wip

Manifest.toml

@@ -11,23 +11,29 @@ git-tree-sha1 = "dedbbb2ddb876f899585c4ec4433265e3017215a"
 uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197"
 version = "2.1.0"
 
+[[ArgTools]]
+uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+
 [[ArnoldiMethod]]
 deps = ["LinearAlgebra", "Random", "StaticArrays"]
 git-tree-sha1 = "f87e559f87a45bece9c9ed97458d3afe98b1ebb9"
 uuid = "ec485272-7323-5ecc-a04f-4719b315124d"
 version = "0.1.0"
 
+[[ArrayInterface]]
+deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays"]
+git-tree-sha1 = "ef91c543a3a8094eba9b1f7171258b9ecae87dfa"
+uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
+version = "3.0.0"
+
 [[Artifacts]]
-deps = ["Pkg"]
-git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
-version = "1.3.0"
 
 [[BangBang]]
 deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"]
-git-tree-sha1 = "f42321255afc37da855b6cd9f2a1fc36c017ceee"
+git-tree-sha1 = "d53b1eaefd48e233545d21f5b764c8ee54df4a09"
 uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66"
-version = "0.3.29"
+version = "0.3.30"
 
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -87,10 +93,8 @@ uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
 version = "3.25.0"
 
 [[CompilerSupportLibraries_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "8e695f735fca77e9708e795eda62afdb869cbb70"
+deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "0.3.4+0"
 
 [[CompositionsBase]]
 git-tree-sha1 = "f3955eb38944e5dd0fabf8ca1e267d94941d34a5"
@@ -114,9 +118,9 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
 version = "4.0.4"
 
 [[DataAPI]]
-git-tree-sha1 = "25ccd31003243d2ce83e474cf11663dddf48035f"
+git-tree-sha1 = "6d64b28d291cb94a0d84e6e41081fb081e7f717f"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
-version = "1.4.1"
+version = "1.5.0"
 
 [[DataFrames]]
 deps = ["CategoricalArrays", "Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
@@ -158,6 +162,10 @@ git-tree-sha1 = "f0e06a5b5ccda38e2fb8f59d91316e657b67047d"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
 version = "0.24.12"
 
+[[Downloads]]
+deps = ["ArgTools", "LibCURL", "NetworkOptions"]
+uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+
 [[EarCut_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "92d8f9f208637e8d2d28c664051a00569c01493d"
@@ -269,6 +277,11 @@ git-tree-sha1 = "c7ec02c4c6a039a98a15f955462cd7aea5df4508"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 version = "0.8.19"
 
+[[IfElse]]
+git-tree-sha1 = "28e837ff3e7a6c3cdb252ce49fb412c8eb3caeef"
+uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
+version = "0.1.0"
+
 [[ImportAll]]
 deps = ["Test"]
 git-tree-sha1 = "5aa65f6204e1b68dfef024421e61fbcacecfbfa6"
@@ -345,16 +358,34 @@ git-tree-sha1 = "c7aebfecb1a60d59c0fe023a68ec947a208b1e6b"
 uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 version = "1.2.0"
 
+[[LabelledArrays]]
+deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "StaticArrays"]
+git-tree-sha1 = "5e288800819c323de5897fa6d5a002bdad54baf7"
+uuid = "2ee39098-c373-598a-b85f-a56591580800"
+version = "1.5.0"
+
 [[Latexify]]
 deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"]
 git-tree-sha1 = "3a0084cec7bf157edcb45a67fac0647f88fe5eaf"
 uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 version = "0.14.7"
 
+[[LibCURL]]
+deps = ["LibCURL_jll", "MozillaCACerts_jll"]
+uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
+
+[[LibCURL_jll]]
+deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
+uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
+
 [[LibGit2]]
-deps = ["Printf"]
+deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
+[[LibSSH2_jll]]
+deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
+uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
+
 [[LibVPX_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "85fcc80c3052be96619affa2fe2e6d2da3908e11"
@@ -442,10 +473,8 @@ uuid = "739be429-bea8-5141-9913-cc70e7f3736d"
 version = "1.0.3"
 
 [[MbedTLS_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "0eef589dd1c26a3ac9d753fe1a8bcad63f956fa6"
+deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
-version = "2.16.8+1"
 
 [[Measures]]
 git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f"
@@ -467,6 +496,9 @@ version = "0.4.5"
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
+[[MozillaCACerts_jll]]
+uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
+
 [[NaNMath]]
 git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
@@ -483,6 +515,9 @@ git-tree-sha1 = "01b5715cdd1b7c5d493c26cc05e4af663ba9a052"
 uuid = "46757867-2c16-5918-afeb-47bfcb05e46a"
 version = "0.3.0"
 
+[[NetworkOptions]]
+uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+
 [[Ogg_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "a42c0f138b9ebe8b58eba2271c5053773bde52d0"
@@ -508,9 +543,9 @@ uuid = "91d4177d-7536-5919-b921-800302f37372"
 version = "1.3.1+3"
 
 [[OrderedCollections]]
-git-tree-sha1 = "cf59cfed2e2c12e8a2ff0a4f1e9b2cd8650da6db"
+git-tree-sha1 = "d45739abcfc03b51f6a42712894a593f74c80a23"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.3.2"
+version = "1.3.3"
 
 [[PCRE_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -542,7 +577,7 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc"
 version = "0.40.0+0"
 
 [[Pkg]]
-deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[PlotThemes]]
@@ -592,7 +627,7 @@ uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 version = "2.4.1"
 
 [[REPL]]
-deps = ["InteractiveUtils", "Markdown", "Sockets"]
+deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 
 [[Random]]
@@ -699,9 +734,9 @@ version = "1.2.1"
 
 [[SplittablesBase]]
 deps = ["Setfield", "Test"]
-git-tree-sha1 = "c2b4f3cd29827787a5f61afe12ea13222197ab98"
+git-tree-sha1 = "edef25a158db82f4940720ebada14a60ef6c4232"
 uuid = "171d559e-b47b-412a-8079-5efa626c420e"
-version = "0.1.12"
+version = "0.1.13"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
@@ -741,6 +776,10 @@ version = "1.2.3"
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 
+[[TOML]]
+deps = ["Dates"]
+uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+
 [[TableTraits]]
 deps = ["IteratorInterfaceExtensions"]
 git-tree-sha1 = "b1ad568ba658d8cbb3b892ed5380a6f3e781a81e"
@@ -753,8 +792,12 @@ git-tree-sha1 = "8dc2bb7d3548e315d890706547b24502ed79504f"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 version = "1.3.1"
 
+[[Tar]]
+deps = ["ArgTools", "SHA"]
+uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
+
 [[Test]]
-deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[ThreadsX]]
@@ -795,9 +838,9 @@ version = "1.18.0+4"
 
 [[XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "be0db24f70aae7e2b89f2f3092e93b8606d659a6"
+git-tree-sha1 = "afd2b541e8fd425cd3b7aa55932a257035ab4a70"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
-version = "2.9.10+3"
+version = "2.9.11+0"
 
 [[XSLT_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Pkg", "XML2_jll"]
@@ -932,10 +975,8 @@ uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10"
 version = "1.4.0+3"
 
 [[Zlib_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "320228915c8debb12cb434c59057290f0834dbf6"
+deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.11+18"
 
 [[Zstd_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -973,6 +1014,10 @@ git-tree-sha1 = "fa14ac25af7a4b8a7f61b287a124df7aab601bcd"
 uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
 version = "1.3.6+6"
 
+[[nghttp2_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+
 [[x264_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "d713c1ce4deac133e3334ee12f4adff07f81778f"

Project.toml

@@ -10,6 +10,7 @@ Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 ImportAll = "c65182e5-40f4-518f-8165-175b85689199"
+LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 NamedTupleTools = "d9ec5142-1e00-5aa0-9d6a-321866360f50"
 NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"

src/CovidAlertVaccinationModel.jl

@@ -45,9 +45,10 @@ function main()
     # display(size.(agent_model.demographic_index_vectors))
     u_0 = get_u_0(length(agent_model.demographics))
     steps = 300
-    @btime solve!($u_0,$get_parameters(),$steps,$agent_model,$vaccinate_uniformly!);
-    # solve!(u_0,get_parameters(),steps,agent_model,vaccinate_uniformly!);
-    # plot_model(agent_model.base_network,graphs,sol1)
+    # @btime solve!($u_0,$get_parameters(),$steps,$agent_model,$vaccinate_uniformly!);
+    sol,graphs = solve!(u_0,get_parameters(),steps,agent_model,vaccinate_uniformly!);
+    return aggregate_timeseries(sol)
+    # plot_model_spatial_gif(agent_model.base_network,graphs,sol1)
 end
 
 

src/plotting.jl

@@ -37,7 +37,7 @@ end
         
 #     gif(anim, "graphplot.gif", fps = 1.0)
 # end
-function plot_model(static_graph,annealed_graph_list::AbstractVector,solution) 
+function plot_model_spatial_gif(static_graph,annealed_graph_list::AbstractVector,solution) 
     plt = plot()
     network_pts = make_layout(annealed_graph_list[1])
     anim = Animation()
@@ -52,4 +52,14 @@ function plot_model(static_graph,annealed_graph_list::AbstractVector,solution)
         end
         
     gif(anim, "graphplot.gif", fps = 1.0)
+end
+using LabelledArrays
+function aggregate_timeseries(sol)
+    agent_statuses = map(Symbol,[AgentStatus(i) for i in 1:AgentStatus.size])
+    return @LArray [count(x -> AgentStatus(i)  == x, u_t) for u_t in sol,  i in 1:AgentStatus.size] namedtuple(agent_statuses,ntuple(i -> (:,i),length(agent_statuses)))
+end
+
+function plot_aggregate_timeseries(sol,network)
+    plot(sol,labels = reshape([string(k) for k in keys(keys(sol))],(1,:)))
+    
 end
\ No newline at end of file