Merge pull request #37 from Evovest/dev

MLJModelInterface integration

Manifest.toml

@@ -27,28 +27,11 @@ git-tree-sha1 = "23d7324164c89638c18f6d7f90d972fa9c4fa9fb"
 uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 version = "0.7.7"
 
-[[ColorTypes]]
-deps = ["FixedPointNumbers", "Random"]
-git-tree-sha1 = "7b62b728a5f3dd6ee3b23910303ccf27e82fad5e"
-uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
-version = "0.8.1"
-
 [[Compat]]
-deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "06be57f11a029927e10d050a6c5496a8695a5437"
+deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
+git-tree-sha1 = "a4839bd26e3e7f4869a4cf6c31f9f93f47aac7c5"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "3.3.0"
-
-[[ComputationalResources]]
-deps = ["Test"]
-git-tree-sha1 = "89e7e7ed20af73d9f78877d2b8d1194e7b6ff13d"
-uuid = "ed09eef8-17a6-5b46-8889-db040fac31e3"
-version = "0.3.0"
-
-[[Crayons]]
-git-tree-sha1 = "cb7a62895da739fe5bb43f1a26d4292baf4b3dc0"
-uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
-version = "4.0.1"
+version = "3.5.0"
 
 [[DataAPI]]
 git-tree-sha1 = "674b67f344687a88310213ddfa8a2b3c76cc4252"
@@ -80,27 +63,16 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
 deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "e063d0b5d27180b98edacd2b1cb90ecfbc171385"
+git-tree-sha1 = "6b19601c0e98de3a8964ed33ad73e130c7165b1d"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.21.12"
+version = "0.22.4"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
 git-tree-sha1 = "fec413d4fc547992eb62a5c544cedb6d7853c1f5"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
 version = "0.8.4"
 
-[[FixedPointNumbers]]
-git-tree-sha1 = "4aaea64dd0c30ad79037084f8ca2b94348e65eaa"
-uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
-version = "0.7.1"
-
-[[Formatting]]
-deps = ["Printf"]
-git-tree-sha1 = "a0c901c29c0e7c763342751c0a94211d56c0de5c"
-uuid = "59287772-0a20-5a39-b81b-1366585eb4c0"
-version = "0.4.1"
-
 [[Future]]
 deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
@@ -109,12 +81,6 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
-[[InvertedIndices]]
-deps = ["Test"]
-git-tree-sha1 = "15732c475062348b0165684ffe28e85ea8396afc"
-uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
-version = "1.0.0"
-
 [[IteratorInterfaceExtensions]]
 git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
 uuid = "82899510-4779-5014-852e-03e436cf321d"
@@ -126,12 +92,6 @@ git-tree-sha1 = "b34d7cef7b337321e97d22242c3c2b91f476748e"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.0"
 
-[[LearnBase]]
-deps = ["LinearAlgebra", "SparseArrays", "StatsBase", "Test"]
-git-tree-sha1 = "c4b5da6d68517f46f70ed5157b28336b56cd2ff3"
-uuid = "7f8f8fb0-2700-5f03-b4bd-41f8cfc144b6"
-version = "0.2.2"
-
 [[LibGit2]]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
@@ -145,17 +105,11 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
-[[LossFunctions]]
-deps = ["InteractiveUtils", "LearnBase", "Markdown", "Random", "RecipesBase", "SparseArrays", "Statistics", "StatsBase", "Test"]
-git-tree-sha1 = "08d87fec43e7d335811dfae5b55dbfc5690e915b"
-uuid = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7"
-version = "0.5.1"
-
-[[MLJBase]]
-deps = ["CategoricalArrays", "ComputationalResources", "DelimitedFiles", "Distributed", "Distributions", "InteractiveUtils", "InvertedIndices", "LinearAlgebra", "LossFunctions", "Missings", "OrderedCollections", "Parameters", "PrettyTables", "ProgressMeter", "Random", "ScientificTypes", "Statistics", "StatsBase", "Tables"]
-git-tree-sha1 = "450fa34dcb0005d0799ffcf9cca5f40aa6d83059"
-uuid = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
-version = "0.10.1"
+[[MLJModelInterface]]
+deps = ["ScientificTypes"]
+git-tree-sha1 = "269deeabed43d68656c80fa57a83fb53ad202728"
+uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea"
+version = "0.1.5"
 
 [[Markdown]]
 deps = ["Base64"]
@@ -194,12 +148,6 @@ git-tree-sha1 = "5f303510529486bb02ac4d70da8295da38302194"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
 version = "0.9.11"
 
-[[Parameters]]
-deps = ["OrderedCollections"]
-git-tree-sha1 = "b62b2558efb1eef1fa44e4be5ff58a515c287e38"
-uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a"
-version = "0.12.0"
-
 [[Parsers]]
 deps = ["Dates", "Test"]
 git-tree-sha1 = "d112c19ccca00924d5d3a38b11ae2b4b268dda39"
@@ -210,22 +158,10 @@ version = "0.3.11"
 deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
-[[PrettyTables]]
-deps = ["Crayons", "Formatting", "Parameters", "Reexport", "Tables"]
-git-tree-sha1 = "2268242f037e0290e87d55c02060320c1d0d6b03"
-uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-version = "0.6.0"
-
 [[Printf]]
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[ProgressMeter]]
-deps = ["Distributed", "Printf"]
-git-tree-sha1 = "ea1f4fa0ff5e8b771bf130d87af5b7ef400760bd"
-uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
-version = "1.2.0"
-
 [[QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
 git-tree-sha1 = "dc84e810393cfc6294248c9032a9cdacc14a3db4"
@@ -240,11 +176,6 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 deps = ["Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
-[[RecipesBase]]
-git-tree-sha1 = "b4ed4a7f988ea2340017916f7c9e5d7560b52cae"
-uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-version = "0.8.0"
-
 [[Reexport]]
 deps = ["Pkg"]
 git-tree-sha1 = "7b1d07f411bc8ddb7977ec7f377b97b158514fe0"
@@ -261,10 +192,9 @@ version = "0.6.0"
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
 [[ScientificTypes]]
-deps = ["CategoricalArrays", "ColorTypes", "PrettyTables", "Tables"]
-git-tree-sha1 = "20fa7448b38ea42eb40da1d66c83cf67d626964a"
+git-tree-sha1 = "9c232034bbee8c53173cdce83787bf8968b09d31"
 uuid = "321657f4-b219-11e9-178b-2701a2544e81"
-version = "0.5.1"
+version = "0.7.1"
 
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
@@ -288,9 +218,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SpecialFunctions]]
 deps = ["OpenSpecFun_jll"]
-git-tree-sha1 = "268052ee908b2c086cc0011f528694f02f3e2408"
+git-tree-sha1 = "e19b98acb182567bcb7b75bb5d9eedf3a3b5ec6c"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "0.9.0"
+version = "0.10.0"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
@@ -304,15 +234,15 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [[StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"]
-git-tree-sha1 = "c53e809e63fe5cf5de13632090bc3520649c9950"
+git-tree-sha1 = "be5c7d45daa449d12868f4466dbf5882242cf2d9"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.32.0"
+version = "0.32.1"
 
 [[StatsFuns]]
 deps = ["Rmath", "SpecialFunctions"]
-git-tree-sha1 = "79982835d2ff3970685cb704500909c94189bde9"
+git-tree-sha1 = "f290ddd5fdedeadd10e961eb3f4d3340f09d030a"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.3"
+version = "0.9.4"
 
 [[SuiteSparse]]
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]

Project.toml

@@ -1,12 +1,12 @@
 name = "EvoTrees"
 uuid = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5"
 authors = ["jeremiedb <[email protected]>"]
-version = "0.4.2"
+version = "0.4.3"
 
 [deps]
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
+MLJModelInterface = "e80e1ace-859a-464e-9ed9-23947d8ae3ea"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SortingAlgorithms = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -18,9 +18,15 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 [compat]
 CategoricalArrays = "0.7"
 Distributions = "0.21, 0.22"
-MLJBase = "0.10"
 SortingAlgorithms = "0.3"
 StaticArrays = "0.12"
 StatsBase = "0.32"
 Tables = "0.2"
 julia = "1"
+
+[extras]
+MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test", "MLJBase"]

experiments/MLJ.jl

@@ -184,7 +184,6 @@ tree.model.nrounds += 10
 pred = predict(tree, selectrows(X,train))
 pred_mean = predict_mean(tree, selectrows(X,train))
 pred_mode = predict_mode(tree, selectrows(X,train))
-pred_median = predict_median(tree, selectrows(X,train))
 
 ##################################################
 ### Gaussian - Larger data
@@ -231,8 +230,7 @@ tree.model.nrounds += 10
 pred = predict(tree, selectrows(X,train))
 pred_mean = predict_mean(tree, selectrows(X,train))
 pred_mode = predict_mode(tree, selectrows(X,train))
-pred_median = predict_median(tree, selectrows(X,train))
-mean(abs.(pred_train - selectrows(Y,train)))
+mean(abs.(pred_mean - selectrows(Y,train)))
 
 q_20 = quantile.(pred, 0.20)
 q_20 = quantile.(pred, 0.80)

src/EvoTrees.jl

@@ -1,19 +1,18 @@
 module EvoTrees
 
-export init_evotree, grow_evotree!, grow_tree, predict, fit_evotree,
+export init_evotree, grow_evotree!, grow_tree, fit_evotree, predict,
     EvoTreeRegressor, EvoTreeCount, EvoTreeClassifier, EvoTreeGaussian,
     EvoTreeRModels, importance
 
 using Statistics
 using Base.Threads: @threads
 using StatsBase: sample, quantile
-import StatsBase: predict
 using Random: seed!
 using StaticArrays
 using Distributions
 using CategoricalArrays
-import MLJBase
-# import MLJ
+import MLJModelInterface: predict
+import MLJModelInterface
 
 include("models.jl")
 include("structs.jl")