diff --git a/16-Chapter 16. Generalized Linear Madness.ipynb b/16-Chapter 16. Generalized Linear Madness.ipynb index 35438b8..cdabddc 100644 --- a/16-Chapter 16. Generalized Linear Madness.ipynb +++ b/16-Chapter 16. Generalized Linear Madness.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": 1, - "id": "866289f6", + "id": "729a30eb", "metadata": {}, "outputs": [], "source": [ @@ -26,7 +26,7 @@ }, { "cell_type": "markdown", - "id": "3caad2f4", + "id": "ed60b20c", "metadata": {}, "source": [ "# 16.1 Geometric people" @@ -34,7 +34,7 @@ }, { "cell_type": "markdown", - "id": "48ce8a44", + "id": "2cd52dfb", "metadata": {}, "source": [ "Code 16.1" @@ -43,7 +43,7 @@ { "cell_type": "code", "execution_count": 2, - "id": "783b9793", + "id": "8bb62561", "metadata": {}, "outputs": [], "source": [ @@ -54,7 +54,7 @@ }, { "cell_type": "markdown", - "id": "8900d312", + "id": "81cbb4d8", "metadata": {}, "source": [ "Code 16.2" @@ -63,7 +63,7 @@ { "cell_type": "code", "execution_count": 3, - "id": "93fe79fe", + "id": "464a86cb", "metadata": {}, "outputs": [], "source": [ @@ -82,7 +82,7 @@ }, { "cell_type": "markdown", - "id": "521cbd88", + "id": "d9fd7f66", "metadata": {}, "source": [ "Code 16.3" @@ -91,7 +91,7 @@ { "cell_type": "code", "execution_count": 4, - "id": "11d92732", + "id": "05618520", "metadata": {}, "outputs": [ { @@ -100,643 +100,643 @@ "\n", "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - 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"\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", - "\n", - "\n", - "\n" ] }, "execution_count": 14, @@ -2216,7 +2378,7 @@ }, { "cell_type": "markdown", - "id": "66717d41", + "id": "9c1475de", "metadata": {}, "source": [ "Code 16.14" @@ -2225,7 +2387,7 @@ { "cell_type": "code", "execution_count": 15, - "id": "321e657f", + "id": "463d111c", "metadata": {}, "outputs": [ { @@ -2259,7 +2421,7 @@ }, { "cell_type": "markdown", - "id": "a9962efa", + "id": "22a1b326", "metadata": {}, "source": [ "Code 16.15" @@ -2268,7 +2430,7 @@ { "cell_type": "code", "execution_count": 16, - "id": "97ed12d5", + "id": "8e19615f", "metadata": {}, "outputs": [ { @@ -2277,87 +2439,87 @@ "\n", "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", "\n", - " \n", + " \n", " \n", " \n", "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - " 0.0) && all(μ_h .> 0.0)\n", + " logμ_l = log.(μ_l)\n", + " logμ_h = log.(μ_h)\n", + " @. L ~ LogNormal(logμ_l, σ_l)\n", + " @. H ~ LogNormal(logμ_h, σ_h)\n", + " else\n", + " Turing.@addlogprob! -Inf\n", + " end\n", + " end\n", + "end" + ] + }, + { + "cell_type": "markdown", + "id": "9e3d91a2", + "metadata": {}, + "source": [ + "Code 16.18" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "b4745c34", + "metadata": {}, + "outputs": [], + "source": [ + "Random.seed!(1)\n", + "m16_5_ch = sample(lynx_hare_model(nrow(d), d.Lynx, d.Hare), NUTS(), 4000)\n", + "m16_5_df = DataFrame(m16_5_ch);" + ] + }, + { + "cell_type": "markdown", + "id": "2a2ceb82", + "metadata": {}, + "source": [ + "Code 16.19" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b422c3cc", + "metadata": {}, + "outputs": [], + "source": [ + "# from row of parameters, get population of Hare and Lynx\n", + "function row_to_population(r, N)\n", + " LH₁ = [r.l₁, r.h₁]\n", + " θ = [r.b_h, r.m_h, r.b_l, r.m_l]\n", + " prob = ODEProblem(lynx_hare!, LH₁, N-1, θ)\n", + " sol = solve(prob, saveat=1)\n", + " L = map(first, sol.u[1:N])\n", + " H = map(last, sol.u[1:N])\n", + " L, H\n", + "end\n", + "\n", + "p = plot(xlab=\"year\", ylab=\"thousands of pelts\")\n", + "plot!(d.Year, d.Hare, lw=1.5, c=:black, lab=\"Lepus\")\n", + "scatter!(d.Year, d.Hare, c=:black)\n", + "plot!(d.Year, d.Lynx, lw=1.5, c=:blue, lab=\"Lynx\")\n", + "scatter!(d.Year, d.Lynx, c=:blue)\n", + "\n", + "for r in first(eachrow(m16_5_df), 21)\n", + " L, H = row_to_population(r, nrow(d))\n", + " L .*= r.p_l\n", + " H .*= r.p_h\n", + " \n", + " plot!(d.Year, L, c=:blue, alpha=0.2)\n", + " plot!(d.Year, H, c=:black, alpha=0.2)\n", + "end\n", + "p" + ] + }, + { + "cell_type": "markdown", + "id": "cdf31d04", + "metadata": {}, + "source": [ + "Code 16.20" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b2d44ac9", + "metadata": {}, + "outputs": [], + "source": [ + "p = plot(xlab=\"year\", ylab=\"thousands animals\")\n", + "\n", + "for r in first(eachrow(m16_5_df), 21)\n", + " L, H = row_to_population(r, nrow(d))\n", + " plot!(d.Year, L, c=:blue, alpha=0.2)\n", + " plot!(d.Year, H, c=:black, alpha=0.2)\n", + "end\n", + "p" + ] + }, { "cell_type": "code", "execution_count": null, - "id": "55d3bc02", + "id": "daabc782", "metadata": {}, "outputs": [], "source": [] diff --git a/17-Chapter 17. Horoscopes.ipynb b/17-Chapter 17. Horoscopes.ipynb new file mode 100644 index 0000000..d47f1c7 --- /dev/null +++ b/17-Chapter 17. Horoscopes.ipynb @@ -0,0 +1,35 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "1d0ee6bb", + "metadata": {}, + "source": [ + "No code in this chapter!" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a5ff8c72", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Julia 1.6.4", + "language": "julia", + "name": "julia-1.6" + }, + "language_info": { + "file_extension": ".jl", + "mimetype": "application/julia", + "name": "julia", + "version": "1.6.4" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/Manifest.toml b/Manifest.toml index ee70375..d1175f0 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -36,15 +36,15 @@ version = "3.3.3" [[AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "Setfield", "Statistics", "StatsBase", "StatsFuns", "UnPack"] -git-tree-sha1 = "189473a73d664fe2496675775b6c8a732b8dfe26" +git-tree-sha1 = "345effa84030f273ee86fcdd706d8484ce9a1a3c" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.3.3" +version = "0.3.5" [[AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "Random", "Requires"] -git-tree-sha1 = "8ad8bfddf8bb627d689ecb91599c349cbf15e971" +git-tree-sha1 = "5d9e09a242d4cf222080398468244389c3428ed1" uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -version = "0.6.6" +version = "0.6.7" [[AdvancedPS]] deps = ["AbstractMCMC", "Distributions", "Libtask", "Random", "StatsFuns"] @@ -54,9 +54,9 @@ version = "0.2.4" [[AdvancedVI]] deps = ["Bijectors", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "130d6b17a3a9d420d9a6b37412cae03ffd6a64ff" +git-tree-sha1 = "e743af305716a527cdb3a67b31a33a7c3832c41f" uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" -version = "0.1.3" +version = "0.1.5" [[ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -86,9 +86,27 @@ version = "3.5.0+3" [[ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "745233d77146ad221629590b6d82fe7f1ddb478f" +git-tree-sha1 = "81f0cb60dc994ca17f68d9fb7c942a5ae70d9ee4" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "4.0.3" +version = "5.0.8" + +[[ArrayInterfaceCore]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "5961f98d226063f2823e0f1b85999e0f0c260127" +uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" +version = "0.1.1" + +[[ArrayInterfaceStaticArrays]] +deps = ["Adapt", "ArrayInterface", "LinearAlgebra", "Static", "StaticArrays"] +git-tree-sha1 = "8973a450b9963b6f5c7a85773d9ddb305ea8c2ac" +uuid = "b0d46f97-bff5-4637-a19a-dd75974142cd" +version = "0.1.1" + +[[ArrayLayouts]] +deps = ["FillArrays", "LinearAlgebra", "SparseArrays"] +git-tree-sha1 = "56c347caf09ad8acb3e261fe75f8e09652b7b05b" +uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" +version = "0.7.10" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -101,9 +119,9 @@ version = "1.0.1" [[AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] -git-tree-sha1 = "d127d5e4d86c7680b20c35d40b503c74b9a39b5e" +git-tree-sha1 = "cf6875678085aed97f52bfc493baaebeb6d40bcb" uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" -version = "0.4.4" +version = "0.4.5" [[AxisKeys]] deps = ["AbstractFFTs", "ChainRulesCore", "CovarianceEstimation", "IntervalSets", "InvertedIndices", "LazyStack", "LinearAlgebra", "NamedDims", "OffsetArrays", "Statistics", "StatsBase", "Tables"] @@ -117,11 +135,17 @@ git-tree-sha1 = "54308218333f6b8967311c76f2cf89ab495542d6" uuid = "488c2830-172b-11e9-1591-253b8a7df96d" version = "0.3.2" +[[BandedMatrices]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "019aa88766e2493c59cbd0a9955e1bac683ffbcd" +uuid = "aae01518-5342-5314-be14-df237901396f" +version = "0.16.13" + [[BangBang]] deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] -git-tree-sha1 = "d648adb5e01b77358511fb95ea2e4d384109fac9" +git-tree-sha1 = "b15a6bc52594f5e4a3b825858d1089618871bf9d" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.35" +version = "0.3.36" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -145,9 +169,15 @@ version = "0.9.11" [[BitTwiddlingConvenienceFunctions]] deps = ["Static"] -git-tree-sha1 = "5e98d6a6aa92e5758c4d58501b7bf23732699fa3" +git-tree-sha1 = "28bbdbf0354959db89358d1d79d421ff31ef0b5e" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" -version = "0.1.2" +version = "0.1.3" + +[[BoundaryValueDiffEq]] +deps = ["BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NLsolve", "Reexport", "SparseArrays"] +git-tree-sha1 = "fe34902ac0c3a35d016617ab7032742865756d7d" +uuid = "764a87c0-6b3e-53db-9096-fe964310641d" +version = "2.7.1" [[Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -155,11 +185,16 @@ git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+0" +[[CEnum]] +git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" +uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" +version = "0.4.2" + [[CPUSummary]] -deps = ["Hwloc", "IfElse", "Static"] -git-tree-sha1 = "849799453de85b55e78550fc7b0c8f442eb497ab" +deps = ["CpuId", "IfElse", "Static"] +git-tree-sha1 = "0eaf4aedad5ccc3e39481db55d72973f856dc564" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.1.8" +version = "0.1.22" [[CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings"] @@ -175,27 +210,33 @@ version = "1.16.1+1" [[CategoricalArrays]] deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] -git-tree-sha1 = "c308f209870fdbd84cb20332b6dfaf14bf3387f8" +git-tree-sha1 = "109664d3a6f2202b1225478335ea8fea3cd8706b" uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" -version = "0.10.2" +version = "0.10.5" [[ChainRules]] deps = ["ChainRulesCore", "Compat", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics"] -git-tree-sha1 = "098b5eeb1170f569a45f363066b0e405868fc210" +git-tree-sha1 = "c03a0bc97fb045e417fe35a4533e6135b59babdc" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.27.0" +version = "1.34.0" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "c9a6160317d1abe9c44b3beb367fd448117679ca" +git-tree-sha1 = "9950387274246d08af38f6eef8cb5480862a435f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.13.0" +version = "1.14.0" [[ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" +git-tree-sha1 = "1e315e3f4b0b7ce40feded39c73049692126cf53" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.2" +version = "0.1.3" + +[[CloseOpenIntervals]] +deps = ["ArrayInterface", "Static"] +git-tree-sha1 = "c892b6671c36d64a4e3caf70ffd57f9d24f4117a" +uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" +version = "0.1.7" [[Clustering]] deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "SparseArrays", "Statistics", "StatsBase"] @@ -210,10 +251,10 @@ uuid = "944b1d66-785c-5afd-91f1-9de20f533193" version = "0.7.0" [[ColorSchemes]] -deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] -git-tree-sha1 = "12fc73e5e0af68ad3137b886e3f7c1eacfca2640" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random"] +git-tree-sha1 = "7297381ccb5df764549818d9a7d57e45f1057d30" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.17.1" +version = "3.18.0" [[ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -221,6 +262,12 @@ git-tree-sha1 = "32a2b8af383f11cbb65803883837a149d10dfe8a" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" version = "0.10.12" +[[ColorVectorSpace]] +deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] +git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322" +uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" +version = "0.9.9" + [[Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" @@ -245,9 +292,9 @@ version = "0.3.0" [[Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "44c37b4636bc54afac5c574d2d02b625349d6582" +git-tree-sha1 = "b153278a25dd42c65abbf4e62344f9d22e59191b" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.41.0" +version = "3.43.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -294,11 +341,23 @@ git-tree-sha1 = "a3e070133acab996660d31dcf479ea42849e368f" uuid = "587fd27a-f159-11e8-2dae-1979310e6154" version = "0.2.7" +[[CpuId]] +deps = ["Markdown"] +git-tree-sha1 = "32d125af0fb8ec3f8935896122c5e345709909e5" +uuid = "adafc99b-e345-5852-983c-f28acb93d879" +version = "0.3.0" + [[Crayons]] git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" +[[DEDataArrays]] +deps = ["ArrayInterface", "DocStringExtensions", "LinearAlgebra", "RecursiveArrayTools", "SciMLBase", "StaticArrays"] +git-tree-sha1 = "5e5f8f363c8c9a2415ef9185c4e0ff6966c87d52" +uuid = "754358af-613d-5f8d-9788-280bf1605d4c" +version = "0.2.2" + [[Dagitty]] deps = ["BenchmarkTools", "Combinatorics", "Compose", "DataStructures", "Documenter", "GraphPlot", "LightGraphs", "Test"] git-tree-sha1 = "f67d4a7d311ac2498ce6e178e22a3bd6b06ef6d6" @@ -308,9 +367,9 @@ uuid = "d56128e0-8113-48cd-82a0-fc808dc30d4b" version = "0.0.1" [[DataAPI]] -git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" +git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.9.0" +version = "1.10.0" [[DataFrames]] deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] @@ -320,9 +379,9 @@ version = "1.3.1" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "3daef5523dd2e769dad2365274f760ff5f282c7d" +git-tree-sha1 = "cc1a8e22627f33c789ab60b36a9132ac050bbf75" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.11" +version = "0.18.12" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -344,6 +403,12 @@ git-tree-sha1 = "0fba8b706d0178b4dc7fd44a96a92382c9065c2c" uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52" version = "0.1.2" +[[DelayDiffEq]] +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "UnPack"] +git-tree-sha1 = "cdd2b2a7d8b48bb0d5628838322c539c56d7b59e" +uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" +version = "5.36.0" + [[DelimitedFiles]] deps = ["Mmap"] uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" @@ -354,6 +419,30 @@ git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" +[[DiffEqBase]] +deps = ["ArrayInterfaceCore", "ChainRulesCore", "DEDataArrays", "DataStructures", "Distributions", "DocStringExtensions", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "IterativeSolvers", "LabelledArrays", "LinearAlgebra", "Logging", "MuladdMacro", "NonlinearSolve", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "StaticArrays", "Statistics", "SuiteSparse", "ZygoteRules"] +git-tree-sha1 = "9f3bddf45d0dcb21ed0957a71ae545daeb27683c" +uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" +version = "6.87.0" + +[[DiffEqCallbacks]] +deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "NLsolve", "OrdinaryDiffEq", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArrays"] +git-tree-sha1 = "c4b99e3a199e293e7290eea94ba89364d47ee557" +uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" +version = "2.22.0" + +[[DiffEqJump]] +deps = ["ArrayInterfaceCore", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "StaticArrays", "TreeViews", "UnPack"] +git-tree-sha1 = "08e1f6a916dafd14e731d40e6c28633a2aaae512" +uuid = "c894b116-72e5-5b58-be3c-e6d8d4ac2b12" +version = "8.5.0" + +[[DiffEqNoiseProcess]] +deps = ["DiffEqBase", "Distributions", "GPUArrays", "LinearAlgebra", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArrays", "Statistics"] +git-tree-sha1 = "915286127c88b9306e29229cde687d46196f4060" +uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" +version = "5.11.0" + [[DiffResults]] deps = ["StaticArrays"] git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805" @@ -362,9 +451,15 @@ version = "1.0.3" [[DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "dd933c4ef7b4c270aacd4eb88fa64c147492acf0" +git-tree-sha1 = "28d605d9a0ac17118fe2c5e9ce0fbb76c3ceb120" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.10.0" +version = "1.11.0" + +[[DifferentialEquations]] +deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqJump", "DiffEqNoiseProcess", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] +git-tree-sha1 = "3f3db9365fedd5fdbecebc3cce86dfdfe5c43c50" +uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" +version = "7.1.0" [[Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] @@ -396,9 +491,9 @@ version = "0.8.6" [[Documenter]] deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "75c6cf9d99e0efc79b724f5566726ad3ad010a01" +git-tree-sha1 = "122d031e8dcb2d3e767ed434bc4d1ae1788b5a7f" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.12" +version = "0.27.17" [[Downloads]] deps = ["ArgTools", "LibCURL", "NetworkOptions"] @@ -418,21 +513,27 @@ version = "2.2.3+0" [[EllipsisNotation]] deps = ["ArrayInterface"] -git-tree-sha1 = "d7ab55febfd0907b285fbf8dc0c73c0825d9d6aa" +git-tree-sha1 = "03b753748fd193a7f2730c02d880da27c5a24508" uuid = "da5c29d0-fa7d-589e-88eb-ea29b0a81949" -version = "1.3.0" +version = "1.6.0" [[EllipticalSliceSampling]] deps = ["AbstractMCMC", "ArrayInterface", "Distributions", "Random", "Statistics"] -git-tree-sha1 = "c25a7254cf745720ddf9051cd0d2792b3baaca0e" +git-tree-sha1 = "0fc0579126b6623857dda209746fe149883c00a7" uuid = "cad2338a-1db2-11e9-3401-43bc07c9ede2" -version = "0.4.6" +version = "0.4.7" [[Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ae13fcbc7ab8f16b0856729b050ef0c446aa3492" +git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.4.4+0" +version = "2.4.8+0" + +[[ExponentialUtilities]] +deps = ["ArrayInterfaceCore", "GPUArrays", "GenericSchur", "LinearAlgebra", "Printf", "SparseArrays", "libblastrampoline_jll"] +git-tree-sha1 = "2a0f80d722d7c5d94ab29c76eefbed79ded3a696" +uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" +version = "1.17.0" [[ExprTools]] git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" @@ -453,9 +554,9 @@ version = "4.4.0+0" [[FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "463cb335fa22c4ebacfd1faba5fde14edb80d96c" +git-tree-sha1 = "505876577b5481e50d089c1c68899dfb6faebc62" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.4.5" +version = "1.4.6" [[FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -463,17 +564,28 @@ git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" version = "3.3.10+0" +[[FastBroadcast]] +deps = ["LinearAlgebra", "Polyester", "Static"] +git-tree-sha1 = "b6bf57ec7a3f294c97ae46124705a9e6b906a209" +uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" +version = "0.1.15" + +[[FastClosures]] +git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" +uuid = "9aa1b823-49e4-5ca5-8b0f-3971ec8bab6a" +version = "0.3.2" + [[FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "80ced645013a5dbdc52cf70329399c35ce007fae" +git-tree-sha1 = "9267e5f50b0e12fdfd5a2455534345c4cf2c7f7a" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.13.0" +version = "1.14.0" [[FilePathsBase]] deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] -git-tree-sha1 = "04d13bfa8ef11720c24e4d840c0033d145537df7" +git-tree-sha1 = "129b104185df66e408edd6625d480b7f9e9823a0" uuid = "48062228-2e41-5def-b9a4-89aafe57970f" -version = "0.9.17" +version = "0.9.18" [[FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" @@ -485,10 +597,10 @@ uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" version = "0.12.8" [[FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "ec299fdc8f49ae450807b0cb1d161c6b76fd2b60" +deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] +git-tree-sha1 = "4fc79c0f63ddfdcdc623a8ce36623346a7ce9ae4" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.10.1" +version = "2.12.0" [[FixedPointNumbers]] deps = ["Statistics"] @@ -510,9 +622,9 @@ version = "0.4.2" [[ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "1bd6fc0c344fc0cbee1f42f8d2e7ec8253dda2d2" +git-tree-sha1 = "2f18915445b248731ec5db4e4a17e451020bf21e" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.25" +version = "0.10.30" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -532,6 +644,11 @@ git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91" uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.10+0" +[[FunctionWrappers]] +git-tree-sha1 = "241552bc2209f0fa068b6415b1942cc0aa486bcc" +uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" +version = "1.1.2" + [[Functors]] git-tree-sha1 = "223fffa49ca0ff9ce4f875be001ffe173b2b7de4" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" @@ -553,6 +670,12 @@ git-tree-sha1 = "f564ce4af5e79bb88ff1f4488e64363487674278" uuid = "38e38edf-8417-5370-95a0-9cbb8c7f171a" version = "1.5.1" +[[GPUArrays]] +deps = ["Adapt", "LLVM", "LinearAlgebra", "Printf", "Random", "Serialization", "Statistics"] +git-tree-sha1 = "c783e8883028bf26fb05ed4022c450ef44edd875" +uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" +version = "8.3.2" + [[GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] git-tree-sha1 = "30f2b340c2fff8410d89bfcdc9c0a6dd661ac5f7" @@ -561,15 +684,21 @@ version = "0.62.1" [[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 = "a6c850d77ad5118ad3be4bd188919ce97fffac47" +git-tree-sha1 = "1e5490a51b4e9d07e8b04836f6008f46b48aaa87" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.64.0+0" +version = "0.64.3+0" + +[[GenericSchur]] +deps = ["LinearAlgebra", "Printf"] +git-tree-sha1 = "fb69b2a645fa69ba5f474af09221b9308b160ce6" +uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" +version = "0.5.3" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "58bcdf5ebc057b085e58d95c138725628dd7453c" +git-tree-sha1 = "83ea630384a13fc4f002b77690bc0afeb4255ac9" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.4.1" +version = "0.4.2" [[Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -595,6 +724,12 @@ git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" version = "1.3.14+0" +[[Graphs]] +deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] +git-tree-sha1 = "57c021de207e234108a6f1454003120a1bf350c4" +uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" +version = "1.6.0" + [[Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" @@ -614,21 +749,9 @@ version = "2.8.1+1" [[HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "3965a3216446a6b020f0d48f1ba94ef9ec01720d" +git-tree-sha1 = "18be5268cf415b5e27f34980ed25a7d34261aa83" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.6" - -[[Hwloc]] -deps = ["Hwloc_jll"] -git-tree-sha1 = "92d99146066c5c6888d5a3abc871e6a214388b91" -uuid = "0e44f5e4-bd66-52a0-8798-143a42290a1d" -version = "2.0.0" - -[[Hwloc_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d8bccde6fc8300703673ef9e1383b11403ac1313" -uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.7.0+0" +version = "0.1.7" [[IJulia]] deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"] @@ -686,21 +809,21 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[Interpolations]] deps = ["AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "b15fc0a95c564ca2e0a7ae12c1f095ca848ceb31" +git-tree-sha1 = "b7bc05649af456efc75d178846f47006c2c4c3c7" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.13.5" +version = "0.13.6" [[IntervalSets]] deps = ["Dates", "EllipsisNotation", "Statistics"] -git-tree-sha1 = "3cc368af3f110a767ac786560045dceddfc16758" +git-tree-sha1 = "bcf640979ee55b652f3b01650444eb7bbe3ea837" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.5.3" +version = "0.5.4" [[InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "a7254c0acd8e62f1ac75ad24d5db43f5f19f3c65" +git-tree-sha1 = "336cc738f03e069ef2cac55a104eb823455dca75" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.2" +version = "0.1.4" [[InvertedIndices]] git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" @@ -717,6 +840,12 @@ git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" version = "1.4.0" +[[IterativeSolvers]] +deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"] +git-tree-sha1 = "1169632f425f79429f245113b775a0e3d121457c" +uuid = "42fd0dbc-a981-5370-80f2-aaf504508153" +version = "0.9.2" + [[IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" @@ -740,18 +869,54 @@ git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" version = "2.1.2+0" +[[KLU]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] +git-tree-sha1 = "cae5e3dfd89b209e01bcd65b3a25e74462c67ee0" +uuid = "ef3ab10e-7fda-4108-b977-705223b18434" +version = "0.3.0" + [[KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] git-tree-sha1 = "591e8dc09ad18386189610acafb970032c519707" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" version = "0.6.3" +[[Krylov]] +deps = ["LinearAlgebra", "Printf", "SparseArrays"] +git-tree-sha1 = "13b16b00144816211cbf92823ded6042490eb009" +uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" +version = "0.8.1" + +[[KrylovKit]] +deps = ["LinearAlgebra", "Printf"] +git-tree-sha1 = "49b0c1dd5c292870577b8f58c51072bd558febb9" +uuid = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" +version = "0.5.4" + [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" version = "3.100.1+0" +[[LERC_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" +uuid = "88015f11-f218-50d7-93a8-a6af411a945d" +version = "3.0.0+1" + +[[LLVM]] +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] +git-tree-sha1 = "c8d47589611803a0f3b4813d9e267cd4e3dbcefb" +uuid = "929cbde3-209d-540e-8aea-75f648917ca0" +version = "4.11.1" + +[[LLVMExtra_jll]] +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg", "TOML"] +git-tree-sha1 = "771bfe376249626d3ca12bcd58ba243d3f961576" +uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" +version = "0.0.16+0" + [[LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" @@ -763,17 +928,23 @@ git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" version = "1.3.0" +[[LabelledArrays]] +deps = ["ArrayInterface", "ArrayInterfaceStaticArrays", "ChainRulesCore", "LinearAlgebra", "MacroTools", "StaticArrays"] +git-tree-sha1 = "90d1465b8c4d22b58da9e00414f0123be3267f46" +uuid = "2ee39098-c373-598a-b85f-a56591580800" +version = "1.10.0" + [[Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "a6552bfeab40de157a297d84e03ade4b8177677f" +git-tree-sha1 = "46a39b9c58749eefb5f2dc1178cb8fab5332b1ab" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.12" +version = "0.15.15" [[LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static"] -git-tree-sha1 = "6dd77ee76188b0365f7d882d674b95796076fa2c" +git-tree-sha1 = "3da92dc6d4bce776cc850c18274a7508b8d752ef" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.5" +version = "0.1.7" [[LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -791,6 +962,12 @@ git-tree-sha1 = "b864cb409e8e445688bc478ef87c0afe4f6d1f8d" uuid = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e" version = "0.1.3" +[[LevyArea]] +deps = ["LinearAlgebra", "Random", "SpecialFunctions"] +git-tree-sha1 = "56513a09b8e0ae6485f34401ea9e2f31357958ec" +uuid = "2d8b4e74-eb68-11e8-0fb9-d5eb67b50637" +version = "1.0.0" + [[LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" @@ -859,10 +1036,10 @@ uuid = "3ae2931a-708c-5973-9c38-ccf7496fb450" version = "0.4.3+0" [[Libtiff_jll]] -deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "340e257aada13f95f98ee352d316c3bed37c8ab9" +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] +git-tree-sha1 = "c9551dd26e31ab17b86cbd00c2ede019c08758eb" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.3.0+0" +version = "4.3.0+1" [[Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -886,26 +1063,38 @@ version = "7.1.1" deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[LinearSolve]] +deps = ["ArrayInterfaceCore", "DocStringExtensions", "GPUArrays", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SuiteSparse", "UnPack"] +git-tree-sha1 = "5b095894601b8d53b025f8a8235a75e4b21c49e4" +uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" +version = "1.17.0" + [[LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "e5718a00af0ab9756305a0392832c8952c7426c1" +git-tree-sha1 = "09e4b894ce6a976c354a69041a04748180d43637" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.6" +version = "0.3.15" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "dfeda1c1130990428720de0024d4516b1902ce98" +git-tree-sha1 = "e9437ef53c3b29a838f4635e748bb38d29d11384" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "0.4.7" +version = "0.4.8" + +[[LoopVectorization]] +deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDDualNumbers", "SLEEFPirates", "SpecialFunctions", "Static", "ThreadingUtilities", "UnPack", "VectorizationBase"] +git-tree-sha1 = "4392c19f0203df81512b6790a0a67446650bdce0" +uuid = "bdcacae8-1622-11e9-2a5c-532679323890" +version = "0.12.110" [[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 = "da663577b5dfc951ad635cec12dfd1ea995152c8" +git-tree-sha1 = "a9e3f4a3460b08dc75870811635b83afbd388ee8" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "5.0.4" +version = "5.3.0" [[MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "Tables"] @@ -915,15 +1104,15 @@ version = "0.1.3" [[MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "5455aef09b40e5020e1520f551fa3135040d4ed0" +git-tree-sha1 = "e595b205efd49508358f7dc670a940c790204629" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2021.1.1+2" +version = "2022.0.0+0" [[MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "8da86dcf5a9ea48413c7e920a990f0ea1869f9cb" +git-tree-sha1 = "74d7fb54c306af241c5f9d4816b735cb4051e125" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.3.6" +version = "1.4.2" [[MacroTools]] deps = ["Markdown", "Random"] @@ -983,13 +1172,18 @@ version = "0.7.3" [[MonteCarloMeasurements]] deps = ["Distributed", "Distributions", "LinearAlgebra", "MacroTools", "Random", "RecipesBase", "Requires", "SLEEFPirates", "StaticArrays", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "bce0a32d6c64165388eec2573b68000ed06f39c1" +git-tree-sha1 = "03619e255664666b352a5e5f6b45e8b00d439870" uuid = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" -version = "1.0.7" +version = "1.0.8" [[MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" +[[MuladdMacro]] +git-tree-sha1 = "c6190f9a7fc5d9d5915ab29f2134421b12d24a68" +uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" +version = "0.2.2" + [[MultivariateStats]] deps = ["Arpack", "LinearAlgebra", "SparseArrays", "Statistics", "StatsBase"] git-tree-sha1 = "8d958ff1854b166003238fe191ec34b9d592860a" @@ -1002,11 +1196,17 @@ git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" version = "7.8.2" +[[NLsolve]] +deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] +git-tree-sha1 = "019f12e9a1a7880459d0173c182e6a99365d7ac1" +uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" +version = "4.5.1" + [[NNlib]] deps = ["Adapt", "ChainRulesCore", "Compat", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "996a3dca9893cb0741bbd08e48b2e2aa0d551898" +git-tree-sha1 = "f89de462a7bc3243f95834e75751d70b3a33e59d" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.8.2" +version = "0.8.5" [[NaNMath]] git-tree-sha1 = "b086b7ea07f8e38cf122f5016af580881ac914fe" @@ -1021,9 +1221,9 @@ version = "0.9.6" [[NamedDims]] deps = ["AbstractFFTs", "ChainRulesCore", "CovarianceEstimation", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "64a54c2992d5da90e3fa19e1bcf65c06bcda2bac" +git-tree-sha1 = "0856b62716585eb90cc1dada226ac9eab5f69aa5" uuid = "356022a1-0364-5f58-8944-0da4b18d706f" -version = "0.2.46" +version = "0.2.47" [[NamedTupleTools]] git-tree-sha1 = "63831dcea5e11db1c0925efe5ef5fc01d528c522" @@ -1037,13 +1237,19 @@ version = "1.0.0" [[NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "16baacfdc8758bc374882566c9187e785e85c2f0" +git-tree-sha1 = "ded92de95031d4a8c61dfb6ba9adb6f1d8016ddd" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.9" +version = "0.4.10" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" +[[NonlinearSolve]] +deps = ["ArrayInterfaceCore", "FiniteDiff", "ForwardDiff", "IterativeSolvers", "LinearAlgebra", "RecursiveArrayTools", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "UnPack"] +git-tree-sha1 = "8c8adff74b454811063fce860e31adb286e298c2" +uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" +version = "0.3.17" + [[Observables]] git-tree-sha1 = "fe29afdef3d0c4a8286128d4e45cc50621b1e43d" uuid = "510215fc-4207-5dde-b226-833fc4488ee2" @@ -1051,9 +1257,9 @@ version = "0.4.0" [[OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "043017e0bdeff61cfbb7afeb558ab29536bbb5ed" +git-tree-sha1 = "52addd9e91df8a6a5781e5c7640787525fd48056" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.10.8" +version = "1.11.2" [[Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1071,9 +1277,9 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112" [[OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "648107615c15d4e09f7eca16307bc821c1f718d8" +git-tree-sha1 = "ab05aa4cc89736e95915b01e7279e61b1bfe33b8" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.13+0" +version = "1.1.14+0" [[OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1098,6 +1304,12 @@ git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.4.1" +[[OrdinaryDiffEq]] +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "ce7260ad4bd075a4627b7d197b1ef73b3213d643" +uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" +version = "6.11.0" + [[PCRE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488" @@ -1130,9 +1342,9 @@ version = "1.1.0" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "13468f237353112a01b2d6b32f3d0f80219944aa" +git-tree-sha1 = "1285416549ccfcdf0c50d4997a94331e88d68413" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.2.2" +version = "2.3.1" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1152,9 +1364,9 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "6f1b25e8ea06279b5689263cc538f51331d7ca17" +git-tree-sha1 = "bb16469fd5224100e422f0b027d26c5a25de1200" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.1.3" +version = "1.2.0" [[Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun"] @@ -1162,11 +1374,29 @@ git-tree-sha1 = "8789439a899b77f4fbb4d7298500a6a5781205bc" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" version = "1.25.0" +[[PoissonRandom]] +deps = ["Random", "Statistics", "Test"] +git-tree-sha1 = "44d018211a56626288b5d3f8c6497d28c26dc850" +uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab" +version = "0.4.0" + +[[Polyester]] +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "efabcabc06030e2b8f072f1b47bc823b6bb3c619" +uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" +version = "0.6.10" + +[[PolyesterWeave]] +deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] +git-tree-sha1 = "7e597df97e46ffb1c8adbaddfa56908a7a20194b" +uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" +version = "0.1.5" + [[PooledArrays]] deps = ["DataAPI", "Future"] -git-tree-sha1 = "db3a23166af8aebf4db5ef87ac5b00d36eb771e2" +git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" -version = "1.4.0" +version = "1.4.2" [[PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -1174,11 +1404,17 @@ git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" +[[PreallocationTools]] +deps = ["Adapt", "ArrayInterfaceCore", "ForwardDiff", "LabelledArrays"] +git-tree-sha1 = "ae8a080dfc68e5615654591d8db5d53ac382353e" +uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" +version = "0.3.1" + [[Preferences]] deps = ["TOML"] -git-tree-sha1 = "de893592a221142f3db370f48290e3a2ef39998f" +git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.2.4" +version = "1.3.0" [[PrettyTables]] deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"] @@ -1208,15 +1444,15 @@ version = "0.1.4" [[ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "afadeba63d90ff223a6a48d2009434ecee2ec9e8" +git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.1" +version = "1.7.2" [[Qt5Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] -git-tree-sha1 = "ad368663a5e20dbb8d6dc2fddeefe4dae0781ae8" +git-tree-sha1 = "c6c0f690d0cc7caddb74cef7aa847b824a16b256" uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" -version = "5.15.3+0" +version = "5.15.3+1" [[QuadGK]] deps = ["DataStructures", "LinearAlgebra"] @@ -1244,6 +1480,18 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" deps = ["Serialization"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +[[Random123]] +deps = ["Random", "RandomNumbers"] +git-tree-sha1 = "afeacaecf4ed1649555a19cb2cad3c141bbc9474" +uuid = "74087812-796a-5b5d-8853-05524746bad3" +version = "1.5.0" + +[[RandomNumbers]] +deps = ["Random", "Requires"] +git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" +uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" +version = "1.5.3" + [[RangeArrays]] git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" uuid = "b3c3ace0-ae52-54e7-9d0b-2c1406fd6b9d" @@ -1251,9 +1499,9 @@ version = "0.3.2" [[Ratios]] deps = ["Requires"] -git-tree-sha1 = "01d341f502250e81f6fec0afe662aa861392a3aa" +git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" -version = "0.4.2" +version = "0.4.3" [[RealDot]] deps = ["LinearAlgebra"] @@ -1273,10 +1521,16 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.4.1" [[RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "ChainRulesCore", "DocStringExtensions", "FillArrays", "LinearAlgebra", "RecipesBase", "Requires", "StaticArrays", "Statistics", "ZygoteRules"] -git-tree-sha1 = "736699f42935a2b19b37a6c790e2355ca52a12ee" +deps = ["Adapt", "ArrayInterfaceCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArrays", "LinearAlgebra", "RecipesBase", "StaticArrays", "Statistics", "ZygoteRules"] +git-tree-sha1 = "2cccbe65fbe6854b3bdb5d8f87dcabaf972f468c" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.24.2" +version = "2.28.0" + +[[RecursiveFactorization]] +deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "StrideArraysCore", "TriangularSolve"] +git-tree-sha1 = "a9a852c7ebb08e2a40e8c0ab9830a744fa283690" +uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" +version = "0.2.10" [[Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1289,6 +1543,12 @@ git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" uuid = "ae029012-a4dd-5104-9daa-d747884805df" version = "1.3.0" +[[ResettableStacks]] +deps = ["StaticArrays"] +git-tree-sha1 = "256eeeec186fa7f26f2801732774ccf277f05db9" +uuid = "ae5879a3-cd67-5da8-be7f-38c6eb64a37b" +version = "1.1.1" + [[Rmath]] deps = ["Random", "Rmath_jll"] git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" @@ -1303,13 +1563,19 @@ version = "0.3.0+0" [[Roots]] deps = ["CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "0abe7fc220977da88ad86d339335a4517944fea2" +git-tree-sha1 = "838b60ee62bebc794864c880a47e331e00c47505" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "1.3.14" +version = "1.4.1" [[SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" +[[SIMDDualNumbers]] +deps = ["ForwardDiff", "IfElse", "SLEEFPirates", "VectorizationBase"] +git-tree-sha1 = "dd4195d308df24f33fb10dde7c22103ba88887fa" +uuid = "3cdde19b-5bb0-4aaf-8931-af3e248e098b" +version = "0.1.1" + [[SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" uuid = "94e857df-77ce-4151-89e5-788b33177be4" @@ -1317,15 +1583,15 @@ version = "0.1.0" [[SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "61a96d8b89083a53fb2b745f3b59a05359651bbe" +git-tree-sha1 = "ac399b5b163b9140f9c310dfe9e9aaa225617ff6" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.30" +version = "0.6.32" [[SciMLBase]] -deps = ["ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "RecipesBase", "RecursiveArrayTools", "StaticArrays", "Statistics", "Tables", "TreeViews"] -git-tree-sha1 = "8ff1bf96965b3878ca5d235752ff1daf519e7a26" +deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "RecipesBase", "RecursiveArrayTools", "StaticArrays", "Statistics", "Tables", "TreeViews"] +git-tree-sha1 = "28bab7640e47e38135c4f11c467076cd79ea7a03" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.26.3" +version = "1.32.2" [[ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -1393,11 +1659,17 @@ version = "1.0.1" deps = ["LinearAlgebra", "Random"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +[[SparseDiffTools]] +deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArrays", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays", "VertexSafeGraphs"] +git-tree-sha1 = "56a100f020fa03ec49f4f9390e3886bd2a672647" +uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" +version = "1.22.0" + [[SpecialFunctions]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "2735e252e72ee0367ebdb10b6148343fd15c2481" +git-tree-sha1 = "cbf21db885f478e4bd73b286af6e67d1beeebe4c" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "1.8.3" +version = "1.8.4" [[SplittablesBase]] deps = ["Setfield", "Test"] @@ -1425,15 +1697,15 @@ version = "4.4.1" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "00b725fffc9a7e9aac8850e4ed75b4c1acbe8cd2" +git-tree-sha1 = "3a2a99b067090deb096edecec1dc291c5b4b31cb" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.5.5" +version = "0.6.5" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "6354dfaf95d398a1a70e0b28238321d5d17b2530" +git-tree-sha1 = "cd56bf18ed715e8b09f06ef8c6b781e6cdc49911" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.4.0" +version = "1.4.4" [[StatisticalRethinking]] deps = ["AxisKeys", "CSV", "DataFrames", "Dates", "Distributions", "DocStringExtensions", "Documenter", "Formatting", "KernelDensity", "LinearAlgebra", "MCMCChains", "MonteCarloMeasurements", "NamedArrays", "NamedTupleTools", "Optim", "OrderedCollections", "Parameters", "ParetoSmooth", "ParetoSmoothedImportanceSampling", "PrettyTables", "Random", "Reexport", "Requires", "Statistics", "StatsBase", "StatsFuns", "StructuralCausalModels", "Tables", "Test", "Unicode"] @@ -1461,9 +1733,9 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "c3d8ba7f3fa0625b062b82853a7d5229cb728b6b" +git-tree-sha1 = "c82aaa13b44ea00134f8c9c89819477bd3986ecd" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.2.1" +version = "1.3.0" [[StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1479,9 +1751,9 @@ version = "0.9.14" [[StatsModels]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "677488c295051568b0b79a77a8c44aa86e78b359" +git-tree-sha1 = "4352d5badd1bc8bf0a8c825e886fa1eda4f0f967" uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" -version = "0.6.28" +version = "0.6.30" [[StatsPlots]] deps = ["Clustering", "DataStructures", "DataValues", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] @@ -1489,11 +1761,29 @@ git-tree-sha1 = "d6956cefe3766a8eb5caae9226118bb0ac61c8ac" uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.14.29" +[[SteadyStateDiffEq]] +deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] +git-tree-sha1 = "785766c07cd4e7e7c2989c27f5b3444e969b1733" +uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" +version = "1.7.0" + +[[StochasticDiffEq]] +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqJump", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "cc2871e5ced6a1264ad86d157ec6eaae20ee69cb" +uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" +version = "6.48.0" + +[[StrideArraysCore]] +deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "ThreadingUtilities"] +git-tree-sha1 = "727eaf73c76f1b8d053345545d9910cd32ce4153" +uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" +version = "0.3.7" + [[StructArrays]] deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] -git-tree-sha1 = "57617b34fa34f91d536eb265df67c2d4519b8b98" +git-tree-sha1 = "e75d82493681dfd884a357952bbd7ab0608e1dc3" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.5" +version = "0.6.7" [[StructuralCausalModels]] deps = ["CSV", "Combinatorics", "DataFrames", "DataStructures", "Distributions", "DocStringExtensions", "LinearAlgebra", "NamedArrays", "Reexport", "Statistics"] @@ -1505,6 +1795,22 @@ version = "1.3.0" deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" +[[SuiteSparse_jll]] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" + +[[Sundials]] +deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SparseArrays", "Sundials_jll"] +git-tree-sha1 = "6549d3b1b5cf86446949c62616675588159ea2fb" +uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" +version = "4.9.4" + +[[Sundials_jll]] +deps = ["CompilerSupportLibraries_jll", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"] +git-tree-sha1 = "013ff4504fc1d475aa80c63b455b6b3a58767db2" +uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164" +version = "5.2.0+1" + [[TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" @@ -1522,15 +1828,21 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "bb1064c9a84c52e277f1096cf41434b675cd368b" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] +git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.6.1" +version = "1.7.0" [[Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" +[[TensorCore]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" +uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" +version = "0.1.1" + [[TerminalLoggers]] deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"] git-tree-sha1 = "62846a48a6cd70e63aa29944b8c4ef704360d72f" @@ -1541,17 +1853,23 @@ version = "0.1.5" deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[ThreadingUtilities]] +deps = ["ManualMemory"] +git-tree-sha1 = "f8629df51cab659d70d2e5618a430b4d3f37f2c3" +uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" +version = "0.5.0" + [[TimeZones]] deps = ["Dates", "Downloads", "InlineStrings", "LazyArtifacts", "Mocking", "Printf", "RecipesBase", "Serialization", "Unicode"] -git-tree-sha1 = "0f1017f68dc25f1a0cb99f4988f78fe4f2e7955f" +git-tree-sha1 = "0a359b0ee27e4fbc90d9b3da1f48ddc6f98a0c9e" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.7.1" +version = "1.7.3" [[Tracker]] deps = ["Adapt", "DiffRules", "ForwardDiff", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "434a953e6ad7abf6a07a1e0b99baaa704753cec0" +git-tree-sha1 = "0874c1b5de1b5529b776cfeca3ec0acfada97b1b" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.19" +version = "0.2.20" [[TranscodingStreams]] deps = ["Random", "Test"] @@ -1561,9 +1879,9 @@ version = "0.9.6" [[Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "1cda71cc967e3ef78aa2593319f6c7379376f752" +git-tree-sha1 = "c76399a3bbe6f5a88faa33c8f8a65aa631d95013" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.72" +version = "0.4.73" [[TreeViews]] deps = ["Test"] @@ -1571,11 +1889,17 @@ git-tree-sha1 = "8d0d7a3fe2f30d6a7f833a5f19f7c7a5b396eae6" uuid = "a2a6695c-b41b-5b7d-aed9-dbfdeacea5d7" version = "0.3.0" +[[TriangularSolve]] +deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] +git-tree-sha1 = "b8d08f55b02625770c09615d96927b3a8396925e" +uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" +version = "0.1.11" + [[Tullio]] deps = ["ChainRulesCore", "DiffRules", "LinearAlgebra", "Requires"] -git-tree-sha1 = "7830c974acc69437a3fee35dd7b510a74cbc862d" +git-tree-sha1 = "859e2e9a7222553a0c052e423557cedb49376da9" uuid = "bc48ee85-29a4-5162-ae0b-a64e1601d4bc" -version = "0.3.3" +version = "0.3.4" [[Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker", "ZygoteRules"] @@ -1607,16 +1931,22 @@ uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" [[VectorizationBase]] -deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "Hwloc", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"] -git-tree-sha1 = "e9a35d501b24c127af57ca5228bcfb806eda7507" +deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"] +git-tree-sha1 = "c95d242ade2d67c1510ce52d107cfca7a83e0b4e" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.24" +version = "0.21.33" [[VersionParsing]] git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868" uuid = "81def892-9a0e-5fdd-b105-ffc91e053289" version = "1.3.0" +[[VertexSafeGraphs]] +deps = ["Graphs"] +git-tree-sha1 = "8351f8d73d7e880bfc042a8b6922684ebeafb35c" +uuid = "19fa3120-7c27-5ec5-8db8-b0b0aa330d6f" +version = "0.2.0" + [[Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" @@ -1631,15 +1961,15 @@ version = "1.25.0+0" [[WeakRefStrings]] deps = ["DataAPI", "InlineStrings", "Parsers"] -git-tree-sha1 = "c69f9da3ff2f4f02e811c3323c22e5dfcb584cfa" +git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" -version = "1.4.1" +version = "1.4.2" [[Widgets]] deps = ["Colors", "Dates", "Observables", "OrderedCollections"] -git-tree-sha1 = "505c31f585405fc375d99d02588f6ceaba791241" +git-tree-sha1 = "fcdae142c1cfc7d89de2d11e08721d0f2f86c98a" uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62" -version = "0.6.5" +version = "0.6.6" [[WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] @@ -1819,6 +2149,12 @@ git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" +[[libblastrampoline_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "576c27f2c23add3ce8f10717d72fbaee6fe120e9" +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "3.1.0+2" + [[libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" diff --git a/Project.toml b/Project.toml index f245eca..747a8f8 100644 --- a/Project.toml +++ b/Project.toml @@ -3,6 +3,7 @@ BSplines = "488c2830-172b-11e9-1591-253b8a7df96d" CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" Dagitty = "d56128e0-8113-48cd-82a0-fc808dc30d4b" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" FreqTables = "da1fdf0e-e0ff-5433-a45f-9bb5ff651cb1" GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a" diff --git a/docs/16-Chapter 16. Generalized Linear Madness.html b/docs/16-Chapter 16. Generalized Linear Madness.html index 9abc835..74a589f 100644 --- a/docs/16-Chapter 16. Generalized Linear Madness.html +++ b/docs/16-Chapter 16. Generalized Linear Madness.html @@ -13216,643 +13216,643 @@

16.1 Geometric people - + - - + - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +16.1 Geometric people - -16.1 Geometric people -16.2 Hidden minds and observed - + - - + - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -14368,374 +14368,465 @@

16.3 Ordinary differential nut - + - - + - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - + + - - - - - - - - - - - - - - - + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - - - + + - - - - - - + + + + + @@ -14827,342 +14918,413 @@

16.3 Ordinary differential nut - + - - + - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + @@ -15221,169 +15383,169 @@

16.4 Population dynamics - + - - + - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - - - - + @@ -15486,87 +15648,87 @@

16.4 Population dynamics - + - - + - - + - - - - - - - - - - - - - - - - - - - - -16.4 Population dynamics -16.4 Population dynamics - + - - + - - + - - - - - - - - - - - - - - - - - - - - - - -16.4 Population dynamics + +
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Code 16.17

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In [18]:
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using DifferentialEquations
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In [19]:
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function lynx_hare!(dLH, LH, θ, t)
+    L, H = LH
+    bh, mh, bl, ml = θ
+
+    dLH[1] = dL = (bl * H - ml) * L
+    dLH[2] = dH = (bh - mh * L) * H
+end
+
+
+@model function lynx_hare_model(N, L, H)
+    b_h ~ TruncatedNormal(1, 0.5, 0.0, Inf)
+    b_l ~ TruncatedNormal(0.05, 0.05, 0.0, Inf)
+    m_h ~ TruncatedNormal(0.05, 0.05, 0.0, Inf)
+    m_l ~ TruncatedNormal(1, 0.5, 0.0, Inf)
+    
+    σ_h ~ Exponential()
+    σ_l ~ Exponential()
+    h₁ ~ LogNormal(log(10), 1)
+    l₁ ~ LogNormal(log(10), 1)
+    p_h ~ Beta(40, 200)
+    p_l ~ Beta(40, 200)
+    
+    LH₁ = [l₁, h₁]
+    θ = [b_h, m_h, b_l, m_l]
+    prob = ODEProblem(lynx_hare!, LH₁, N-1, θ)
+    sol = solve(prob, saveat=1)
+    if length(sol.u) < N
+        Turing.@addlogprob! -Inf
+    else
+        μ_l = map(first, sol.u[1:N]) .* p_l
+        μ_h = map(last, sol.u[1:N]) .* p_h
+        # sometime solution might end up with negative population :)
+        if all(μ_l .> 0.0) && all(μ_h .> 0.0)
+            logμ_l = log.(μ_l)
+            logμ_h = log.(μ_h)
+            @. L ~ LogNormal(logμ_l, σ_l)
+            @. H ~ LogNormal(logμ_h, σ_h)
+        else
+            Turing.@addlogprob! -Inf
+        end
+    end
+end
+
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+

Code 16.18

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In [20]:
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Random.seed!(1)
+m16_5_ch = sample(lynx_hare_model(nrow(d), d.Lynx, d.Hare), NUTS(), 4000)
+m16_5_df = DataFrame(m16_5_ch);
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Code 16.19

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In [ ]:
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# from row of parameters, get population of Hare and Lynx
+function row_to_population(r, N)
+    LH₁ = [r.l₁, r.h₁]
+    θ = [r.b_h, r.m_h, r.b_l, r.m_l]
+    prob = ODEProblem(lynx_hare!, LH₁, N-1, θ)
+    sol = solve(prob, saveat=1)
+    L = map(first, sol.u[1:N])
+    H = map(last, sol.u[1:N])
+    L, H
+end
+
+p = plot(xlab="year", ylab="thousands of pelts")
+plot!(d.Year, d.Hare, lw=1.5, c=:black, lab="Lepus")
+scatter!(d.Year, d.Hare, c=:black)
+plot!(d.Year, d.Lynx, lw=1.5, c=:blue, lab="Lynx")
+scatter!(d.Year, d.Lynx, c=:blue)
+
+for r in first(eachrow(m16_5_df), 21)
+    L, H = row_to_population(r, nrow(d))
+    L .*= r.p_l
+    H .*= r.p_h
+    
+    plot!(d.Year, L, c=:blue, alpha=0.2)
+    plot!(d.Year, H, c=:black, alpha=0.2)
+end
+p
+
+ +
+
+
+ +
+
+
+
+

Code 16.20

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p = plot(xlab="year", ylab="thousands animals")
+
+for r in first(eachrow(m16_5_df), 21)
+    L, H = row_to_population(r, nrow(d))
+    plot!(d.Year, L, c=:blue, alpha=0.2)
+    plot!(d.Year, H, c=:black, alpha=0.2)
+end
+p
+
+ +
+
+
+
diff --git a/docs/17-Chapter 17. Horoscopes.html b/docs/17-Chapter 17. Horoscopes.html new file mode 100644 index 0000000..47182c7 --- /dev/null +++ b/docs/17-Chapter 17. Horoscopes.html @@ -0,0 +1,13110 @@ + + + + +17-Chapter 17. Horoscopes + + + + + + + + + + + + + + + + + + + + + + +
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No code in this chapter!

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+ + + + + + diff --git a/docs/index.md b/docs/index.md index 8a81d3a..47bebe5 100644 --- a/docs/index.md +++ b/docs/index.md @@ -28,5 +28,6 @@ but please first try to solve them yourself, as it is much more fun (in addition * [Chapter 14. Adventures in Covariance](14-Chapter 14. Adventures in Covariance.html) * [Chapter 15. Missing Data and Other Opportunities](15-Chapter 15. Missing Data and Other Opportunities.html) * [Chapter 16. Generalized Linear Madness](16-Chapter 16. Generalized Linear Madness.html) +* [Chapter 17. Horoscopes (no code)](17-Chapter 17. Horoscopes.html) Besides Julia, second edition examples were also [ported to NumPyro](https://fehiepsi.github.io/rethinking-numpyro/).