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updated Turing version and fixed link in 07
1 parent 1c88b69 commit c998e96

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-817
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32 files changed

+997
-817
lines changed

tutorials/00-introduction/Manifest.toml

Lines changed: 58 additions & 53 deletions
Original file line numberDiff line numberDiff line change
@@ -5,9 +5,9 @@ manifest_format = "2.0"
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project_hash = "b45878f3df6dffef908d7ec87e98124988d559f6"
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[[deps.ADTypes]]
8-
git-tree-sha1 = "401c87ea437e9d5b74dc283a77198ad75e50811f"
8+
git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224"
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uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
10-
version = "1.1.0"
10+
version = "1.2.1"
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[deps.ADTypes.extensions]
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ADTypesChainRulesCoreExt = "ChainRulesCore"
@@ -133,10 +133,10 @@ version = "0.2.5"
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Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
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[[deps.AliasTables]]
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deps = ["Random"]
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git-tree-sha1 = "82b912bb5215792fd33df26f407d064d3602af98"
136+
deps = ["PtrArrays", "Random"]
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git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff"
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uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8"
139-
version = "1.1.2"
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version = "1.1.3"
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[[deps.ArgCheck]]
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git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4"
@@ -240,9 +240,9 @@ version = "0.1.1"
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[[deps.Bijectors]]
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deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"]
243-
git-tree-sha1 = "c12f0e123d21091546d11164d2665e70558a32b3"
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git-tree-sha1 = "49491db48b1c70eefa5115e626100dbd6c0ff4c0"
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uuid = "76274a88-744f-5084-9051-94815aaf08c4"
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version = "0.13.11"
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version = "0.13.12"
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[deps.Bijectors.extensions]
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BijectorsDistributionsADExt = "DistributionsAD"
@@ -278,9 +278,9 @@ version = "0.5.0"
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[[deps.Cairo_jll]]
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deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
281-
git-tree-sha1 = "a4c43f59baa34011e303e76f5c8c91bf58415aaf"
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git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd"
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uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
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version = "1.18.0+1"
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version = "1.18.0+2"
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[[deps.Calculus]]
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deps = ["LinearAlgebra"]
@@ -350,9 +350,9 @@ weakdeps = ["SpecialFunctions"]
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[[deps.Colors]]
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deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
353-
git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a"
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git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0"
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uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
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version = "0.12.10"
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version = "0.12.11"
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[[deps.Combinatorics]]
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git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860"
@@ -540,9 +540,9 @@ version = "0.6.8"
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[[deps.DynamicPPL]]
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deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"]
543-
git-tree-sha1 = "e590becab0719330d8cc2a31fc07ef7a5804072b"
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git-tree-sha1 = "882510df0da64bae763a65240b07fb4b1c462317"
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uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
545-
version = "0.25.4"
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version = "0.27.1"
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[deps.DynamicPPL.extensions]
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DynamicPPLChainRulesCoreExt = ["ChainRulesCore"]
@@ -635,9 +635,9 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"]
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[[deps.FixedPointNumbers]]
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deps = ["Statistics"]
638-
git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc"
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git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172"
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uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
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version = "0.8.4"
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version = "0.8.5"
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[[deps.Fontconfig_jll]]
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deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"]
@@ -662,9 +662,9 @@ weakdeps = ["StaticArrays"]
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[[deps.FreeType2_jll]]
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deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"]
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git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0"
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git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc"
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uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7"
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version = "2.13.1+0"
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version = "2.13.2+0"
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[[deps.FriBidi_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -725,9 +725,9 @@ version = "0.21.0+0"
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[[deps.Glib_jll]]
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deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
728-
git-tree-sha1 = "359a1ba2e320790ddbe4ee8b4d54a305c0ea2aff"
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git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba"
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uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
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version = "2.80.0+0"
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version = "2.80.2+0"
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[[deps.Graphite2_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -742,9 +742,9 @@ version = "1.0.2"
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[[deps.HTTP]]
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deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
745-
git-tree-sha1 = "ab5b37dc4f98fc037527968852a6f9b2bdf9f32d"
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git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed"
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uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
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version = "1.10.7"
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version = "1.10.8"
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[[deps.HarfBuzz_jll]]
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deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"]
@@ -856,9 +856,9 @@ version = "3.0.3+0"
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[[deps.KernelAbstractions]]
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deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"]
859-
git-tree-sha1 = "ed7167240f40e62d97c1f5f7735dea6de3cc5c49"
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git-tree-sha1 = "db02395e4c374030c53dc28f3c1d33dec35f7272"
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uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
861-
version = "0.9.18"
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version = "0.9.19"
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[deps.KernelAbstractions.extensions]
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EnzymeExt = "EnzymeCore"
@@ -1011,9 +1011,9 @@ version = "1.17.0+0"
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[[deps.Libmount_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "4b683b19157282f50bfd5dcaa2efe5295814ea22"
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git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e"
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uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9"
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version = "2.40.0+0"
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version = "2.40.1+0"
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[[deps.Libtask]]
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deps = ["FunctionWrappers", "LRUCache", "LinearAlgebra", "Statistics"]
@@ -1029,9 +1029,9 @@ version = "4.5.1+1"
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[[deps.Libuuid_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "27fd5cc10be85658cacfe11bb81bee216af13eda"
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git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807"
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uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
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version = "2.40.0+0"
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version = "2.40.1+0"
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[[deps.LinearAlgebra]]
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deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
@@ -1172,9 +1172,9 @@ version = "0.10.2"
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[[deps.NNlib]]
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deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"]
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git-tree-sha1 = "5055845dd316575ae2fc1f6dcb3545ff15fe547a"
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git-tree-sha1 = "e0cea7ec219ada9ac80ec2e82e374ab2f154ae05"
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uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
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version = "0.9.14"
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version = "0.9.16"
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[deps.NNlib.extensions]
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NNlibAMDGPUExt = "AMDGPU"
@@ -1304,9 +1304,9 @@ version = "1.3.0"
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[[deps.Pixman_jll]]
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deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"]
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git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87"
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git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b"
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uuid = "30392449-352a-5448-841d-b1acce4e97dc"
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version = "0.42.2+0"
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version = "0.43.4+0"
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[[deps.Pkg]]
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deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
@@ -1379,6 +1379,11 @@ git-tree-sha1 = "763a8ceb07833dd51bb9e3bbca372de32c0605ad"
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uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
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version = "1.10.0"
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[[deps.PtrArrays]]
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git-tree-sha1 = "077664975d750757f30e739c870fbbdc01db7913"
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uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d"
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version = "1.1.0"
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[[deps.Qt6Base_jll]]
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deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"]
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git-tree-sha1 = "37b7bb7aabf9a085e0044307e1717436117f2b3b"
@@ -1446,9 +1451,9 @@ version = "0.6.12"
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[[deps.RecursiveArrayTools]]
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deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
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git-tree-sha1 = "f599a896fb28043dd63a4d372231dfcbdd117394"
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git-tree-sha1 = "758bc86b90e9fee2edc4af2a750b0d3f2d5c02c5"
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uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
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version = "3.16.0"
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version = "3.19.0"
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[deps.RecursiveArrayTools.extensions]
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RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
@@ -1492,10 +1497,10 @@ uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa"
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version = "0.7.1"
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[[deps.Rmath_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
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git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da"
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "d483cd324ce5cf5d61b77930f0bbd6cb61927d21"
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uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f"
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version = "0.4.0+0"
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version = "0.4.2+0"
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[[deps.Roots]]
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deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"]
@@ -1533,9 +1538,9 @@ version = "0.1.1"
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[[deps.SciMLBase]]
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deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
1536-
git-tree-sha1 = "397367599b9526a49cc06a4db70835807498b561"
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git-tree-sha1 = "265f1a7a804d8093fa0b17e33e45373a77e56ca5"
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uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
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version = "2.36.1"
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version = "2.38.0"
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[deps.SciMLBase.extensions]
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SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -1563,9 +1568,9 @@ uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
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version = "0.3.8"
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[[deps.SciMLStructures]]
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git-tree-sha1 = "5833c10ce83d690c124beedfe5f621b50b02ba4d"
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git-tree-sha1 = "d778a74df2f64059c38453b34abad1953b2b8722"
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uuid = "53ae85a6-f571-4167-b2af-e1d143709226"
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version = "1.1.0"
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version = "1.2.0"
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[[deps.ScientificTypesBase]]
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git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b"
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[[deps.SentinelArrays]]
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deps = ["Dates", "Random"]
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git-tree-sha1 = "0e7508ff27ba32f26cd459474ca2ede1bc10991f"
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git-tree-sha1 = "363c4e82b66be7b9f7c7c7da7478fdae07de44b9"
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uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
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version = "1.4.1"
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version = "1.4.2"
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[[deps.Serialization]]
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uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
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[[deps.StaticArrays]]
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deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
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git-tree-sha1 = "bf074c045d3d5ffd956fa0a461da38a44685d6b2"
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git-tree-sha1 = "9ae599cd7529cfce7fea36cf00a62cfc56f0f37c"
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uuid = "90137ffa-7385-5640-81b9-e52037218182"
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version = "1.9.3"
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version = "1.9.4"
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weakdeps = ["ChainRulesCore", "Statistics"]
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[deps.StaticArrays.extensions]
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[[deps.Turing]]
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deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
1827-
git-tree-sha1 = "2798b422eb107bdf4433068d22ce054a44c4dd44"
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git-tree-sha1 = "cfb3b446a5e52e1da4cc71b77a9350c309c581f0"
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uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
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version = "0.31.4"
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version = "0.32.0"
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[deps.Turing.extensions]
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TuringDynamicHMCExt = "DynamicHMC"
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[[deps.Unitful]]
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deps = ["Dates", "LinearAlgebra", "Random"]
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git-tree-sha1 = "3c793be6df9dd77a0cf49d80984ef9ff996948fa"
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git-tree-sha1 = "dd260903fdabea27d9b6021689b3cd5401a57748"
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uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
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version = "1.19.0"
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version = "1.20.0"
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weakdeps = ["ConstructionBase", "InverseFunctions"]
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[deps.Unitful.extensions]
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[[deps.XML2_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
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git-tree-sha1 = "532e22cf7be8462035d092ff21fada7527e2c488"
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git-tree-sha1 = "52ff2af32e591541550bd753c0da8b9bc92bb9d9"
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uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
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version = "2.12.6+0"
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version = "2.12.7+0"
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[[deps.XSLT_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"]
@@ -2115,10 +2120,10 @@ uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70"
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[[deps.libaom_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
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git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4"
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d"
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uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b"
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version = "3.4.0+0"
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version = "3.9.0+0"
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[[deps.libass_jll]]
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deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]

tutorials/00-introduction/index.qmd

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@@ -181,7 +181,7 @@ sampler = NUTS();
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We approximate the posterior distribution with 1000 samples:
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```{julia}
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chain = sample(model, sampler, 1_000; progress=false);
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chain = sample(model, sampler, 2_000, progress=false);
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```
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The `sample` function and common keyword arguments are explained more extensively in the documentation of [AbstractMCMC.jl](https://turinglang.github.io/AbstractMCMC.jl/dev/api/).

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