From 53c6d66011c3f75ae416b7839f4d4f8615239f59 Mon Sep 17 00:00:00 2001 From: Rob J Goedman Date: Wed, 14 Dec 2022 07:36:00 -0700 Subject: [PATCH] Rel 9.10.5 - InferenceObjects v0.3, drop BridgeStan example notebook --- Examples_Notebooks/BridgeStan.jl | 1823 ------------------------ Examples_Notebooks/InferenceObjects.jl | 84 +- Examples_Notebooks/PosteriorDB.jl | 1276 +---------------- Examples_Notebooks/PosteriorDB_01.jl | 588 ++++++++ Project.toml | 4 +- README.md | 2 +- test/runtests.jl | 4 +- 7 files changed, 678 insertions(+), 3103 deletions(-) delete mode 100644 Examples_Notebooks/BridgeStan.jl create mode 100644 Examples_Notebooks/PosteriorDB_01.jl diff --git a/Examples_Notebooks/BridgeStan.jl b/Examples_Notebooks/BridgeStan.jl deleted file mode 100644 index c58a4bb8..00000000 --- a/Examples_Notebooks/BridgeStan.jl +++ /dev/null @@ -1,1823 +0,0 @@ -### A Pluto.jl notebook ### -# v0.19.16 - -using Markdown -using InteractiveUtils - -# ╔═╡ 5084b8f0-65ac-4704-b1fc-2a9008132bd7 -using Pkg - -# ╔═╡ 550371ad-d411-4e66-9d63-7329322c6ea1 -begin - # Specific to ROSStanPluto - using StanSample - - # Graphics related - using GLMakie - - # Include basic packages - using RegressionAndOtherStories -end - -# ╔═╡ fa1ee718-a00b-4969-860b-798409045a51 -md" ##### Experimental use of BridgeStan." - -# ╔═╡ cf39df58-3371-4535-88e4-f3f6c0404500 -md" ##### Widen the cells." - -# ╔═╡ 0616ece8-ccf8-4281-bfed-9c1192edf88e -html""" - -""" - -# ╔═╡ 4755dab0-d228-41d3-934a-56f2863a5652 -md"###### A typical set of Julia packages to include in notebooks." - -# ╔═╡ 5fdc1b11-ce9b-4f67-8e2e-5ab22cd75b70 -md" -!!! note - -All data files are available (as .csv files) in the data subdirectory of package RegressionAndOtherStories.jl. -" - -# ╔═╡ 100e2ea9-17e5-4eef-b880-823311f5d496 -ros_datadir() - -# ╔═╡ d830f41c-0fb6-4bff-9fe0-0bd51f444779 -hibbs = CSV.read(ros_datadir("ElectionsEconomy", "hibbs.csv"), DataFrame) - -# ╔═╡ bdc2ae99-233f-4bf7-9426-906029fd71f0 -tmpdir = mktempdir() - -# ╔═╡ 5727d281-2c11-4b65-b492-58a7afcac0ac -md" ##### Quick test if smb (Stan Model Bridge-to-stan) is ok." - -# ╔═╡ 4f2e4d69-35c7-4693-ae12-503f37b771f1 -bernoulli_model = " -data { - int N; - int y[N]; -} -parameters { - real theta; -} -model { - theta ~ beta(1,1); - y ~ bernoulli(theta); -} -"; - -# ╔═╡ 060268ec-c4bc-4d97-874d-37f1b192e399 -begin - data = Dict("N" => 10, "y" => [0, 1, 0, 1, 0, 0, 0, 0, 0, 1]) - sm = SampleModel("bernoulli", bernoulli_model) - rc = stan_sample(sm; data) - success(rc) && read_summary(sm) -end - -# ╔═╡ f1f43a67-d5e1-48c6-8b69-893f4d2e9c1e -smb = create_smb(sm, joinpath(sm.tmpdir, sm.name * "_data_4.json")); - -# ╔═╡ 0a2c175e-1d75-4c3e-89b7-88a5caa1bf07 -typeof(smb) - -# ╔═╡ 1c1b1cfd-dc7b-40f5-8a63-aa332d42d2f8 -let - x = rand(BridgeStan.param_unc_num(smb)) - q = @. log(x / (1 - x)) # unconstrained scale - lp, grad = BridgeStan.log_density_gradient(smb, q, jacobian = 0) - DataFrame(x=x, q=q, log_density=lp, gradient=grad) -end - -# ╔═╡ 478e931b-3be1-44b1-ac4d-e470c574874f -let - x = 0.33 - q = @. log(x / (1 - x)) # unconstrained scale - lp, grad = BridgeStan.log_density_gradient(smb, [q], jacobian = 0) - DataFrame(x=x, q=q, log_density=lp, gradient=grad) -end - -# ╔═╡ feda7416-1195-489f-991d-8a876507db45 -function sim(smb::BridgeStan.StanModel, x=LinRange(0.1, 0.9, 100)) - q = zeros(length(x)) - ld = zeros(length(x)) - g = Vector{Vector{Float64}}(undef, length(x)) - for (i, p) in enumerate(x) - q[i] = @. log(p / (1 - p)) # unconstrained scale - ld[i], g[i] = BridgeStan.log_density_gradient(smb, q[i:i], jacobian = 0) - end - return DataFrame(x=x, q=q, log_density=ld, gradient=[x[1] for x in g]) -end - -# ╔═╡ 2775bef8-9f19-48fa-a92f-536060e59aad -@time sim_df = sim(smb) - -# ╔═╡ a6f798cf-8ec1-4b3a-bebc-77c5371530be -let - fm = findmax(sim_df.log_density) - x = sim_df.x[fm[2]] - - f = Figure() - ax = Axis(f[1, 1]; title="BridgeStan example") - dens = lines!(sim_df.x, sim_df.log_density) - scatter!(x, fm[1]) - lines!([x, x], [fm[1], minimum(sim_df.log_density)]; color=:grey, linestyle=:dash) - annotations!("$([round(x; digits=2), round(fm[1]; digits=2)])"; position=(0.31, -6)) - gra = lines!(sim_df.x, sim_df.gradient) - Legend(f[1, 2], [dens, gra], ["log_density", "gradient"]) - f -end - -# ╔═╡ e936c5c3-f5c7-423d-846b-529f77499b34 -sim_df[findmax(sim_df.log_density)[2], :] - -# ╔═╡ 9fb10ce6-9ea3-4857-bc4d-5b139d27eb06 -md" ##### Try a simple model." - -# ╔═╡ 1f512a86-6a42-4f3c-bb50-ebb53791c1b9 -stan1_2 = " -data { - int N; - vector[N] x; - vector[N] y; -} -parameters { - real a; // Coefficient independent variable - real sigma; // dispersion parameter -} -model { - vector[N] mu; - mu = a * x; - // priors including constants - a ~ normal(0, 1); - sigma ~ normal(0, 1); - y ~ normal(mu, sigma); -}"; - -# ╔═╡ bdd4422c-0eea-4f08-b9ae-efc396c0bce4 -let - N = 100 - x = rand(Normal(2, 1), N) - y = 2 * x + rand(Normal(0, 1), N) - data = (N = 100, x = x, y = y) - global m1_2s = SampleModel("m1_2s", stan1_2) - global rc1_2s = stan_sample(m1_2s; data) - if success(rc1_2s) - global sum1_2s = read_summary(m1_2s) - end -end - -# ╔═╡ 44eccff8-f882-45aa-879e-3b245770196e -let - global smb1_2s = create_smb(m1_2s, joinpath(m1_2s.tmpdir, m1_2s.name * "_data_4.json")) - q = [2.0, 0.0] # unconstrained scale - lp, grad = BridgeStan.log_density_gradient(smb1_2s, q, jacobian = 0) - DataFrame(q=q, log_density=lp, gradient=grad) -end - -# ╔═╡ c6792359-c10a-4c1a-a764-c12b85cf24e8 -BridgeStan.param_names(smb1_2s) - -# ╔═╡ 3539edb8-bb39-402a-8641-cadcedae905a -md" ##### Return to m1_1s." - -# ╔═╡ 274dc84c-b416-4f9e-8ff2-6ca0f08a40cf -stan1_1 = " -data { - int N; // total number of observations - vector[N] growth; // Independent variable: growth - vector[N] vote; // Dependent variable: votes -} -parameters { - real b; // Coefficient independent variable - real a; // Intercept - real sigma; // Dispersion parameter -} -model { - vector[N] mu; - mu = a + b * growth; - - // priors including constants - a ~ normal(50, 20); - b ~ normal(2, 10); - sigma ~ exponential(1); - - // likelihood including constants - vote ~ normal(mu, sigma); -}"; - -# ╔═╡ 953eea61-f05f-4233-86aa-d5af3b47b41e -let - data = (N=16, vote=hibbs.vote, growth=hibbs.growth) - global m1_1s = SampleModel("m1_1s", stan1_1, tmpdir) - global rc1_1s = stan_sample(m1_1s; data) - success(rc1_1s) && describe(m1_1s, [:a, :b, :sigma]) -end - -# ╔═╡ 9d1a8b9a-2b0c-4b8d-af31-1717e7a5ecd7 -if success(rc1_1s) - post1_1s = read_samples(m1_1s, :dataframe) - ms1_1s = model_summary(post1_1s, [:a, :b, :sigma]) -end - -# ╔═╡ b222454b-6f4d-4d91-8374-a264873870bf -success(rc1_1s) && describe(m1_1s, [:a, :b, :sigma]) - -# ╔═╡ 7e6a43cb-8789-422c-80d2-6a154b576c56 -if success(rc1_1s) - sum1_1s = read_summary(m1_1s) -end - -# ╔═╡ 1503a0c8-20ff-4821-8dc8-7299617628ef -sum1_1s[9, :mean] - -# ╔═╡ e5129e29-9281-4796-88b6-020d9e8d580c -begin - smb1_1s = create_smb(m1_1s, joinpath(m1_1s.tmpdir, m1_1s.name * "_data_4.json")) - q = rand(BridgeStan.param_unc_num(smb1_1s)) # unconstrained scale - lp, grad = BridgeStan.log_density_gradient(smb1_1s, q, jacobian = 0) - DataFrame(q=q, log_density=lp, gradient=grad) -end - -# ╔═╡ 0c17b7d0-cb6e-4ccc-8685-1fa962aebebf -let - qmax = [sum1_1s[8, :mean], sum1_1s[9, :mean], 1.03] # unconstrained scale - lp, grad = BridgeStan.log_density_gradient(smb1_1s, qmax, jacobian = 0) - DataFrame(q=qmax, log_density=lp, gradient=grad) -end - -# ╔═╡ 9c82419f-3577-46a4-b759-2badbcd1411f -mean(rand(Exponential(1), 1000)) - -# ╔═╡ 450c557d-5e11-4061-b807-fffb429212f7 -BridgeStan.param_unc_num(smb1_1s) - -# ╔═╡ 7a709a1a-e8b1-4c3f-abcb-e3facd87fee9 -BridgeStan.param_names(smb1_1s) - -# ╔═╡ 4b433a67-2a29-41c2-a04a-83572eb09dd2 -let - smb1_1s = create_smb(m1_1s, joinpath(m1_1s.tmpdir, m1_1s.name * "_data_4.json")) - q = [3.04, 43.32, 1.0] # unconstrained scale - lp, grad = BridgeStan.log_density_gradient(smb1_1s, q, jacobian = 0) - DataFrame(q=q, log_density=lp, gradient=grad) -end - -# ╔═╡ 79aa12f4-abef-479a-8644-25a9f5588f22 -function sim2(smb1_1s::BridgeStan.StanModel, x=LinRange(1, 6, 100)) - q = Vector{Vector{Float64}}(undef, length(x)) - ld = zeros(length(x)) - g = Vector{Vector{Float64}}(undef, length(x)) - for (i, p) in enumerate(x) - q[i] = [x[i], 43.32, 1.0] # unconstrained scale - ld[i], g[i] = BridgeStan.log_density_gradient(smb1_1s, q[i], - jacobian = 0) - end - return DataFrame(x=x, q=q, log_density=ld, gradient=[x[1] for x in g]) -end - -# ╔═╡ 3648ec90-7fda-4047-b0dc-0c448f795431 -@time sim_df_2 = sim2(smb1_1s) - -# ╔═╡ 52c42c16-03f7-4416-9180-835b7ed9d942 -sim_df_2[findmax(sim_df_2.log_density)[2], :] - -# ╔═╡ dca12cf4-6d3c-4899-8b70-c7d974705064 -sim_df_2[59:70, :] - -# ╔═╡ 00000000-0000-0000-0000-000000000001 -PLUTO_PROJECT_TOML_CONTENTS = """ -[deps] -GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" -Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -RegressionAndOtherStories = "21324389-b050-441a-ba7b-9a837781bda0" -StanSample = 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"JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] -git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" -uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" -version = "1.5.2+4" - -[[deps.Xorg_libXrender_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" -uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.10+4" - -[[deps.Xorg_libpthread_stubs_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" -uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.0+3" - -[[deps.Xorg_libxcb_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" -uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.13.0+3" - -[[deps.Xorg_xtrans_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" -uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.4.0+3" - -[[deps.Zlib_jll]] -deps = ["Libdl"] -uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+0" - -[[deps.isoband_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c" -uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4" -version = "0.2.3+0" - -[[deps.libaom_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" -uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.4.0+0" - -[[deps.libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" -uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.1+0" - -[[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.2.0+0" - -[[deps.libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" -uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" - -[[deps.libpng_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" -uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.38+0" - -[[deps.libsixel_jll]] -deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] -git-tree-sha1 = "d4f63314c8aa1e48cd22aa0c17ed76cd1ae48c3c" -uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" -version = "1.10.3+0" - -[[deps.libvorbis_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" -uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" - -[[deps.nghttp2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" - -[[deps.p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" - -[[deps.x264_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" -uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2021.5.5+0" - -[[deps.x265_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" -uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.5.0+0" -""" - -# ╔═╡ Cell order: -# ╟─fa1ee718-a00b-4969-860b-798409045a51 -# ╟─cf39df58-3371-4535-88e4-f3f6c0404500 -# ╠═0616ece8-ccf8-4281-bfed-9c1192edf88e -# ╟─4755dab0-d228-41d3-934a-56f2863a5652 -# ╠═5084b8f0-65ac-4704-b1fc-2a9008132bd7 -# ╠═550371ad-d411-4e66-9d63-7329322c6ea1 -# ╟─5fdc1b11-ce9b-4f67-8e2e-5ab22cd75b70 -# ╠═100e2ea9-17e5-4eef-b880-823311f5d496 -# ╠═d830f41c-0fb6-4bff-9fe0-0bd51f444779 -# ╠═bdc2ae99-233f-4bf7-9426-906029fd71f0 -# ╟─5727d281-2c11-4b65-b492-58a7afcac0ac -# ╠═4f2e4d69-35c7-4693-ae12-503f37b771f1 -# ╠═060268ec-c4bc-4d97-874d-37f1b192e399 -# ╠═f1f43a67-d5e1-48c6-8b69-893f4d2e9c1e -# ╠═0a2c175e-1d75-4c3e-89b7-88a5caa1bf07 -# ╠═1c1b1cfd-dc7b-40f5-8a63-aa332d42d2f8 -# ╠═478e931b-3be1-44b1-ac4d-e470c574874f -# ╠═feda7416-1195-489f-991d-8a876507db45 -# ╠═2775bef8-9f19-48fa-a92f-536060e59aad -# ╠═a6f798cf-8ec1-4b3a-bebc-77c5371530be -# ╠═e936c5c3-f5c7-423d-846b-529f77499b34 -# ╟─9fb10ce6-9ea3-4857-bc4d-5b139d27eb06 -# ╠═1f512a86-6a42-4f3c-bb50-ebb53791c1b9 -# ╠═bdd4422c-0eea-4f08-b9ae-efc396c0bce4 -# ╠═44eccff8-f882-45aa-879e-3b245770196e -# ╠═c6792359-c10a-4c1a-a764-c12b85cf24e8 -# ╟─3539edb8-bb39-402a-8641-cadcedae905a -# ╠═274dc84c-b416-4f9e-8ff2-6ca0f08a40cf -# ╠═953eea61-f05f-4233-86aa-d5af3b47b41e -# ╠═9d1a8b9a-2b0c-4b8d-af31-1717e7a5ecd7 -# ╠═b222454b-6f4d-4d91-8374-a264873870bf -# ╠═7e6a43cb-8789-422c-80d2-6a154b576c56 -# ╠═1503a0c8-20ff-4821-8dc8-7299617628ef -# ╠═e5129e29-9281-4796-88b6-020d9e8d580c -# ╠═0c17b7d0-cb6e-4ccc-8685-1fa962aebebf -# ╠═9c82419f-3577-46a4-b759-2badbcd1411f -# ╠═450c557d-5e11-4061-b807-fffb429212f7 -# ╠═7a709a1a-e8b1-4c3f-abcb-e3facd87fee9 -# ╠═4b433a67-2a29-41c2-a04a-83572eb09dd2 -# ╠═79aa12f4-abef-479a-8644-25a9f5588f22 -# ╠═3648ec90-7fda-4047-b0dc-0c448f795431 -# ╠═52c42c16-03f7-4416-9180-835b7ed9d942 -# ╠═dca12cf4-6d3c-4899-8b70-c7d974705064 -# ╟─00000000-0000-0000-0000-000000000001 -# ╟─00000000-0000-0000-0000-000000000002 diff --git a/Examples_Notebooks/InferenceObjects.jl b/Examples_Notebooks/InferenceObjects.jl index 0bf5c31f..4d3e7679 100644 --- a/Examples_Notebooks/InferenceObjects.jl +++ b/Examples_Notebooks/InferenceObjects.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.16 +# v0.19.18 using Markdown using InteractiveUtils @@ -79,15 +79,8 @@ end; # ╔═╡ d572fb32-4ccf-4ba9-a995-48877e90f232 if success(rc) - idata = inferencedata(m_schools) - - nt = namedtuple(data) - - # Until InferenceObjects issue #36 is merged - ntu=(sigma=nt.sigma, J=[4], y=nt.y) - - idata = merge(idata, from_namedtuple(; observed_data = ntu)) - + idata = inferencedata(m_schools; log_likelihood_var=:log_lik, posterior_predictive_var=:y_hat) + idata = merge(idata, from_namedtuple(; observed_data = namedtuple(data))) else @warn "Sampling failed." end @@ -96,6 +89,9 @@ end # ╔═╡ 150f9cea-91da-4648-8469-dfb4c852227a md" ##### To see more details, click on any of the triangles above or specify group as shown below." +# ╔═╡ 3b2eee33-a2f2-4dc8-a4a1-89fa036a1385 +idata.posterior + # ╔═╡ 4d703d31-d03e-4c37-b4b9-c29f29b5cc62 if :observed_data in propertynames(idata) idata.observed_data @@ -113,6 +109,15 @@ post_schools = read_samples(m_schools, :dataframe; start=1001) # ╔═╡ 4da97b66-2c45-4c19-aa32-487a95fb23e9 posterior_schools = DataFrame(idata.posterior) +# ╔═╡ 8f52ef47-46e2-4028-83f1-c9cd183bc799 +DataFrame(inferencedata(m_schools).posterior) |> size + +# ╔═╡ 2e19a32a-4a26-4b53-8173-ea3d74eb19f4 +DataFrame(inferencedata(m_schools; dims=(theta=[:school], theta_tilde=[:school])).posterior) + +# ╔═╡ 30b9724d-73f4-4888-9698-b01f0ed1c720 +DataFrame(inferencedata(m_schools; dims=(theta=[:school], theta_tilde=[:school])).posterior) |> size + # ╔═╡ 00000000-0000-0000-0000-000000000001 PLUTO_PROJECT_TOML_CONTENTS = """ [deps] @@ -124,11 +129,11 @@ Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" StanSample = "c1514b29-d3a0-5178-b312-660c88baa699" [compat] -CSV = "~0.10.7" +CSV = "~0.10.8" DataFrames = "~1.4.4" -InferenceObjects = "~0.2.5" -NamedTupleTools = "~0.14.1" -StanSample = "~6.13.7" +InferenceObjects = "~0.3.0" +NamedTupleTools = "~0.14.2" +StanSample = "~6.13.8" """ # ╔═╡ 00000000-0000-0000-0000-000000000002 @@ -137,7 +142,7 @@ PLUTO_MANIFEST_TOML_CONTENTS = """ julia_version = "1.10.0-DEV" manifest_format = "2.0" -project_hash = "04f1bdf71c794e2f6ac06ca8d047f7f659ab5ecb" +project_hash = "ae44de63df444ba476e72c536643e3f4974df324" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" @@ -156,9 +161,9 @@ version = "1.1.1" [[deps.ArrayInterfaceCore]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c46fb7dd1d8ca1d213ba25848a5ec4e47a1a1b08" +git-tree-sha1 = "badccc4459ffffb6bce5628461119b7057dec32c" uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.26" +version = "0.1.27" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -167,10 +172,10 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[deps.CSV]] -deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings"] -git-tree-sha1 = "c5fd7cd27ac4aed0acf4b73948f0110ff2a854b2" +deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "SnoopPrecompile", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] +git-tree-sha1 = "8c73e96bd6817c2597cfd5615b91fca5deccf1af" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.7" +version = "0.10.8" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] @@ -240,9 +245,9 @@ version = "1.9.0" [[deps.DimensionalData]] deps = ["Adapt", "ArrayInterfaceCore", "ConstructionBase", "Dates", "Extents", "IntervalSets", "IteratorInterfaceExtensions", "LinearAlgebra", "Random", "RecipesBase", "SparseArrays", "Statistics", "TableTraits", "Tables"] -git-tree-sha1 = "0da97e5280d6e3d375e992f687c413a4789e1fa9" +git-tree-sha1 = "48eef48335b34aa69699a33060d4cea7b499024d" uuid = "0703355e-b756-11e9-17c0-8b28908087d0" -version = "0.23.1" +version = "0.23.2" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -250,9 +255,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "c36550cb29cbe373e95b3f40486b9a4148f89ffd" +git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.2" +version = "0.9.3" [[deps.Documenter]] deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] @@ -296,10 +301,10 @@ uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" version = "0.2.2" [[deps.InferenceObjects]] -deps = ["Compat", "Dates", "DimensionalData"] -git-tree-sha1 = "96726b5b80563e1bccb453e0d1f7022ddbd5115b" +deps = ["Compat", "Dates", "DimensionalData", "Tables"] +git-tree-sha1 = "71bfda0025595c30cc162ac8a7019ab7e200866f" uuid = "b5cf5a8d-e756-4ee3-b014-01d49d192c00" -version = "0.2.5" +version = "0.3.0" [[deps.InlineStrings]] deps = ["Parsers"] @@ -390,9 +395,9 @@ uuid = "14a3606d-f60d-562e-9121-12d972cd8159" version = "2022.10.11" [[deps.NamedTupleTools]] -git-tree-sha1 = "17eeb975b00de066fb343aa8d56884f51d4a651c" +git-tree-sha1 = "e43cec005f0d7b51851669d3c4726dd4481aef80" uuid = "d9ec5142-1e00-5aa0-9d6a-321866360f50" -version = "0.14.1" +version = "0.14.2" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" @@ -416,9 +421,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates", "SnoopPrecompile"] -git-tree-sha1 = "b64719e8b4504983c7fca6cc9db3ebc8acc2a4d6" +git-tree-sha1 = "6466e524967496866901a78fca3f2e9ea445a559" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.5.1" +version = "2.5.2" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] @@ -499,15 +504,15 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.StanBase]] deps = ["CSV", "DataFrames", "DelimitedFiles", "Distributed", "DocStringExtensions", "Documenter", "JSON", "NamedTupleTools", "Parameters", "Random", "Unicode"] -git-tree-sha1 = "9c1be7357e148627c5c2c0afaf2ba287fc81b48b" +git-tree-sha1 = "70258a57edc0eff2a1e11185b49c7d66e3de075b" uuid = "d0ee94f6-a23d-54aa-bbe9-7f572d6da7f5" -version = "4.7.4" +version = "4.7.5" [[deps.StanSample]] deps = ["CSV", "CompatHelperLocal", "DataFrames", "DelimitedFiles", "Distributed", "DocStringExtensions", "JSON", "NamedTupleTools", "OrderedCollections", "Parameters", "Random", "Reexport", "Requires", "Serialization", "StanBase", "TableOperations", "Tables", "Unicode"] -git-tree-sha1 = "7b8c4ab8bb993296e93a64d1a4a09b9f79b8ffb5" +git-tree-sha1 = "18c30df5440f6d569a570ef4b6f1afc7fc5586a6" uuid = "c1514b29-d3a0-5178-b312-660c88baa699" -version = "6.13.7" +version = "6.13.8" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -584,6 +589,11 @@ git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" version = "1.4.2" +[[deps.WorkerUtilities]] +git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7" +uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" +version = "1.6.1" + [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" @@ -614,10 +624,14 @@ version = "17.4.0+0" # ╠═a1e486d9-ad7f-48ae-8d51-9ae446e6c030 # ╠═d572fb32-4ccf-4ba9-a995-48877e90f232 # ╟─150f9cea-91da-4648-8469-dfb4c852227a +# ╠═3b2eee33-a2f2-4dc8-a4a1-89fa036a1385 # ╠═4d703d31-d03e-4c37-b4b9-c29f29b5cc62 # ╠═8a6367b7-92f9-498e-874d-868b0a402d3e # ╠═5bf5c448-5b76-4c77-9529-9106f94bc1ef # ╠═9a15cd96-2863-4b87-b3eb-3d14fb128b6d # ╠═4da97b66-2c45-4c19-aa32-487a95fb23e9 +# ╠═8f52ef47-46e2-4028-83f1-c9cd183bc799 +# ╠═2e19a32a-4a26-4b53-8173-ea3d74eb19f4 +# ╠═30b9724d-73f4-4888-9698-b01f0ed1c720 # ╟─00000000-0000-0000-0000-000000000001 # ╟─00000000-0000-0000-0000-000000000002 diff --git a/Examples_Notebooks/PosteriorDB.jl b/Examples_Notebooks/PosteriorDB.jl index 9c274e67..8b7f588d 100644 --- a/Examples_Notebooks/PosteriorDB.jl +++ b/Examples_Notebooks/PosteriorDB.jl @@ -10,8 +10,9 @@ using Pkg # ╔═╡ e4d98ecf-1dd3-414b-ba5c-b6a7d71df3eb begin using DataFrames + using Statistics using PosteriorDB - using Stan + using StanSample end # ╔═╡ 34a9e246-547e-11ed-2c8e-5d545ad2b268 @@ -39,13 +40,13 @@ posterior_names(pdb) dataset_names(pdb) # ╔═╡ 54dd2074-76f0-4bd7-9406-94e9720d0daf -post = posterior(pdb, "eight_schools-eight_schools_centered") +posterior_pdb = posterior(pdb, "eight_schools-eight_schools_centered") # ╔═╡ a0260880-429c-4888-a4be-9b1d6457de53 -mod = model(post) +mod = model(posterior_pdb) # ╔═╡ 829195fc-adab-4f39-a69c-4c5c8d4916db -info(post) +info(posterior_pdb) # ╔═╡ 8feb8740-b286-4877-8587-7fde4419f90d begin @@ -57,7 +58,7 @@ end impl = implementation(mod, "stan") # ╔═╡ 438253a2-5b62-46f9-a85e-8a89e42e1c82 -let +begin code = load(impl) println(code) end @@ -66,19 +67,19 @@ end info(mod) # ╔═╡ 0247e72a-afc8-4072-9fd6-78b4a0e1baf7 -data = dataset(post) +post = dataset(posterior_pdb) # ╔═╡ e18e0655-1785-47e6-a322-d7e2f84e6f6f -info(data) +info(posterior_pdb) # ╔═╡ 302ce3e8-e3c0-4111-8065-71a3b622779f -path(data) +path(post) # ╔═╡ a9ba650f-76f3-483e-bc3a-c0ff039e08c8 -load(data) +data = load(post) # ╔═╡ 69c80caa-cc31-4409-9f73-2580e7620fd2 -ref = reference_posterior(post) +ref = reference_posterior(posterior_pdb) # ╔═╡ 719112ef-f399-4664-8843-16723289bd1d info(ref) @@ -87,7 +88,21 @@ info(ref) path(ref) # ╔═╡ 26030da6-920f-47bd-ad55-29444e78c1c8 -DataFrame(load(ref)) +pdb_df = DataFrame(load(ref)) + +# ╔═╡ 20738a8e-a50d-4682-884b-a84e33e6146a +pdb_df.mu + +# ╔═╡ 4ac7fa99-6ba1-46dd-abae-ed0655a71f6f +begin + sm = SampleModel("PDB", code) + rc = stan_sample(sm; data) +end; + +# ╔═╡ 1e6593dd-956e-40b1-a715-6223fc7c56d8 +if success(rc) + df = read_samples(sm, :dataframe) +end # ╔═╡ 00000000-0000-0000-0000-000000000001 PLUTO_PROJECT_TOML_CONTENTS = """ @@ -95,12 +110,13 @@ PLUTO_PROJECT_TOML_CONTENTS = """ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" PosteriorDB = "1c4bc282-d2f5-44f9-b6d1-8c4424a23ad4" -Stan = "682df890-35be-576f-97d0-3d8c8b33a550" +StanSample = "c1514b29-d3a0-5178-b312-660c88baa699" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [compat] DataFrames = "~1.4.4" PosteriorDB = "~0.3.1" -Stan = "~9.10.3" +StanSample = "~6.13.7" """ # ╔═╡ 00000000-0000-0000-0000-000000000002 @@ -109,216 +125,35 @@ PLUTO_MANIFEST_TOML_CONTENTS = """ julia_version = "1.10.0-DEV" manifest_format = "2.0" -project_hash = "2bc51eaf36066fb2ab3481a94ed6efa1ea014ce1" +project_hash = "6d33b3d450b408a8aa6cd319e36f66b7d977b0a9" [[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" version = "0.0.1" -[[deps.AbstractFFTs]] -deps = ["ChainRulesCore", "LinearAlgebra"] -git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" -uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.2.1" - -[[deps.AbstractMCMC]] -deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] -git-tree-sha1 = "5c26c7759412ffcaf0dd6e3172e55d783dd7610b" -uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -version = "4.1.3" - -[[deps.AbstractTrees]] -git-tree-sha1 = "52b3b436f8f73133d7bc3a6c71ee7ed6ab2ab754" -uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.3" - -[[deps.Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" -uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.4.0" - -[[deps.ArgCheck]] -git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" -uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" -version = "2.3.0" - [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" -[[deps.Arpack]] -deps = ["Arpack_jll", "Libdl", "LinearAlgebra", "Logging"] -git-tree-sha1 = "9b9b347613394885fd1c8c7729bfc60528faa436" -uuid = 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["Arpack", "LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI", "StatsBase"] -git-tree-sha1 = "efe9c8ecab7a6311d4b91568bd6c88897822fabe" -uuid = "6f286f6a-111f-5878-ab1e-185364afe411" -version = "0.10.0" - -[[deps.NaNMath]] -deps = ["OpenLibm_jll"] -git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" -uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.1" - -[[deps.NamedArrays]] -deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "2fd5787125d1a93fbe30961bd841707b8a80d75b" -uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.9.6" - [[deps.NamedTupleTools]] git-tree-sha1 = "17eeb975b00de066fb343aa8d56884f51d4a651c" uuid = "d9ec5142-1e00-5aa0-9d6a-321866360f50" version = "0.14.1" -[[deps.NaturalSort]] -git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" -uuid = "c020b1a1-e9b0-503a-9c33-f039bfc54a85" -version = "1.0.0" - 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"Libdl"] -uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+0" - -[[deps.OpenSSL]] -deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "df6830e37943c7aaa10023471ca47fb3065cc3c4" -uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.3.2" - -[[deps.OpenSSL_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004" -uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.19+0" - -[[deps.OpenSpecFun_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" -uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" -version = "0.5.5+0" - -[[deps.Opus_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" -uuid = "91d4177d-7536-5919-b921-800302f37372" -version = "1.3.2+0" - [[deps.OrderedCollections]] git-tree-sha1 = 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"Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "7c5d624a2cb080c2bf41dc5da8fbb837c427048a" -uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.37.0" - [[deps.PooledArrays]] deps = ["DataAPI", "Future"] git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7" @@ -1124,12 +390,6 @@ git-tree-sha1 = "574cb927d335c7caed89342e714cb6bd50051e1b" uuid = "1c4bc282-d2f5-44f9-b6d1-8c4424a23ad4" version = "0.3.1" -[[deps.Preferences]] -deps = ["TOML"] -git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" -uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.3.0" - [[deps.PrettyTables]] deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] git-tree-sha1 = "96f6db03ab535bdb901300f88335257b0018689d" @@ -1140,30 +400,6 @@ version = "2.2.2" deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -[[deps.ProgressLogging]] -deps = ["Logging", "SHA", "UUIDs"] -git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539" -uuid = "33c8b6b6-d38a-422a-b730-caa89a2f386c" -version = "0.1.4" - -[[deps.ProgressMeter]] -deps = ["Distributed", "Printf"] -git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" -uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.2" - -[[deps.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"] -git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" -uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" -version = "5.15.3+2" - -[[deps.QuadGK]] -deps = ["DataStructures", "LinearAlgebra"] 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-[[deps.Xorg_xcb_util_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] -git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" -uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" -version = "0.4.0+1" - -[[deps.Xorg_xcb_util_keysyms_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" -uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" -version = "0.4.0+1" - -[[deps.Xorg_xcb_util_renderutil_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" -uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" -version = "0.3.9+1" - -[[deps.Xorg_xcb_util_wm_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" -uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" -version = "0.4.1+1" - -[[deps.Xorg_xkbcomp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] -git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" -uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" -version = "1.4.2+4" - -[[deps.Xorg_xkeyboard_config_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] -git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" -uuid = "33bec58e-1273-512f-9401-5d533626f822" -version = "2.27.0+4" - -[[deps.Xorg_xtrans_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" -uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.4.0+3" - [[deps.ZipFile]] deps = ["Libdl", "Printf", "Zlib_jll"] git-tree-sha1 = "f492b7fe1698e623024e873244f10d89c95c340a" @@ -1693,59 +550,11 @@ deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" version = "1.2.13+0" -[[deps.Zstd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" -uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.2+0" - -[[deps.ZygoteRules]] -deps = ["MacroTools"] -git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.2" - -[[deps.fzf_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" -uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.29.0+0" - -[[deps.libaom_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" -uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.4.0+0" - -[[deps.libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" -uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.1+0" - [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" version = "5.2.0+0" -[[deps.libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" -uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" - -[[deps.libpng_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" -uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.38+0" - -[[deps.libvorbis_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" -uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" - [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" @@ -1755,24 +564,6 @@ version = "1.48.0+0" deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" version = "17.4.0+0" - -[[deps.x264_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" -uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2021.5.5+0" - -[[deps.x265_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" -uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.5.0+0" - -[[deps.xkbcommon_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" -uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+0" """ # ╔═╡ Cell order: @@ -1798,5 +589,8 @@ version = "1.4.1+0" # ╠═719112ef-f399-4664-8843-16723289bd1d # ╠═9e152cf5-2916-42a5-85cb-2c41e3590c3a # ╠═26030da6-920f-47bd-ad55-29444e78c1c8 +# ╠═20738a8e-a50d-4682-884b-a84e33e6146a +# ╠═4ac7fa99-6ba1-46dd-abae-ed0655a71f6f +# ╠═1e6593dd-956e-40b1-a715-6223fc7c56d8 # ╟─00000000-0000-0000-0000-000000000001 # ╟─00000000-0000-0000-0000-000000000002 diff --git a/Examples_Notebooks/PosteriorDB_01.jl b/Examples_Notebooks/PosteriorDB_01.jl new file mode 100644 index 00000000..d0abb45f --- /dev/null +++ b/Examples_Notebooks/PosteriorDB_01.jl @@ -0,0 +1,588 @@ +### A Pluto.jl notebook ### +# v0.19.17 + +using Markdown +using InteractiveUtils + +# ╔═╡ 9339e545-32ee-4304-ba49-d34befb45fe3 +using Pkg + +# ╔═╡ e4d98ecf-1dd3-414b-ba5c-b6a7d71df3eb +begin + using DataFrames + using Statistics + using PosteriorDB + using StanSample +end + +# ╔═╡ 34a9e246-547e-11ed-2c8e-5d545ad2b268 +html""" + +""" + +# ╔═╡ 22ffe9ac-a7d7-4066-a6a0-58e0b60d0352 +pdb = database() + +# ╔═╡ 97fd910a-2972-48f9-a512-e5975b51351f +pdb.path + +# ╔═╡ bdf2a2eb-89df-401f-b113-6ea178d67500 +posterior_names(pdb) + +# ╔═╡ 5cebec86-cb13-4bf2-850a-3c6510e3fb5e +dataset_names(pdb) + +# ╔═╡ 54dd2074-76f0-4bd7-9406-94e9720d0daf +posterior_pdb = posterior(pdb, "M0_data-M0_model") + +# ╔═╡ a0260880-429c-4888-a4be-9b1d6457de53 +mod = model(posterior_pdb) + +# ╔═╡ 829195fc-adab-4f39-a69c-4c5c8d4916db +info(posterior_pdb) + +# ╔═╡ 8feb8740-b286-4877-8587-7fde4419f90d +begin + mod_code = implementation(mod, "stan") + mod_code +end + +# ╔═╡ 46d29033-58c8-48a0-998e-944ad9d0ee62 +impl = implementation(mod, "stan") + +# ╔═╡ 438253a2-5b62-46f9-a85e-8a89e42e1c82 +begin + code = load(impl) + println(code) +end + +# ╔═╡ 3068fb12-0c37-466d-9721-99f746006f03 +info(mod) + +# ╔═╡ 0247e72a-afc8-4072-9fd6-78b4a0e1baf7 +post = dataset(posterior_pdb) + +# ╔═╡ 32831937-e82c-41b3-83bd-0f25a62b6540 +DataFrame(post.posterior) + +# ╔═╡ e18e0655-1785-47e6-a322-d7e2f84e6f6f +info(posterior_pdb) + +# ╔═╡ 302ce3e8-e3c0-4111-8065-71a3b622779f +path(post) + +# ╔═╡ a9ba650f-76f3-483e-bc3a-c0ff039e08c8 +data = load(post) + +# ╔═╡ 48e0b38c-e72b-439d-aac4-dad55f8c05bc +data["y"] = data["y"]' + +# ╔═╡ b201d58c-2145-4f02-aedf-c56bb71aa527 +model_1=model(posterior_pdb) + +# ╔═╡ 4ac7fa99-6ba1-46dd-abae-ed0655a71f6f +begin + sm = SampleModel("PDB", code) + rc = stan_sample(sm; data) +end; + +# ╔═╡ 1e6593dd-956e-40b1-a715-6223fc7c56d8 +if success(rc) + df = read_samples(sm, :dataframe) +end + +# ╔═╡ 00000000-0000-0000-0000-000000000001 +PLUTO_PROJECT_TOML_CONTENTS = """ +[deps] +DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" +PosteriorDB = "1c4bc282-d2f5-44f9-b6d1-8c4424a23ad4" +StanSample = "c1514b29-d3a0-5178-b312-660c88baa699" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" + +[compat] +DataFrames = "~1.4.4" +PosteriorDB = "~0.3.1" +StanSample = "~6.13.7" +""" + +# ╔═╡ 00000000-0000-0000-0000-000000000002 +PLUTO_MANIFEST_TOML_CONTENTS = """ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.0-DEV" +manifest_format = "2.0" +project_hash = "67fbb3a1844a1c0ebfac7799670a254337429f45" + +[[deps.ANSIColoredPrinters]] +git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" +uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" +version = "0.0.1" + +[[deps.ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" + +[[deps.Artifacts]] +uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" + +[[deps.Base64]] +uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" + +[[deps.CSV]] +deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings"] +git-tree-sha1 = "c5fd7cd27ac4aed0acf4b73948f0110ff2a854b2" +uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +version = "0.10.7" + +[[deps.CodecZlib]] +deps = ["TranscodingStreams", "Zlib_jll"] +git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da" +uuid = "944b1d66-785c-5afd-91f1-9de20f533193" +version = "0.7.0" + +[[deps.Compat]] +deps = ["Dates", "LinearAlgebra", "UUIDs"] +git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" +uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" +version = "4.5.0" + +[[deps.CompatHelperLocal]] +deps = ["DocStringExtensions", "Pkg", "UUIDs"] +git-tree-sha1 = "be25ab802a22a212ce4da944fe60d7c250ddcfe1" +uuid = "5224ae11-6099-4aaa-941d-3aab004bd678" +version = "0.1.25" + +[[deps.CompilerSupportLibraries_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +version = "1.0.1+0" + +[[deps.Crayons]] +git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" +uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" +version = "4.1.1" + +[[deps.DataAPI]] +git-tree-sha1 = "e08915633fcb3ea83bf9d6126292e5bc5c739922" +uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" +version = "1.13.0" + +[[deps.DataFrames]] +deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "d4f69885afa5e6149d0cab3818491565cf41446d" +uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +version = 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+[[deps.Tables]] +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] +git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" +uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" +version = "1.10.0" + +[[deps.Tar]] +deps = ["ArgTools", "SHA"] +uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" +version = "1.10.0" + +[[deps.Test]] +deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] +uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + +[[deps.TranscodingStreams]] +deps = ["Random", "Test"] +git-tree-sha1 = "e4bdc63f5c6d62e80eb1c0043fcc0360d5950ff7" +uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" +version = "0.9.10" + +[[deps.UUIDs]] +deps = ["Random", "SHA"] +uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" + +[[deps.UnPack]] +git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" +uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" +version = "1.0.2" + +[[deps.Unicode]] +uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" + +[[deps.WeakRefStrings]] +deps = ["DataAPI", "InlineStrings", "Parsers"] +git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" +uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" +version = "1.4.2" + +[[deps.ZipFile]] +deps = ["Libdl", "Printf", "Zlib_jll"] +git-tree-sha1 = "f492b7fe1698e623024e873244f10d89c95c340a" +uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea" +version = "0.10.1" + +[[deps.Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.13+0" + +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.2.0+0" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.48.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" +""" + +# ╔═╡ Cell order: +# ╠═34a9e246-547e-11ed-2c8e-5d545ad2b268 +# ╠═9339e545-32ee-4304-ba49-d34befb45fe3 +# ╠═e4d98ecf-1dd3-414b-ba5c-b6a7d71df3eb +# ╠═22ffe9ac-a7d7-4066-a6a0-58e0b60d0352 +# ╠═97fd910a-2972-48f9-a512-e5975b51351f +# ╠═bdf2a2eb-89df-401f-b113-6ea178d67500 +# ╠═5cebec86-cb13-4bf2-850a-3c6510e3fb5e +# ╠═54dd2074-76f0-4bd7-9406-94e9720d0daf +# ╠═a0260880-429c-4888-a4be-9b1d6457de53 +# ╠═829195fc-adab-4f39-a69c-4c5c8d4916db +# ╠═8feb8740-b286-4877-8587-7fde4419f90d +# ╠═46d29033-58c8-48a0-998e-944ad9d0ee62 +# ╠═438253a2-5b62-46f9-a85e-8a89e42e1c82 +# ╠═3068fb12-0c37-466d-9721-99f746006f03 +# ╠═0247e72a-afc8-4072-9fd6-78b4a0e1baf7 +# ╠═32831937-e82c-41b3-83bd-0f25a62b6540 +# ╠═e18e0655-1785-47e6-a322-d7e2f84e6f6f +# ╠═302ce3e8-e3c0-4111-8065-71a3b622779f +# ╠═a9ba650f-76f3-483e-bc3a-c0ff039e08c8 +# ╠═48e0b38c-e72b-439d-aac4-dad55f8c05bc +# ╠═b201d58c-2145-4f02-aedf-c56bb71aa527 +# ╠═4ac7fa99-6ba1-46dd-abae-ed0655a71f6f +# ╠═1e6593dd-956e-40b1-a715-6223fc7c56d8 +# ╟─00000000-0000-0000-0000-000000000001 +# ╟─00000000-0000-0000-0000-000000000002 diff --git a/Project.toml b/Project.toml index 08ce753d..daf42114 100644 --- a/Project.toml +++ b/Project.toml @@ -43,7 +43,7 @@ DataStructures = "0.18.13" DimensionalData = "0.23" Distributions = "0.25" DocStringExtensions = "0.9" -InferenceObjects = "0.2" +InferenceObjects = "0.3" JSON = "0.21" JSON3 = "1.12" MCMCChains = "5.5" @@ -55,7 +55,7 @@ StanBase = "4" StanDiagnose = "4" StanOptimize = "4" StanQuap = "4" -StanSample = "6.13.7" +StanSample = "6.13.8" StanVariational = "4" StatsBase = "0.33" StatsFuns = "1" diff --git a/README.md b/README.md index d9f20d42..4a710a58 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ In Stan.jl v7 all of cmdstan's methods were moved to separate packages, i.e. Sta Stan.jl v9 uses StanSample.jl v6, StanOptimize.jl v4, StanQuap.jl v4, StanDiagnose.jl v4 and StanVariational v4 and supports multithreading on C++ level. Stan.jl v9 also uses JSON.jl to generate data and init input files for cmdstan. -Stan.jl v9 also supports BridgeStan.jl, InferenceObjects.jl and PosteriorDB.jl. See the example notebooks in the Examples_Notebooks subdirectory. Note that these are new packages and updates are to be expected. +Stan.jl v9 also supports InferenceObjects.jl and PosteriorDB.jl. See the example notebooks in the Examples_Notebooks subdirectory. Note that these are new packages and updates are to be expected. Unfortunately BridgeStan v1.0 is no longer supported. The StanJulia ecosystem includes 2 additional packages, StanQuap.jl (to compute [MAP](https://en.wikipedia.org/wiki/Maximum_a_posteriori_estimation) estimates) and DiffEqBayesStan.jl. diff --git a/test/runtests.jl b/test/runtests.jl index 7628a111..c8429150 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -52,7 +52,7 @@ examples = [ "Examples/Dyes/dyes.jl", "Examples/EightSchools/schools8.jl", "Examples/InferenceData/inferencedata.jl", - "Examples/BridgeStan/bridgestan.jl", + #"Examples/BridgeStan/bridgestan.jl", "Examples/PosteriorDB/posteriordb.jl", "Examples_Stan_Methods/Diagnose/diagnose.jl", @@ -86,6 +86,8 @@ if haskey(ENV, "JULIA_CMDSTAN_HOME") || haskey(ENV, "CMDSTAN") end end + + println("Tests completed.") else println("\nCMDSTAN or JULIA_CMDSTAN_HOME not set. Skipping tests") end