GWIS configuration

.github/workflows/CI.yml

@@ -18,11 +18,11 @@ jobs:
           - x64
     steps:
       - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:

.gitignore

@@ -36,3 +36,4 @@ sandbox.jl
 src/generate_results.jl
 test_grid.csv
 test/tl_inputs/real_data.jl
+test/data/scratch/

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.4"
 manifest_format = "2.0"
-project_hash = "2b58dcc0ffd21f9ddd37c869a6c32c55af516134"
+project_hash = "026a4a228f2fe6f789f0bbad2d45493e7ed45f99"
 
 [[deps.ARFFFiles]]
 deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"]
@@ -936,6 +936,24 @@ git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
 uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe"
 version = "1.0.2"
 
+[[deps.HDF5]]
+deps = ["Compat", "HDF5_jll", "Libdl", "MPIPreferences", "Mmap", "Preferences", "Printf", "Random", "Requires", "UUIDs"]
+git-tree-sha1 = "e856eef26cf5bf2b0f95f8f4fc37553c72c8641c"
+uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+version = "0.17.2"
+
+    [deps.HDF5.extensions]
+    MPIExt = "MPI"
+
+    [deps.HDF5.weakdeps]
+    MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
+
+[[deps.HDF5_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"]
+git-tree-sha1 = "82a471768b513dc39e471540fdadc84ff80ff997"
+uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
+version = "1.14.3+3"
+
 [[deps.HTTP]]
 deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
 git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed"
@@ -954,6 +972,12 @@ git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293"
 uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0"
 version = "0.1.17"
 
+[[deps.Hwloc_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "50aedf345a709ab75872f80a2779568dc0bb461b"
+uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8"
+version = "2.11.2+3"
+
 [[deps.HypergeometricFunctions]]
 deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
 git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb"
@@ -1137,9 +1161,9 @@ version = "1.0.0"
 
 [[deps.JLD2]]
 deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"]
-git-tree-sha1 = "a0746c21bdc986d0dc293efa6b1faee112c37c28"
+git-tree-sha1 = "89e1e5c3d43078d42eed2306cab2a11b13e5c6ae"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.53"
+version = "0.4.54"
 
 [[deps.JLLWrappers]]
 deps = ["Artifacts", "Preferences"]
@@ -1358,9 +1382,9 @@ weakdeps = ["ChainRulesCore", "SparseArrays", "Statistics"]
 
 [[deps.LogExpFunctions]]
 deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea"
+git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.28"
+version = "0.3.29"
 
     [deps.LogExpFunctions.extensions]
     LogExpFunctionsChainRulesCoreExt = "ChainRulesCore"
@@ -1503,6 +1527,24 @@ git-tree-sha1 = "b45738c2e3d0d402dffa32b2c1654759a2ac35a4"
 uuid = "f1d291b0-491e-4a28-83b9-f70985020b54"
 version = "0.4.4"
 
+[[deps.MPICH_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
+git-tree-sha1 = "7715e65c47ba3941c502bffb7f266a41a7f54423"
+uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
+version = "4.2.3+0"
+
+[[deps.MPIPreferences]]
+deps = ["Libdl", "Preferences"]
+git-tree-sha1 = "c105fe467859e7f6e9a852cb15cb4301126fac07"
+uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
+version = "0.1.11"
+
+[[deps.MPItrampoline_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
+git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142"
+uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748"
+version = "5.5.1+2"
+
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
 git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df"
@@ -1564,6 +1606,12 @@ git-tree-sha1 = "44d32db644e84c75dab479f1bc15ee76a1a3618f"
 uuid = "128add7d-3638-4c79-886c-908ea0c25c34"
 version = "0.2.0"
 
+[[deps.MicrosoftMPI_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "bc95bf4149bf535c09602e3acdf950d9b4376227"
+uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf"
+version = "10.1.4+3"
+
 [[deps.Missings]]
 deps = ["DataAPI"]
 git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d"
@@ -1697,6 +1745,12 @@ git-tree-sha1 = "6efb039ae888699d5a74fb593f6f3e10c7193e33"
 uuid = "8b6db2d4-7670-4922-a472-f9537c81ab66"
 version = "0.3.1"
 
+[[deps.OpenMPI_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
+git-tree-sha1 = "e25c1778a98e34219a00455d6e4384e017ea9762"
+uuid = "fe0851c0-eecd-5654-98d4-656369965a5c"
+version = "4.1.6+0"
+
 [[deps.OpenSSL]]
 deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"]
 git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4"
@@ -2236,10 +2290,10 @@ uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
 version = "1.7.0"
 
 [[deps.StatsBase]]
-deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21"
+deps = ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
+git-tree-sha1 = "29321314c920c26684834965ec2ce0dacc9cf8e5"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.34.3"
+version = "0.34.4"
 
 [[deps.StatsFuns]]
 deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
@@ -2300,15 +2354,20 @@ version = "7.2.1+1"
 
 [[deps.TMLE]]
 deps = ["AbstractDifferentiation", "AutoHashEquals", "CategoricalArrays", "Combinatorics", "Distributions", "GLM", "Graphs", "HypothesisTests", "LogExpFunctions", "MLJBase", "MLJGLMInterface", "MLJModels", "MetaGraphsNext", "Missings", "OrderedCollections", "PrecompileTools", "Random", "SplitApplyCombine", "Statistics", "TableOperations", "Tables", "Zygote"]
-git-tree-sha1 = "2928dc0b1c3e26d8dcaaa7585dedefe33f687020"
+git-tree-sha1 = "01d5f62021293388d0d7a1fb6b3618312d543a33"
 uuid = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf"
-version = "0.17.0"
-weakdeps = ["JSON", "YAML"]
+version = "0.17.1"
 
     [deps.TMLE.extensions]
+    CausalTablesExt = "CausalTables"
     JSONExt = "JSON"
     YAMLExt = "YAML"
 
+    [deps.TMLE.weakdeps]
+    CausalTables = "6af48e0c-efc2-4bf7-a92f-a553ccf79fd6"
+    JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+    YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
+
 [[deps.TMLECLI]]
 deps = ["ArgParse", "Arrow", "CSV", "CategoricalArrays", "Combinatorics", "Configurations", "DataFrames", "EvoTrees", "GLMNet", "JLD2", "JSON", "MKL", "MLJ", "MLJBase", "MLJLinearModels", "MLJModelInterface", "MLJModels", "MLJXGBoostInterface", "Mmap", "PackageCompiler", "Random", "Serialization", "TMLE", "Tables", "YAML"]
 git-tree-sha1 = "eb8a7aa2a17c0dd2fb165dd79a860c1aea0df55a"
@@ -2628,6 +2687,12 @@ git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c"
 uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4"
 version = "0.2.3+0"
 
+[[deps.libaec_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997"
+uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0"
+version = "1.1.2+2"
+
 [[deps.libaom_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
 git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d"

Project.toml

@@ -13,8 +13,10 @@ CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
 MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
 Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
@@ -24,6 +26,7 @@ Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 SnpArrays = "4e780e97-f5bf-4111-9dc4-b70aaf691b06"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 TMLE = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf"
 TMLECLI = "2573d147-4098-46ba-9db2-8608d210ccac"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
@@ -37,12 +40,12 @@ CairoMakie = "0.12"
 CategoricalArrays = "0.10"
 Combinatorics = "1.0"
 DataFrames = "1.2"
+MKL = "0.7"
 OrderedCollections = "1.6.3"
 PackageCompiler = "2.1.17"
 SnpArrays = "0.3"
 StableRNGs = "1.0.1"
 Statistics = "1.10"
 TMLE = "0.17"
-MKL = "0.7"
 YAML = "0.4.9"
 julia = "1.10, 1"

src/TargeneCore.jl

@@ -25,6 +25,7 @@ using TMLECLI
 using HypothesisTests
 using OrderedCollections
 using Mmap
+using StatsBase
 
 ###############################################################################
 ###                               INCLUDES                                  ###