ff2bf" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.3.2" +version = "2.5.8" + +[[deps.Pipe]] +git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" +uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" +version = "1.3.0" [[deps.Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -837,24 +1310,37 @@ version = "0.40.1+0" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" +version = "1.8.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "8162b2f8547bc23876edd0c5181b27702ae58dce" +git-tree-sha1 = 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"79830c17fe30f234931767238c584b3a75b3329d" +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 = "f49a45a239e13333b8b936120fe6d793fe58a972" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.31.6" +version = "1.38.8" + +[[deps.Polyester]] +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "0fe4e7c4d8ff4c70bfa507f0dd96fa161b115777" +uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" +version = "0.7.3" + +[[deps.PolyesterWeave]] +deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] +git-tree-sha1 = "240d7170f5ffdb285f9427b92333c3463bf65bf6" +uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" +version = "0.2.1" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] @@ -862,6 +1348,12 @@ git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" version = "1.4.2" +[[deps.PreallocationTools]] +deps = ["Adapt", "ArrayInterface", "ForwardDiff", "Requires"] +git-tree-sha1 = "f739b1b3cc7b9949af3b35089931f2b58c289163" +uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" +version = "0.4.12" + [[deps.Preferences]] deps = ["TOML"] git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" @@ -869,10 +1361,16 @@ uuid = "21216c6a-2e73-6563-6e65-726566657250" version = "1.3.0" [[deps.PrettyTables]] -deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"] -git-tree-sha1 = 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"IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" +git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.7.0" +version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" +version = "1.10.1" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1118,37 +1754,105 @@ git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" version = "0.1.1" +[[deps.TermInterface]] +git-tree-sha1 = "7aa601f12708243987b88d1b453541a75e3d8c7a" +uuid = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c" +version = "0.2.3" + [[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"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[deps.TextWrap]] +git-tree-sha1 = "9250ef9b01b66667380cf3275b3f7488d0e25faf" +uuid = "b718987f-49a8-5099-9789-dcd902bef87d" +version = "1.0.1" + +[[deps.ThreadingUtilities]] +deps = ["ManualMemory"] +git-tree-sha1 = "c97f60dd4f2331e1a495527f80d242501d2f9865" +uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" +version = "0.5.1" + +[[deps.ThreadsX]] +deps = ["ArgCheck", "BangBang", "ConstructionBase", "InitialValues", "MicroCollections", "Referenceables", "Setfield", "SplittablesBase", "Transducers"] +git-tree-sha1 = "34e6bcf36b9ed5d56489600cf9f3c16843fa2aa2" +uuid = "ac1d9e8a-700a-412c-b207-f0111f4b6c0d" +version = "0.1.11" + +[[deps.TimerOutputs]] +deps = ["ExprTools", "Printf"] +git-tree-sha1 = "f2fd3f288dfc6f507b0c3a2eb3bac009251e548b" +uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" +version = "0.5.22" + +[[deps.Tracker]] +deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] +git-tree-sha1 = "77817887c4b414b9c6914c61273910e3234eb21c" +uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" +version = "0.2.23" + [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" +git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.6" +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 = "c76399a3bbe6f5a88faa33c8f8a65aa631d95013" +git-tree-sha1 = "c42fa452a60f022e9e087823b47e5a5f8adc53d5" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.73" +version = "0.4.75" + +[[deps.TreeViews]] +deps = ["Test"] +git-tree-sha1 = "8d0d7a3fe2f30d6a7f833a5f19f7c7a5b396eae6" +uuid = "a2a6695c-b41b-5b7d-aed9-dbfdeacea5d7" +version = "0.3.0" + +[[deps.TriangularSolve]] +deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] +git-tree-sha1 = "31eedbc0b6d07c08a700e26d31298ac27ef330eb" +uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" +version = "0.1.19" + +[[deps.Tricks]] +git-tree-sha1 = "aadb748be58b492045b4f56166b5188aa63ce549" +uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" +version = "0.1.7" + +[[deps.TruncatedStacktraces]] +deps = ["InteractiveUtils", "MacroTools", "Preferences"] +git-tree-sha1 = "7bc1632a4eafbe9bd94cf1a784a9a4eb5e040a91" +uuid = "781d530d-4396-4725-bb49-402e4bee1e77" +version = "1.3.0" + +[[deps.Turing]] +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "Setfield", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker"] +git-tree-sha1 = "bc3e1000da9d84aca4f8ed66cc1dd59b3f793760" +uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" +version = "0.24.3" [[deps.URIs]] -git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355" +git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.3.0" +version = "1.4.2" [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" +[[deps.UnPack]] +git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" +uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" +version = "1.0.2" + [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" @@ -1159,15 +1863,21 @@ uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" [[deps.Unzip]] -git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" +git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" -version = "0.1.2" +version = "0.2.0" + +[[deps.VectorizationBase]] +deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] +git-tree-sha1 = "f78fc4c3abbf5ab65108a41664e88fb131ab8946" +uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" +version = "0.21.63" [[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"] @@ -1193,11 +1903,16 @@ git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3" uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "0.5.5" +[[deps.WorkerUtilities]] +git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7" +uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" +version = "1.6.1" + [[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"] @@ -1334,18 +2049,37 @@ version = "1.4.0+3" [[deps.Zlib_jll]] deps = ["Libdl"] 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.Zygote]] +deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "Requires", "SnoopPrecompile", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] +git-tree-sha1 = "4df8f470806a45a8630ac8f597304821dc8e8838" +uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" +version = "0.6.59" [[deps.ZygoteRules]] -deps = ["MacroTools"] -git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" +deps = ["ChainRulesCore", "MacroTools"] +git-tree-sha1 = "977aed5d006b840e2e40c0b48984f7463109046d" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.2" +version = "0.2.3" + +[[deps.fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.29.0+0" + +[[deps.libaom_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" +uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" +version = "3.4.0+0" [[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1356,6 +2090,7 @@ version = "0.15.1+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.1.1+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1378,10 +2113,12 @@ version = "1.3.7+1" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.48.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1397,6 +2134,6 @@ version = "3.5.0+0" [[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" +git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "0.9.1+5" +version = "1.4.1+0" diff --git a/scripts/Project.toml b/scripts/Project.toml index 4098d9b..61146c5 100644 --- a/scripts/Project.toml +++ b/scripts/Project.toml @@ -2,13 +2,19 @@ CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" +DifferenceEquations = "e0ca9c66-1f9e-11ec-127a-1304ce62169c" +DifferentiableStateSpaceModels = "beacd9db-9e5e-4956-9b09-459a4b2028df" +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" +HMCExamples = "04c4e5f0-d543-11eb-2b99-3f716ccaf3f5" JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" MAT = "23992714-dd62-5051-b70f-ba57cb901cac" MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" MCMCChainsStorage = "51a256e2-afd8-4c38-88d8-a98ba8ad53ca" Measures = "442fdcdd-2543-5da2-b0f3-8c86c306513e" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" +SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b" diff --git a/scripts/rbc_sv_replication/statplots.jl b/scripts/rbc_sv_replication/statplots.jl index 907afa4..4221306 100644 --- a/scripts/rbc_sv_replication/statplots.jl +++ b/scripts/rbc_sv_replication/statplots.jl @@ -1,4 +1,8 @@ using HDF5, MCMCChains, MCMCChainsStorage, CSV, DataFrames, StatsPlots, Measures, Dates +using HMCExamples, DifferentiableStateSpaceModels, DifferenceEquations, Random, Distributions, RecursiveArrayTools + + +Random.seed!(0) # fix a seed for reproducibility function generate_plots() println("generating plots") @@ -19,32 +23,63 @@ function generate_plots() density_plot = density(chain_joint_1[include_vars], left_margin = 20mm, top_margin = 5mm, bottom_margin = 10mm, label = "NUTS, joint") vline!(density_plot, pseudotrues, linestyle = :dash, color = :black, label = "", legend = :outertopright, size = (600, 1000)) savefig(density_plot, ".figures/densityplots_rbc_sv.png") - + for (batch, chain) in [("2_joint", chain_joint_1)] - # epsilons + # time series plots + + m = PerturbationModel(HMCExamples.rbc_sv) + p_f = nothing + T = 200 + symbol_to_int(s) = parse(Int, replace(string(s), "ϵ_draw["=>"", "]"=>"")) - ϵ_chain = sort(chain[:, [Symbol("ϵ_draw[$a]") for a in 1:201], 1], lt = (x,y) -> symbol_to_int(x) < symbol_to_int(y)) - tmp = describe(ϵ_chain) - ϵ_mean = tmp[1][:, 2] - ϵ_std = tmp[1][:, 3] + ϵ_chain = sort(chain[:, [Symbol("ϵ_draw[$a]") for a in 1:2:401], 1], lt = (x,y) -> symbol_to_int(x) < symbol_to_int(y)) + ϵ_stats = describe(ϵ_chain) + ϵ_data = hcat(get_params(ϵ_chain[:, :, 1]).ϵ_draw...) + ϵ_mean = ϵ_stats[1][:, 2] + ϵ_std = ϵ_stats[1][:, 3] + + vol_chain = sort(chain[:, [Symbol("ϵ_draw[$a]") for a in 2:2:402], 1], lt = (x,y) -> symbol_to_int(x) < symbol_to_int(y)) + vol_stats = describe(vol_chain) + vol_data = hcat(get_params(vol_chain[:, :, 1]).ϵ_draw...) + vol_mean = vol_stats[1][:, 2] + vol_std = vol_stats[1][:, 3] + + p_data = get_params(chain[include_vars]) + num_samples = size(chain)[1] + save_zlag = zeros(num_samples, T+1) + save_ν = zeros(num_samples, T+1) - # Import the true shock values - ϵ_true = Matrix(DataFrame(CSV.File("data/rbc_sv_$(batch)_shocks.csv")))' + for i in 1:num_samples + p_d = (; α=p_data.α[i], β=1 / (p_data.β_draw[i] / 100 + 1), ρ=p_data.ρ[i], δ=0.025, σ=0.01, Ω_1=0.01, ρ_σ=0.5, μ_σ=1.0, σ_σ=0.1) + mod_perturb = generate_perturbation(m, p_d, p_f, Val(2)) + x0 = rand(MvNormal(mod_perturb.x_ergodic_var)) + prob = QuadraticStateSpaceProblem(mod_perturb, x0, (0, T); noise=vcat(ϵ_data[i:i, 2:end], vol_data[i:i, 2:end]), observables_noise = nothing) + sol = solve(prob, DirectIteration()) + u_vec = VectorOfArray(sol.u) + save_zlag[i, :] = u_vec[2, :] + save_ν[i, :] = u_vec[3, :] + end + + # Import the true values + shock_true = Matrix(DataFrame(CSV.File("data/rbc_sv_$(batch)_shocks.csv")))' + latent_true = Matrix(DataFrame(CSV.File("data/rbc_sv_$(batch)_latents.csv")))' # Plot and save ϵ_plot = plot(ϵ_mean[2:end], ribbon=2 * ϵ_std[2:end], label="Posterior mean") - ϵ_plot = plot!(ϵ_true[1, :], label="True values") + ϵ_plot = plot!(shock_true[1, :], label="True values") savefig(ϵ_plot, ".figures/epsilons_rbc_sv_$(batch).png") - ϵ_chain = sort(chain[:, [Symbol("ϵ_draw[$a]") for a in 202:402], 1], lt = (x,y) -> symbol_to_int(x) < symbol_to_int(y)) - tmp = describe(ϵ_chain) - ϵ_mean = tmp[1][:, 2] - ϵ_std = tmp[1][:, 3] + vol_plot = plot(vol_mean[2:end], ribbon=2 * vol_std[2:end], label="Posterior mean") + vol_plot = plot!(shock_true[2, :], label="True values") + savefig(vol_plot, ".figures/volshocks_rbc_sv_$(batch).png") - # Plot and save - ϵ_plot = plot(ϵ_mean[2:end], ribbon=2 * ϵ_std[2:end], label="Posterior mean") - ϵ_plot = plot!(ϵ_true[2, :], label="True values") - savefig(ϵ_plot, ".figures/volshocks_rbc_sv_$(batch).png") + zlag_plot = plot(vec(mean(save_zlag, dims = 1)), ribbon=2 * vec(std(save_zlag, dims = 1)), label="Posterior mean") + zlag_plot = plot!(latent_true[1, :], label="True values") + savefig(zlag_plot, ".figures/zlag_rbc_sv_$(batch).png") + + ν_plot = plot(vec(mean(save_ν, dims = 1)), ribbon=2 * vec(std(save_ν, dims = 1)), label="Posterior mean") + ν_plot = plot!(latent_true[2, :], label="True values") + savefig(ν_plot, ".figures/nu_rbc_sv_$(batch).png") end println(" plots complete")