From b8ac501033ed0cb7d07a996e78f864150b51effd Mon Sep 17 00:00:00 2001
From: pjentsch <pjentsch@uwaterloo.ca>
Date: Wed, 21 Apr 2021 11:08:18 -0400
Subject: [PATCH] revert prev change
---
CovidAlertVaccinationModel/Manifest.toml | 89 +++++++++++--------
.../src/ABM/mixing_graphs.jl | 2 +
.../src/CovidAlertVaccinationModel.jl | 8 +-
.../src/IntervalsModel/intervals_model.jl | 1 -
CovidAlertVaccinationModel/src/data.jl | 6 +-
5 files changed, 61 insertions(+), 45 deletions(-)
diff --git a/CovidAlertVaccinationModel/Manifest.toml b/CovidAlertVaccinationModel/Manifest.toml
index 439fc5d..f0134ef 100644
--- a/CovidAlertVaccinationModel/Manifest.toml
+++ b/CovidAlertVaccinationModel/Manifest.toml
@@ -93,21 +93,21 @@ version = "0.9.5"
[[ChainRulesCore]]
deps = ["Compat", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "44e9f638aa9ed1ad58885defc568c133010140aa"
+git-tree-sha1 = "42e3c181483fbd2c416087a0a93838803e358358"
uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "0.9.37"
+version = "0.9.38"
[[CheapThreads]]
deps = ["ArrayInterface", "IfElse", "Requires", "Static", "StrideArraysCore", "ThreadingUtilities", "VectorizationBase"]
-git-tree-sha1 = "5b11b7aba0d4b53f46559b25055d3f0d4376fb36"
+git-tree-sha1 = "6596dbdb8fadd45ef9dff0087ef3a6ec9c5473bc"
uuid = "b630d9fa-e28e-4980-896d-83ce5e2106b2"
-version = "0.2.2"
+version = "0.2.3"
[[ColorSchemes]]
deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random", "StaticArrays"]
-git-tree-sha1 = "d3cf83862f70d430d4b34e43ed65e74bd50ae0e0"
+git-tree-sha1 = "9d7dfad1326b1ad29afa1366587806a14d727745"
uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
-version = "3.11.0"
+version = "3.12.0"
[[ColorTypes]]
deps = ["FixedPointNumbers", "Random"]
@@ -138,9 +138,9 @@ version = "0.1.0"
[[Conda]]
deps = ["JSON", "VersionParsing"]
-git-tree-sha1 = "6231e40619c15148bcb80aa19d731e629877d762"
+git-tree-sha1 = "299304989a5e6473d985212c28928899c74e9421"
uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
-version = "1.5.1"
+version = "1.5.2"
[[ConsoleProgressMonitor]]
deps = ["Logging", "ProgressMeter"]
@@ -218,9 +218,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
[[Distributions]]
deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "e64debe8cd174cc52d7dd617ebc5492c6f8b698c"
+git-tree-sha1 = "09b3d464f5cbeaf1a2a422afe20d82eff421a7ca"
uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.24.15"
+version = "0.24.17"
[[DocStringExtensions]]
deps = ["LibGit2", "Markdown", "Pkg", "Test"]
@@ -268,10 +268,10 @@ uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
version = "4.3.1+4"
[[FFTW]]
-deps = ["AbstractFFTs", "FFTW_jll", "IntelOpenMP_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Reexport"]
-git-tree-sha1 = "1b48dbde42f307e48685fa9213d8b9f8c0d87594"
+deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
+git-tree-sha1 = "1dc6ca6ad69eb9beadd3ce82b90910f4fa63d7c3"
uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
-version = "1.3.2"
+version = "1.4.0"
[[FFTW_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -327,9 +327,9 @@ version = "3.3.3+0"
[[GR]]
deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"]
-git-tree-sha1 = "82a03d9c331d181bf33c99c9af04202cc4533d48"
+git-tree-sha1 = "011458b83178ac913dc4eb73b229af45bdde5d83"
uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
-version = "0.57.3"
+version = "0.57.4"
[[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"]
@@ -422,9 +422,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
[[Interpolations]]
deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"]
-git-tree-sha1 = "eb1dd6d5b2275faaaa18533e0fc5f9171cec25fa"
+git-tree-sha1 = "1e0e51692a3a77f1eeb51bf741bdd0439ed210e7"
uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
-version = "0.13.1"
+version = "0.13.2"
[[Intervals]]
deps = ["Dates", "Printf", "RecipesBase", "Serialization", "TimeZones"]
@@ -449,9 +449,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d"
version = "1.0.0"
[[JLLWrappers]]
-git-tree-sha1 = "a431f5f2ca3f4feef3bd7a5e94b8b8d4f2f647a0"
+deps = ["Preferences"]
+git-tree-sha1 = "642a199af8b68253517b80bd3bfd17eb4e84df6e"
uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
-version = "1.2.0"
+version = "1.3.0"
[[JSON]]
deps = ["Dates", "Mmap", "Parsers", "Unicode"]
@@ -502,9 +503,9 @@ version = "1.6.0"
[[Latexify]]
deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"]
-git-tree-sha1 = "7c72983c6daf61393ee8a0b29a419c709a06cede"
+git-tree-sha1 = "1925f6838df247e7853f3f9727dd8a52a78f60f4"
uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
-version = "0.14.12"
+version = "0.15.2"
[[Lazy]]
deps = ["MacroTools"]
@@ -605,6 +606,12 @@ version = "1.3.5"
deps = ["Libdl"]
uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+[[LogExpFunctions]]
+deps = ["DocStringExtensions"]
+git-tree-sha1 = "9809b844f0ff853f0620e0cac7a712e1818671e5"
+uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
+version = "0.2.1"
+
[[Logging]]
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
@@ -788,9 +795,9 @@ version = "1.0.10"
[[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 = "cc4eb1be2576984d7a0f7f51478827dee816138b"
+git-tree-sha1 = "30004ffb10118498f38eb0f22cffe802b0aae45f"
uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.11.2"
+version = "1.12.0"
[[PooledArrays]]
deps = ["DataAPI", "Future"]
@@ -798,6 +805,12 @@ git-tree-sha1 = "cde4ce9d6f33219465b55162811d8de8139c0414"
uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
version = "1.2.1"
+[[Preferences]]
+deps = ["TOML"]
+git-tree-sha1 = "ea79e4c9077208cd3bc5d29631a26bc0cff78902"
+uuid = "21216c6a-2e73-6563-6e65-726566657250"
+version = "1.2.1"
+
[[PrettyTables]]
deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"]
git-tree-sha1 = "574a6b3ea95f04e8757c0280bb9c29f1a5e35138"
@@ -822,9 +835,9 @@ version = "1.5.0"
[[PyCall]]
deps = ["Conda", "Dates", "Libdl", "LinearAlgebra", "MacroTools", "Serialization", "VersionParsing"]
-git-tree-sha1 = "dd1a970b543bd02efce2984582e996af28cab27f"
+git-tree-sha1 = "169bb8ea6b1b143c5cf57df6d34d022a7b60c6db"
uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-version = "1.92.2"
+version = "1.92.3"
[[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"]
@@ -976,9 +989,9 @@ version = "0.2.4"
[[StaticArrays]]
deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "2f01a51c23eed210ff4a1be102c4cc8236b66e5b"
+git-tree-sha1 = "e8cd1b100d37f5b4cfd2c83f45becf61c762eaf7"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.1.0"
+version = "1.1.1"
[[Statistics]]
deps = ["LinearAlgebra", "SparseArrays"]
@@ -991,10 +1004,10 @@ uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
version = "0.33.5"
[[StatsFuns]]
-deps = ["Rmath", "SpecialFunctions"]
-git-tree-sha1 = "ced55fd4bae008a8ea12508314e725df61f0ba45"
+deps = ["LogExpFunctions", "Rmath", "SpecialFunctions"]
+git-tree-sha1 = "30cd8c360c54081f806b1ee14d2eecbef3c04c49"
uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.7"
+version = "0.9.8"
[[StrideArraysCore]]
deps = ["ArrayInterface", "Requires", "ThreadingUtilities", "VectorizationBase"]
@@ -1010,9 +1023,9 @@ version = "0.5.1"
[[StructTypes]]
deps = ["Dates", "UUIDs"]
-git-tree-sha1 = "5eaf731e88587bb72a6c1262c0a014cd1859a08d"
+git-tree-sha1 = "ad4558dee74c5d26ab0d0324766b1a3ee6ae777a"
uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
-version = "1.5.2"
+version = "1.7.1"
[[SuiteSparse]]
deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
@@ -1036,9 +1049,9 @@ version = "1.0.1"
[[Tables]]
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
-git-tree-sha1 = "a9ff3dfec713c6677af435d6a6d65f9744feef67"
+git-tree-sha1 = "c9d2d262e9a327be1f35844df25fe4561d258dc9"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "1.4.1"
+version = "1.4.2"
[[Tar]]
deps = ["ArgTools", "SHA"]
@@ -1074,9 +1087,9 @@ version = "1.5.3"
[[Transducers]]
deps = ["ArgCheck", "BangBang", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"]
-git-tree-sha1 = "721dc0b917a43e6d191f07a6ea095ced164f08ce"
+git-tree-sha1 = "d0aa4681564aa1c68bb1e146dd181817f139697b"
uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999"
-version = "0.4.62"
+version = "0.4.63"
[[URIs]]
git-tree-sha1 = "7855809b88d7b16e9b029afd17880930626f54a2"
@@ -1097,9 +1110,9 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
[[VectorizationBase]]
deps = ["ArrayInterface", "Hwloc", "IfElse", "Libdl", "LinearAlgebra", "Static"]
-git-tree-sha1 = "ec513821175957ffb4a33af7d4b96065e3c0cdf6"
+git-tree-sha1 = "4f9b7b3e40da418518e0282e7397fd0ca17a7527"
uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
-version = "0.19.27"
+version = "0.19.28"
[[VersionParsing]]
git-tree-sha1 = "80229be1f670524750d905f8fc8148e5a8c4537f"
diff --git a/CovidAlertVaccinationModel/src/ABM/mixing_graphs.jl b/CovidAlertVaccinationModel/src/ABM/mixing_graphs.jl
index 00bdc2d..87d12b0 100644
--- a/CovidAlertVaccinationModel/src/ABM/mixing_graphs.jl
+++ b/CovidAlertVaccinationModel/src/ABM/mixing_graphs.jl
@@ -11,9 +11,11 @@ function Base.isequal(e1::GraphEdge,e2::GraphEdge)
end
function sample_mixing_graph!(mixing_graph,population_demographics)
mixing_edges = mixing_graph.mixing_edges
+ # display( mixing_edges.sampler_matrix)
for i in 1:size(mixing_edges.contact_array)[1], j in 1:i #diagonal
demo_i = Int(population_demographics[i])
demo_j = Int(population_demographics[j])
+
rand!(RNG, mixing_edges.sampler_matrix[demo_i,demo_j],mixing_edges.sample_cache[i,j])
for k in 1:length(mixing_edges.contact_array[i,j][1])
kth_node_i = mixing_edges.contact_array[i,j][1][k]
diff --git a/CovidAlertVaccinationModel/src/CovidAlertVaccinationModel.jl b/CovidAlertVaccinationModel/src/CovidAlertVaccinationModel.jl
index 0e2d09b..3e0897f 100644
--- a/CovidAlertVaccinationModel/src/CovidAlertVaccinationModel.jl
+++ b/CovidAlertVaccinationModel/src/CovidAlertVaccinationModel.jl
@@ -28,18 +28,20 @@ using StaticArrays
export intervalsmodel, hh, ws, rest, abm
const DNDEBUG = false
-macro c_assert(boolean)
+macro c_assert(boolean) #this is a version of @assert that turns itself off when DNDEBUG=false, should use more
if DNDEBUG
message = string("Assertion: ", boolean, " failed")
:($(esc(boolean)) || error($message))
end
end
+const durmax = 144
const PACKAGE_FOLDER = dirname(dirname(pathof(CovidAlertVaccinationModel)))
const RNG = Xoroshiro128Star(1)
-#consts that let give us nicer names for the indices
const color_palette = palette(:seaborn_pastel) #color theme for the plots
+#consts that let give us nicer names for the indices
+
include("utils.jl")
include("data.jl")
include("ABM/contact_vectors.jl")
@@ -52,11 +54,11 @@ include("ABM/output.jl")
include("ABM/solve.jl")
include("ABM/abm.jl")
+
include("IntervalsModel/intervals_model.jl")
include("IntervalsModel/interval_overlap_sampling.jl")
include("IntervalsModel/hh_durations_model.jl")
include("IntervalsModel/ws_durations_model.jl")
include("IntervalsModel/rest_durations_model.jl")
include("IntervalsModel/plotting_functions.jl")
-
end
diff --git a/CovidAlertVaccinationModel/src/IntervalsModel/intervals_model.jl b/CovidAlertVaccinationModel/src/IntervalsModel/intervals_model.jl
index 3e4fce9..9605d5a 100644
--- a/CovidAlertVaccinationModel/src/IntervalsModel/intervals_model.jl
+++ b/CovidAlertVaccinationModel/src/IntervalsModel/intervals_model.jl
@@ -4,7 +4,6 @@ Number of start times to sample for a given set of distribution parameters.
const comparison_samples = 100
const distribution_support = 0:94
const YOUNG, MIDDLE,OLD = 1,2,3
-const durmax = 144
const sample_repeat = 100
const sparam = (60,12)
diff --git a/CovidAlertVaccinationModel/src/data.jl b/CovidAlertVaccinationModel/src/data.jl
index b3d825e..a84afeb 100644
--- a/CovidAlertVaccinationModel/src/data.jl
+++ b/CovidAlertVaccinationModel/src/data.jl
@@ -108,12 +108,12 @@ function load_contact_time_distributions()
ws = "ws",
rest = "rest"
)
- function make_sampler(λ) #our samples can only be in 0:143 so we can fake a poisson distribution by explicitly sampling
- return Distributions.DiscreteNonParametricSampler(0:durmax,[pdf(Poisson(λ),x) for x in 0:durmax])
+ function make_sampler(λ)
+ return Distributions.PoissonADSampler(λ)#Distributions.DiscreteNonParametricSampler(0:durmax,[pdf(Poisson(λ),x) for x in 0:durmax])
end
contact_distributions_tuple = map(fnames) do fname
dat = deserialize(joinpath(PACKAGE_FOLDER,"intervals_model_output","simulation_output","$fname.dat"))
- return map(p -> Poisson(mode(p.particles)), as_symmetric_matrix(dat[distkey].P))
+ return map(p -> make_sampler(mode(p.particles)), as_symmetric_matrix(dat[distkey].P))
end
return contact_distributions_tuple
end
--
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