Merge pull request #3 from rcqls/main

Update VAM to VirtualAgeModels
ReliableTeam · Jun 26, 2023 · d4c4a3c · d4c4a3c
2 parents 0fb9b58 + 580bc40
commit d4c4a3c
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Showing 13 changed files with 52 additions and 41 deletions.
diff --git a/Manifest.toml b/Manifest.toml
@@ -1,8 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.9.0"
+julia_version = "1.9.1"
 manifest_format = "2.0"
-project_hash = "360fa5c287212c41321ca17e534c448f3f688a14"
+project_hash = "d74d8905f2c948a04e769adc098911ffce34eaa3"
 
 [[deps.Adapt]]
 deps = ["LinearAlgebra", "Requires"]
@@ -22,9 +22,9 @@ version = "1.1.1"
 
 [[deps.ArrayInterface]]
 deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "d3f758863a47ceef2248d136657cb9c033603641"
+git-tree-sha1 = "f83ec24f76d4c8f525099b2ac475fc098138ec31"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "7.4.8"
+version = "7.4.11"
 
     [deps.ArrayInterface.extensions]
     ArrayInterfaceBandedMatricesExt = "BandedMatrices"
@@ -62,9 +62,9 @@ version = "0.3.0"
 
 [[deps.Compat]]
 deps = ["UUIDs"]
-git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957"
+git-tree-sha1 = "4e88377ae7ebeaf29a047aa1ee40826e0b708a5d"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.6.1"
+version = "4.7.0"
 weakdeps = ["Dates", "LinearAlgebra"]
 
     [deps.Compat.extensions]
@@ -128,19 +128,19 @@ version = "1.1.0"
 
 [[deps.DiffRules]]
 deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"]
-git-tree-sha1 = "158232a81d43d108837639d3fd4c66cc3988c255"
+git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272"
 uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
-version = "1.14.0"
+version = "1.15.1"
 
 [[deps.Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[deps.Distributions]]
 deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "Test"]
-git-tree-sha1 = "c72970914c8a21b36bbc244e9df0ed1834a0360b"
+git-tree-sha1 = "db40d3aff76ea6a3619fdd15a8c78299221a2394"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.95"
+version = "0.25.97"
 
     [deps.Distributions.extensions]
     DistributionsChainRulesCoreExt = "ChainRulesCore"
@@ -172,9 +172,9 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
 
 [[deps.FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"]
-git-tree-sha1 = "ed569cb9e7e3590d5ba884da7edc50216aac5811"
+git-tree-sha1 = "0b3b52afd0f87b0a3f5ada0466352d125c9db458"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "1.1.0"
+version = "1.2.1"
 
 [[deps.FiniteDiff]]
 deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"]
@@ -216,9 +216,9 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
 [[deps.HypergeometricFunctions]]
 deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
-git-tree-sha1 = "84204eae2dd237500835990bcade263e27674a93"
+git-tree-sha1 = "0ec02c648befc2f94156eaef13b0f38106212f3f"
 uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a"
-version = "0.3.16"
+version = "0.3.17"
 
 [[deps.InlineStrings]]
 deps = ["Parsers"]
@@ -366,9 +366,9 @@ version = "0.5.5+0"
 
 [[deps.Optim]]
 deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"]
-git-tree-sha1 = "a89b11f0f354f06099e4001c151dffad7ebab015"
+git-tree-sha1 = "e3a6546c1577bfd701771b477b794a52949e7594"
 uuid = "429524aa-4258-5aef-a3af-852621145aeb"
-version = "1.7.5"
+version = "1.7.6"
 
 [[deps.OrderedCollections]]
 git-tree-sha1 = "d321bf2de576bf25ec4d3e4360faca399afca282"
@@ -389,9 +389,9 @@ version = "0.12.3"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "a5aef8d4a6e8d81f171b2bd4be5265b01384c74c"
+git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.5.10"
+version = "2.7.1"
 
 [[deps.Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
@@ -412,9 +412,9 @@ version = "0.2.4"
 
 [[deps.PrecompileTools]]
 deps = ["Preferences"]
-git-tree-sha1 = "259e206946c293698122f63e2b513a7c99a244e8"
+git-tree-sha1 = "9673d39decc5feece56ef3940e5dafba15ba0f81"
 uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
-version = "1.1.1"
+version = "1.1.2"
 
 [[deps.Preferences]]
 deps = ["TOML"]
@@ -499,19 +499,19 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
 [[deps.SortingAlgorithms]]
 deps = ["DataStructures"]
-git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00"
+git-tree-sha1 = "c60ec5c62180f27efea3ba2908480f8055e17cee"
 uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
-version = "1.1.0"
+version = "1.1.1"
 
 [[deps.SparseArrays]]
 deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[deps.SpecialFunctions]]
 deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880"
+git-tree-sha1 = "7beb031cf8145577fbccacd94b8a8f4ce78428d3"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "2.2.0"
+version = "2.3.0"
 
     [deps.SpecialFunctions.extensions]
     SpecialFunctionsChainRulesCoreExt = "ChainRulesCore"
@@ -537,9 +537,9 @@ version = "1.6.0"
 
 [[deps.StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916"
+git-tree-sha1 = "75ebe04c5bed70b91614d684259b661c9e6274a4"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.33.21"
+version = "0.34.0"
 
 [[deps.StatsFuns]]
 deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
@@ -615,7 +615,7 @@ version = "1.2.13+0"
 [[deps.libblastrampoline_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-version = "5.7.0+0"
+version = "5.8.0+0"
 
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]

diff --git a/Project.toml b/Project.toml
@@ -1,10 +1,13 @@
-name = "VAM"
+name = "VirtualAgeModels"
 uuid = "b276bca3-8be3-40c5-b17b-0eb635c89c3b"
-authors = ["R cqls <[email protected]>"]
+authors = ["Rcqls <[email protected]>"]
 version = "0.1.0"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[compat]
+julia = "1.9"
diff --git a/README.md b/README.md
@@ -1 +1 @@
-## Moving VAM to julia
+## VirtualAgeModels Moving VAM to julia
diff --git a/examples/vam_bayesian.jl b/examples/vam_bayesian.jl
@@ -1,4 +1,4 @@
-using VAM
+using VirtualAgeModels
 
 m = @vam(Temps & Type ~ (ARA1(.4) | Weibull(0.01,2.5)))
 df = rand(m, @stop (size < 30))

diff --git a/examples/vam_covariates.jl b/examples/vam_covariates.jl
@@ -1,4 +1,4 @@
-using VAM
+using VirtualAgeModels
 using DataFrames
 using Distributions
 using RCall
@@ -37,8 +37,8 @@ mbis = @vam(System & Time & Type ~ (ARAInf(0.8)|Weibull(0.15,2.3|0.6cov1 + -0.9c
 ml = mle(mbis,dataDF,dataCov;method=NelderMead())
 mlbis = mle(mbis,dataDF,dataCov)
 
-VAM.params(ml.mle)
-sum(VAM.params(ml.mle) .- cres)
+params(ml.mle)
+sum(params(ml.mle) .- cres)
 contrast(ml.mle)
 
 m2 = @vam( time & type ~ (ARAInf(0.4) | Weibull(0.001,1.5)) )

diff --git a/examples/vam_mle_amc_amb.jl b/examples/vam_mle_amc_amb.jl
@@ -1,4 +1,4 @@
-using VAM
+using VirtualAgeModels
 using DataFrames
 #using RData
 using RCall
@@ -15,5 +15,5 @@ res <- coef(AMC_mle)
 
 m = @vam(Time & Type ~ (ARA∞(0.6) | Weibull(1.0,3.0)))
 mle(m, AMC_Amb)
-VAM.params(m)
+params(m)
 sum(abs.(res .- params(m)))
diff --git a/examples/vam_mle_contrast.jl b/examples/vam_mle_contrast.jl
@@ -1,4 +1,4 @@
-using VAM
+using VirtualAgeModels
 using DataFrames
 
 data = DataFrame(time=[3.36],type=[-1])

diff --git a/examples/vam_model.jl b/examples/vam_model.jl
@@ -1,4 +1,4 @@
-using VAM
+using VirtualAgeModels
 using Distributions
 
 vam = @vam(time & type ~ (ARAInf(0.4) | Weibull(0.001,2.5)))

diff --git a/examples/vam_sim.jl b/examples/vam_sim.jl
@@ -1,4 +1,4 @@
-using VAM
+using VirtualAgeModels
 using DataFrames
 
 s = simulator(

diff --git a/src/VAM.jl → src/VirtualAgeModels.jl b/src/VAM.jl → src/VirtualAgeModels.jl
@@ -1,4 +1,4 @@
-module VAM
+module VirtualAgeModels
 
 using Random, DataFrames, Optim, Distributions
 export @vam, @stop, params, params!, nbparams, data, data!, simulator, sim, simulate, mle, bayesian

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,5 +1,5 @@
 using Test
-using VAM
+using VirtualAgeModels
 using DataFrames
 using RCall
 

diff --git a/test/test/Manifest.toml b/test/test/Manifest.toml
@@ -0,0 +1,7 @@
+# This file is machine-generated - editing it directly is not advised
+
+julia_version = "1.9.1"
+manifest_format = "2.0"
+project_hash = "da39a3ee5e6b4b0d3255bfef95601890afd80709"
+
+[deps]
diff --git a/test/test/Project.toml b/test/test/Project.toml
@@ -0,0 +1 @@
+[deps]
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		## Moving VAM to julia
		## VirtualAgeModels Moving VAM to julia