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Recursive Array Tools Notebook #281

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c75462a
param plots
sumedha-k Oct 4, 2020
cb07929
chains tests
sumedha-k Oct 4, 2020
9ed7abc
Merge branch 'master' into newPlotting
aarmey Oct 5, 2020
3348745
added DataFrames dependency
sumedha-k Oct 5, 2020
ec3be81
Merge branch 'newPlotting' of github.com:meyer-lab/TAMode.jl into new…
sumedha-k Oct 5, 2020
d0db670
Merge branch 'master' into newPlotting
aarmey Oct 5, 2020
81c4572
Merge branch 'master' into newPlotting
aarmey Oct 5, 2020
b30ea7c
added Gadfly
sumedha-k Oct 5, 2020
bc36b02
Manifest merge conflict
sumedha-k Oct 5, 2020
f1f79fa
fixed build error
sumedha-k Oct 5, 2020
687a76c
Update testChains.jl
aarmey Oct 6, 2020
6829519
added sampling file
sumedha-k Oct 8, 2020
84ba918
Merge branch 'newPlotting' of github.com:meyer-lab/TAMode.jl into new…
sumedha-k Oct 8, 2020
b98a9bb
recursivearraytools notebook
sumedha-k Oct 24, 2020
c91d3db
Merge branch 'master' into newPlotting
aarmey Oct 24, 2020
3b160f1
update recursive notebook
sumedha-k Oct 24, 2020
d501730
Merge branch 'newPlotting' of github.com:meyer-lab/TAMode.jl into new…
sumedha-k Oct 24, 2020
59d7364
Fixed?
aarmey Oct 25, 2020
f25d064
labelled arrays notebook update
sumedha-k Nov 10, 2020
170a21a
labelled arrays notebook update
sumedha-k Nov 10, 2020
d932be1
Merge branch 'master' into newPlotting
aarmey Nov 10, 2020
4ed013b
Fix Manifest
aarmey Nov 10, 2020
3bce3cb
Merge branch 'master' into newPlotting
aarmey Nov 20, 2020
6b8e520
added flatten and unflatten functions
sumedha-k Nov 23, 2020
6650596
Merge branch 'newPlotting' of github.com:meyer-lab/TAMode.jl into new…
sumedha-k Nov 23, 2020
424a3da
updated Manifest
sumedha-k Nov 28, 2020
a672484
Merge branch 'master' into newPlotting
aarmey Nov 28, 2020
fde4a35
bug fix
sumedha-k Nov 28, 2020
69a2de8
Merge branch 'newPlotting' of github.com:meyer-lab/TAMode.jl into new…
sumedha-k Nov 28, 2020
811211b
update to manifest
sumedha-k Nov 29, 2020
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90 changes: 45 additions & 45 deletions Manifest.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -88,9 +88,9 @@ version = "0.5.0"

[[Bijectors]]
deps = ["ArgCheck", "Compat", "Distributions", "LinearAlgebra", "MappedArrays", "NNlib", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics", "StatsFuns"]
git-tree-sha1 = "3e2637ad074d5e626da6298632e05e57cc4ff27f"
git-tree-sha1 = "9a0f332a5873e81c420477ad9cea001c7484e3d0"
uuid = "76274a88-744f-5084-9051-94815aaf08c4"
version = "0.8.7"
version = "0.8.8"

[[BinaryProvider]]
deps = ["Libdl", "Logging", "SHA"]
Expand Down Expand Up @@ -118,15 +118,15 @@ version = "0.8.3"

[[ChainRules]]
deps = ["ChainRulesCore", "ChainRulesTestUtils", "Compat", "LinearAlgebra", "Random", "Reexport", "Requires", "Statistics"]
git-tree-sha1 = "f6265a7e32d2c82e9462a06e0d5066284c29b89e"
git-tree-sha1 = "118fad132f286ac9df765e0dda94ddba2f0fb279"
uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2"
version = "0.7.32"
version = "0.7.33"

[[ChainRulesCore]]
deps = ["LinearAlgebra", "MuladdMacro", "SparseArrays"]
git-tree-sha1 = "aebbda0a7c644bd8739b34f2a1b1e48f114aab49"
git-tree-sha1 = "007f084f0136c0e2d87d3ac53e9d8eab06cec27f"
uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
version = "0.9.17"
version = "0.9.19"

[[ChainRulesTestUtils]]
deps = ["ChainRulesCore", "Compat", "FiniteDifferences", "LinearAlgebra", "Random", "Test"]
Expand Down Expand Up @@ -222,10 +222,10 @@ uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
version = "1.4.0"

[[DataFrames]]
deps = ["CategoricalArrays", "Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "Missings", "PooledArrays", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
git-tree-sha1 = "ecd850f3d2b815431104252575e7307256121548"
deps = ["CategoricalArrays", "Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
git-tree-sha1 = "20159837c2e5e196793a313cd700b8199fd8f985"
uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
version = "0.21.8"
version = "0.22.1"

[[DataStructures]]
deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
Expand Down Expand Up @@ -260,9 +260,9 @@ version = "1.0.2"

[[DiffRules]]
deps = ["NaNMath", "Random", "SpecialFunctions"]
git-tree-sha1 = "eb0c34204c8410888844ada5359ac8b96292cfd1"
git-tree-sha1 = "214c3fcac57755cfda163d91c58893a8723f93e9"
uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
version = "1.0.1"
version = "1.0.2"

[[Distances]]
deps = ["LinearAlgebra", "Statistics"]
Expand All @@ -282,9 +282,9 @@ version = "0.23.12"

[[DistributionsAD]]
deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "DiffRules", "Distributions", "FillArrays", "ForwardDiff", "LinearAlgebra", "NaNMath", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsBase", "StatsFuns", "ZygoteRules"]
git-tree-sha1 = "309458fa6cd189cb080a349130918ace2bce0256"
git-tree-sha1 = "f9348ae225e7168a04f7cec7a562bd0d86657e53"
uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c"
version = "0.6.9"
version = "0.6.11"

[[DocStringExtensions]]
deps = ["LibGit2", "Markdown", "Pkg", "Test"]
Expand Down Expand Up @@ -373,9 +373,9 @@ version = "2.7.1"

[[FiniteDifferences]]
deps = ["ChainRulesCore", "LinearAlgebra", "Printf", "Random", "Richardson"]
git-tree-sha1 = "5ef56eea8b65c2ed2d11bd394629892201369b23"
git-tree-sha1 = "e62dc2e6c482bbbe97e79f875063285257daa142"
uuid = "26cc04aa-876d-5657-8c51-4c34ba976000"
version = "0.11.2"
version = "0.11.3"

[[FixedPointNumbers]]
deps = ["Statistics"]
Expand Down Expand Up @@ -735,15 +735,15 @@ version = "0.8.26"

[[LoweredCodeUtils]]
deps = ["JuliaInterpreter"]
git-tree-sha1 = "6f681c69f95cf2b9b04328bea3f03122b750d34e"
git-tree-sha1 = "9af25a91bda16307caff2a50f9c744c432b8bc1b"
uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b"
version = "1.2.5"
version = "1.2.6"

[[MCMCChains]]
deps = ["AbstractFFTs", "AbstractMCMC", "AxisArrays", "Compat", "Distributions", "Formatting", "IteratorInterfaceExtensions", "LinearAlgebra", "MLJModelInterface", "NaturalSort", "PrettyTables", "Random", "RecipesBase", "Serialization", "SpecialFunctions", "Statistics", "StatsBase", "TableTraits", "Tables"]
git-tree-sha1 = "878a89e412ec091baccfad98da59dc230a2f1e04"
git-tree-sha1 = "1915b448ec72dcd7adc87e957500976e1c07cd62"
uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
version = "4.2.4"
version = "4.3.1"

[[MKL_jll]]
deps = ["IntelOpenMP_jll", "Libdl", "Pkg"]
Expand Down Expand Up @@ -823,15 +823,15 @@ uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
version = "4.4.1"

[[NNlib]]
deps = ["Libdl", "LinearAlgebra", "Pkg", "Requires", "Statistics"]
git-tree-sha1 = "a8180fd1445e31c0b1add98dae8da694ac2c23fd"
deps = ["Compat", "Libdl", "LinearAlgebra", "Pkg", "Requires", "Statistics"]
git-tree-sha1 = "1ae42464fea5258fd2ff49f1c4a40fc41cba3860"
uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
version = "0.7.6"
version = "0.7.7"

[[NaNMath]]
git-tree-sha1 = "c84c576296d0e2fbb3fc134d3e09086b3ea617cd"
git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb"
uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
version = "0.3.4"
version = "0.3.5"

[[NamedArrays]]
deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"]
Expand Down Expand Up @@ -881,9 +881,9 @@ version = "1.3.2"

[[OrdinaryDiffEq]]
deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "ExponentialUtilities", "FastClosures", "FiniteDiff", "ForwardDiff", "GenericSVD", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "NLsolve", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
git-tree-sha1 = "7ea4d187575fb5256409d755819afb66e1812f2b"
git-tree-sha1 = "e782c1ff432a6ba8677b6fced19a92a6878a5c68"
uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
version = "5.45.0"
version = "5.45.1"

[[PCRE_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
Expand Down Expand Up @@ -933,9 +933,9 @@ version = "1.0.7"

[[Plots]]
deps = ["Base64", "Contour", "Dates", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"]
git-tree-sha1 = "892484bb5c9feefb46a3e3064721d4e50d02e5cf"
git-tree-sha1 = "173c7250ccd7c98615b04c669eb13fa7fab494b0"
uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
version = "1.9.0"
version = "1.9.1"

[[PooledArrays]]
deps = ["DataAPI"]
Expand All @@ -944,10 +944,10 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
version = "0.5.3"

[[PrettyTables]]
deps = ["Crayons", "Formatting", "Parameters", "Reexport", "Tables"]
git-tree-sha1 = "8458dc04a493ae5c2fed3796c1d3117972c69694"
deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"]
git-tree-sha1 = "237170206bf38a66fee4d845f4ae57f63788eeb0"
uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
version = "0.9.1"
version = "0.10.1"

[[Printf]]
deps = ["Unicode"]
Expand Down Expand Up @@ -976,10 +976,10 @@ uuid = "784f63db-0788-585a-bace-daefebcd302b"
version = "2019.1.0+2"

[[Qt_jll]]
deps = ["Fontconfig_jll", "Glib_jll", "Libdl", "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 = "b3979580c712b167a131bd1a4152a840d6df89cb"
deps = ["Artifacts", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "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 = "72244a8e084251aea25968c61bbf5c001aaa7d5a"
uuid = "ede63266-ebff-546c-83e0-1c6fb6d0efc8"
version = "5.15.0+3"
version = "5.15.1+0"

[[QuadGK]]
deps = ["DataStructures", "LinearAlgebra"]
Expand Down Expand Up @@ -1036,15 +1036,15 @@ version = "0.2.0"

[[Requires]]
deps = ["UUIDs"]
git-tree-sha1 = "2fc2e1ab606a5dca7bbad9036a694553c3a57926"
git-tree-sha1 = "e05c53ebc86933601d36212a93b39144a2733493"
uuid = "ae029012-a4dd-5104-9daa-d747884805df"
version = "1.0.3"
version = "1.1.1"

[[Revise]]
deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "Pkg", "REPL", "Requires", "UUIDs", "Unicode"]
git-tree-sha1 = "3afd4b8001d03475369e6eb55c00bf15609b9289"
git-tree-sha1 = "637d03a5262b9f1d334cd63aaf092297fbc4f168"
uuid = "295af30f-e4ad-537b-8983-00126c2a3abe"
version = "3.1.7"
version = "3.1.9"

[[Richardson]]
deps = ["LinearAlgebra"]
Expand Down Expand Up @@ -1086,9 +1086,9 @@ uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa"
version = "0.5.5"

[[ScientificTypes]]
git-tree-sha1 = "b06fff5c17a20aa69494a3d9da62d9c88ec6b764"
git-tree-sha1 = "1d3f5f8bdf5dd0c9951eb9c595ee08a728aec331"
uuid = "321657f4-b219-11e9-178b-2701a2544e81"
version = "1.1.0"
version = "1.1.1"

[[Scratch]]
deps = ["Dates"]
Expand Down Expand Up @@ -1158,9 +1158,9 @@ version = "0.33.2"

[[StatsFuns]]
deps = ["Rmath", "SpecialFunctions"]
git-tree-sha1 = "04a5a8e6ab87966b43f247920eab053fd5fdc925"
git-tree-sha1 = "3b9f665c70712af3264b61c27a7e1d62055dafd1"
uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
version = "0.9.5"
version = "0.9.6"

[[StructArrays]]
deps = ["Adapt", "DataAPI", "Tables"]
Expand Down Expand Up @@ -1220,9 +1220,9 @@ version = "0.3.0"

[[Turing]]
deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedVI", "Bijectors", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker", "ZygoteRules"]
git-tree-sha1 = "0ee8eae03fc19c1ce36d6e598dffa2b523d4a8e2"
git-tree-sha1 = "d35cab4bd3f1d8feec9eea4855ee481ff310e4f4"
uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
version = "0.14.10"
version = "0.14.11"

[[UUIDs]]
deps = ["Random", "SHA"]
Expand Down Expand Up @@ -1462,4 +1462,4 @@ version = "3.0.0+3"
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"]
git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6"
uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd"
version = "0.9.1+5"
version = "0.9.1+5"
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