SIR Notebook

README.md

SIR Model Prototype Notebook in Julia

Manifest.toml

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uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

[[Logging]]
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"

[[LoggingExtras]]
git-tree-sha1 = "c867b50bfc564f0beded1c566f4fc66cfd8b5418"
uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36"
version = "0.4.0"

[[MLStyle]]
git-tree-sha1 = "67f9a88611bc79f992aa705d9bbc833a2547dec7"
uuid = "d8e11817-5142-5d16-987a-aa16d5891078"
version = "0.3.1"

[[MacroTools]]
deps = ["Markdown", "Random"]
git-tree-sha1 = "f7d2e3f654af75f01ec49be82c231c382214223a"
uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
version = "0.5.5"

[[Markdown]]
deps = ["Base64"]
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"

[[MbedTLS]]
deps = ["Dates", "MbedTLS_jll", "Random", "Sockets"]
git-tree-sha1 = "a9e2221f06b42f56052f43ad7edecb01d0ef5ab4"
uuid = "739be429-bea8-5141-9913-cc70e7f3736d"
version = "1.0.1"

[[MbedTLS_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "066a4467008745eed36dad973ceb66405785a621"
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
version = "2.16.0+1"

[[Measures]]
git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f"
uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
version = "0.3.1"

[[Missings]]
deps = ["DataAPI"]
git-tree-sha1 = "de0a5ce9e5289f27df672ffabef4d1e5861247d5"
uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
version = "0.4.3"

[[Mmap]]
uuid = "a63ad114-7e13-5084-954f-fe012c677804"

[[ModelingToolkit]]
deps = ["DiffEqBase", "DiffRules", "Distributed", "DocStringExtensions", "GeneralizedGenerated", "Latexify", "LinearAlgebra", "MacroTools", "NaNMath", "SparseArrays", "SpecialFunctions", "StaticArrays"]
git-tree-sha1 = "fbd6b367d0d37b1533f71a44c20abc237eab6bc6"
uuid = "961ee093-0014-501f-94e3-6117800e7a78"
version = "1.4.2"

[[MuladdMacro]]
git-tree-sha1 = "c6190f9a7fc5d9d5915ab29f2134421b12d24a68"
uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
version = "0.2.2"

[[MultiScaleArrays]]
deps = ["DiffEqBase", "RecursiveArrayTools", "Statistics", "StochasticDiffEq", "TreeViews"]
git-tree-sha1 = "c69e4a0db8d482a825c7ac76a433759ade2a5af2"
uuid = "f9640e96-87f6-5992-9c3b-0743c6a49ffa"
version = "1.6.0"

[[NLSolversBase]]
deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"]
git-tree-sha1 = "7c4e66c47848562003250f28b579c584e55becc0"
uuid = "d41bc354-129a-5804-8e4c-c37616107c6c"
version = "7.6.1"

[[NLsolve]]
deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"]
git-tree-sha1 = "cce0463af83a0f36c7bfa5820e373ac090cc46ad"
uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
version = "4.3.0"

[[NaNMath]]
git-tree-sha1 = "928b8ca9b2791081dc71a51c55347c27c618760f"
uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
version = "0.3.3"

[[NameResolution]]
deps = ["DataStructures", "PrettyPrint"]
git-tree-sha1 = "f4119274d5a410c64a1d9f546312bb6ae54d41c0"
uuid = "71a1bf82-56d0-4bbc-8a3c-48b961074391"
version = "0.1.3"

[[Observables]]
deps = ["Test"]
git-tree-sha1 = "dc02cec22747d1d10d9f70d8a1c03432b5bfbcd0"
uuid = "510215fc-4207-5dde-b226-833fc4488ee2"
version = "0.2.3"

[[Ogg_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "f4d4d03c562f40652c0baabd3e4cb2e756e157b7"
uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051"
version = "1.3.3+0"

[[OpenSSL_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "33661eb9d5484220b4367d067f499b30bafc9c12"
uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
version = "1.1.1+1"

[[OpenSpecFun_jll]]
deps = ["CompilerSupportLibraries_jll", "Libdl", "Pkg"]
git-tree-sha1 = "d51c416559217d974a1113522d5919235ae67a87"
uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
version = "0.5.3+3"

[[Opus_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "c9931bf2fcdb57b48c227395c61ea82603212f7d"
uuid = "91d4177d-7536-5919-b921-800302f37372"
version = "1.3.1+0"

[[OrderedCollections]]
deps = ["Random", "Serialization", "Test"]
git-tree-sha1 = "c4c13474d23c60d20a67b217f1d7f22a40edf8f1"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.1.0"

[[OrdinaryDiffEq]]
deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "ExponentialUtilities", "FiniteDiff", "ForwardDiff", "GenericSVD", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "NLsolve", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
git-tree-sha1 = "8351ae59bb662f19464691823aaf8a235e8005db"
uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
version = "5.32.0"

[[ParameterizedFunctions]]
deps = ["DataStructures", "DiffEqBase", "LinearAlgebra", "ModelingToolkit"]
git-tree-sha1 = "23ccaee3dd3a6d104a381011d715964dd2943491"
uuid = "65888b18-ceab-5e60-b2b9-181511a3b968"
version = "5.0.3"

[[Parameters]]
deps = ["OrderedCollections"]
git-tree-sha1 = "b62b2558efb1eef1fa44e4be5ff58a515c287e38"
uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a"
version = "0.12.0"

[[Parsers]]
deps = ["Dates", "Test"]
git-tree-sha1 = "0c16b3179190d3046c073440d94172cfc3bb0553"
uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
version = "0.3.12"

[[Pidfile]]
deps = ["FileWatching", "Test"]
git-tree-sha1 = "1ffd82728498b5071cde851bbb7abd780d4445f3"
uuid = "fa939f87-e72e-5be4-a000-7fc836dbe307"
version = "1.1.0"

[[Pkg]]
deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Test", "UUIDs"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

[[PlotThemes]]
deps = ["PlotUtils", "Requires", "Statistics"]
git-tree-sha1 = "df772cc7c78862da96af1ee85cd0111c6640e44e"
uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a"
version = "1.0.1"

[[PlotUtils]]
deps = ["Colors", "Dates", "Printf", "Random", "Reexport"]
git-tree-sha1 = "132e468bf7d67ee6c997c160b982a7ab2e7c3e37"
uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043"
version = "0.6.4"

[[Plots]]
deps = ["Base64", "Contour", "Dates", "FFMPEG", "FixedPointNumbers", "GR", "GeometryTypes", "JSON", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "Reexport", "Requires", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"]
git-tree-sha1 = "a4b22be3bb271cf46466e44009b5788ef4aaef7d"
uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
version = "0.29.8"

[[PoissonRandom]]
deps = ["Random", "Statistics", "Test"]
git-tree-sha1 = "44d018211a56626288b5d3f8c6497d28c26dc850"
uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab"
version = "0.4.0"

[[PrettyPrint]]
git-tree-sha1 = "21e1f88cb73589ec39a1181f77eb444b5276151e"
uuid = "8162dcfd-2161-5ef2-ae6c-7681170c5f98"
version = "0.1.0"

[[Printf]]
deps = ["Unicode"]
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"

[[ProgressLogging]]
deps = ["Logging", "SHA", "UUIDs"]
git-tree-sha1 = "e47914361d124d8760f5e356403daeb7f3b81633"
uuid = "33c8b6b6-d38a-422a-b730-caa89a2f386c"
version = "0.1.2"

[[ProgressMeter]]
deps = ["Distributed", "Printf"]
git-tree-sha1 = "ea1f4fa0ff5e8b771bf130d87af5b7ef400760bd"
uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
version = "1.2.0"

[[REPL]]
deps = ["InteractiveUtils", "Markdown", "Sockets"]
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

[[Random]]
deps = ["Serialization"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

[[RandomNumbers]]
deps = ["Random", "Requires"]
git-tree-sha1 = "441e6fc35597524ada7f85e13df1f4e10137d16f"
uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143"
version = "1.4.0"

[[RecipesBase]]
git-tree-sha1 = "b4ed4a7f988ea2340017916f7c9e5d7560b52cae"
uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
version = "0.8.0"

[[RecursiveArrayTools]]
deps = ["ArrayInterface", "RecipesBase", "Requires", "StaticArrays", "Statistics", "ZygoteRules"]
git-tree-sha1 = "bd13db2a3561fb3a3635220c5ee21e3356d7631e"
uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
version = "2.1.0"

[[RecursiveFactorization]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "6761a5d1f9646affb2a369ff932841fff77934a3"
uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4"
version = "0.1.0"

[[Reexport]]
deps = ["Pkg"]
git-tree-sha1 = "7b1d07f411bc8ddb7977ec7f377b97b158514fe0"
uuid = "189a3867-3050-52da-a836-e630ba90ab69"
version = "0.2.0"

[[Requires]]
deps = ["UUIDs"]
git-tree-sha1 = "d37400976e98018ee840e0ca4f9d20baa231dc6b"
uuid = "ae029012-a4dd-5104-9daa-d747884805df"
version = "1.0.1"

[[ResettableStacks]]
deps = ["StaticArrays"]
git-tree-sha1 = "d19e9c93de6020a96dbb2820567c78d0ab8f7248"
uuid = "ae5879a3-cd67-5da8-be7f-38c6eb64a37b"
version = "1.0.0"

[[Roots]]
deps = ["Printf"]
git-tree-sha1 = "955ce06c1f424ca7043c7827f5cb14d8eb397065"
uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
version = "1.0.1"

[[SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"

[[Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"

[[SharedArrays]]
deps = ["Distributed", "Mmap", "Random", "Serialization"]
uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"

[[Showoff]]
deps = ["Dates"]
git-tree-sha1 = "e032c9df551fb23c9f98ae1064de074111b7bc39"
uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f"
version = "0.3.1"

[[SimpleTraits]]
deps = ["InteractiveUtils", "MacroTools"]
git-tree-sha1 = "2bdf3b6300a9d66fe29ee8bb51ba100c4df9ecbc"
uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
version = "0.9.1"

[[Sockets]]
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"

[[SortingAlgorithms]]
deps = ["DataStructures", "Random", "Test"]
git-tree-sha1 = "03f5898c9959f8115e30bc7226ada7d0df554ddd"
uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
version = "0.3.1"

[[SparseArrays]]
deps = ["LinearAlgebra", "Random"]
uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

[[SparseDiffTools]]
deps = ["Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "InteractiveUtils", "LightGraphs", "LinearAlgebra", "Requires", "SparseArrays", "VertexSafeGraphs"]
git-tree-sha1 = "6429f706e7da24a8c1c5e0416c3f0ce9974ab991"
uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804"
version = "1.4.0"

[[SpecialFunctions]]
deps = ["OpenSpecFun_jll"]
git-tree-sha1 = "e19b98acb182567bcb7b75bb5d9eedf3a3b5ec6c"
uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
version = "0.10.0"

[[StaticArrays]]
deps = ["LinearAlgebra", "Random", "Statistics"]
git-tree-sha1 = "5a3bcb6233adabde68ebc97be66e95dcb787424c"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
version = "0.12.1"

[[Statistics]]
deps = ["LinearAlgebra", "SparseArrays"]
uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[[StatsBase]]
deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"]
git-tree-sha1 = "19bfcb46245f69ff4013b3df3b977a289852c3a1"
uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
version = "0.32.2"

[[SteadyStateDiffEq]]
deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport"]
git-tree-sha1 = "9a2de84a1618e1702dbb95ebdbb84dbf7f24d1ab"
uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
version = "1.5.0"

[[StochasticDiffEq]]
deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "FillArrays", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "Parameters", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays"]
git-tree-sha1 = "d7c979f831943fb1d870c862a0d60c5f475c56af"
uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
version = "6.19.1"

[[SuiteSparse]]
deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"

[[Sundials]]
deps = ["BinaryProvider", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SparseArrays", "SuiteSparse"]
git-tree-sha1 = "d6e23d712b0ec7161174acbc82fd224cde3e3103"
uuid = "c3572dad-4567-51f8-b174-8c6c989267f4"
version = "3.9.0"

[[TableTraits]]
deps = ["IteratorInterfaceExtensions"]
git-tree-sha1 = "b1ad568ba658d8cbb3b892ed5380a6f3e781a81e"
uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
version = "1.0.0"

[[TerminalLoggers]]
deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"]
git-tree-sha1 = "8c05be75dfe73d90e5dfb6293e0c852013f7282d"
uuid = "5d786b92-1e48-4d6f-9151-6b4477ca9bed"
version = "0.1.1"

[[Test]]
deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[[TreeViews]]
deps = ["Test"]
git-tree-sha1 = "8d0d7a3fe2f30d6a7f833a5f19f7c7a5b396eae6"
uuid = "a2a6695c-b41b-5b7d-aed9-dbfdeacea5d7"
version = "0.3.0"

[[UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

[[UnPack]]
git-tree-sha1 = "e0cb9715adda456f7657e45377fd3063bf87179a"
uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
version = "0.1.0"

[[Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[[VertexSafeGraphs]]
deps = ["LightGraphs"]
git-tree-sha1 = "35060f8047a2b79bdc8e4961bbbd2b7e30e62709"
uuid = "19fa3120-7c27-5ec5-8db8-b0b0aa330d6f"
version = "0.1.1"

[[WebIO]]
deps = ["AssetRegistry", "Base64", "Distributed", "FunctionalCollections", "JSON", "Logging", "Observables", "Pkg", "Random", "Requires", "Sockets", "UUIDs", "WebSockets", "Widgets"]
git-tree-sha1 = "b8eb800251c06efd635bcdc4ec7f83643f0b9a61"
uuid = "0f1e0344-ec1d-5b48-a673-e5cf874b6c29"
version = "0.8.13"

[[WebSockets]]
deps = ["Base64", "Dates", "Distributed", "HTTP", "Logging", "Random", "Sockets", "Test"]
git-tree-sha1 = "13f763d38c7a05688938808b49cb29b18b60c8c8"
uuid = "104b5d7c-a370-577a-8038-80a2059c5097"
version = "1.5.2"

[[Widgets]]
deps = ["Colors", "Dates", "Observables", "OrderedCollections"]
git-tree-sha1 = "fc0feda91b3fef7fe6948ee09bb628f882b49ca4"
uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62"
version = "0.6.2"

[[Zlib_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "fd36a6739e256527287c5444960d0266712cd49e"
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.11+8"

[[ZygoteRules]]
deps = ["MacroTools"]
git-tree-sha1 = "b3b4882cc9accf6731a08cc39543fbc6b669dca8"
uuid = "700de1a5-db45-46bc-99cf-38207098b444"
version = "0.2.0"

[[libass_jll]]
deps = ["Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "Libdl", "Pkg", "Zlib_jll"]
git-tree-sha1 = "3fd3ea3525f2e3d337c54a52b2ca78a5a272bbf5"
uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0"
version = "0.14.0+0"

[[libfdk_aac_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "0e4ace600c20714a8dd67700c4502714d8473e8e"
uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280"
version = "0.1.6+1"

[[libvorbis_jll]]
deps = ["Libdl", "Ogg_jll", "Pkg"]
git-tree-sha1 = "71e54fb89ac3e0344c7185d1876fd96b0f246952"
uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
version = "1.3.6+2"

[[x264_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "23664c0757c3740050ca0e22944c786c165ca25a"
uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a"
version = "2019.5.25+1"

[[x265_jll]]
deps = ["Libdl", "Pkg"]
git-tree-sha1 = "9345e417084421a8e91373d6196bc58e660eed2a"
uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76"
version = "3.0.0+0"

postBuild

#!/bin/bash
julia -e 'using WebIO; WebIO.install_jupyter_nbextension();'

Project.toml

[deps]
DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
Interact = "c601a237-2ae4-5e1e-952c-7a85b0c7eef1"
ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
WebIO = "0f1e0344-ec1d-5b48-a673-e5cf874b6c29"

sir_prototype.ipynb