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 = "c1514b29-d3a0-5178-b312-660c88baa699"
-
-[compat]
-GLMakie = "~0.8.0"
-RegressionAndOtherStories = "~0.7.4"
-StanSample = "~6.13.7"
-"""
-
-# ╔═╡ 00000000-0000-0000-0000-000000000002
-PLUTO_MANIFEST_TOML_CONTENTS = """
-# This file is machine-generated - editing it directly is not advised
-
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-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]]
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-version = "0.4.3"
-
-[[deps.Adapt]]
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-version = "3.4.0"
-
-[[deps.ArgCheck]]
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-
[[deps.ArgTools]]
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
version = "1.1.1"
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-version = "0.5.4"
-
-[[deps.Arpack_jll]]
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-git-tree-sha1 = "5ba6c757e8feccf03a1554dfaf3e26b3cfc7fd5e"
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-
-[[deps.ArrayInterfaceOffsetArrays]]
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-uuid = "015c0d05-e682-4f19-8f0a-679ce4c54826"
-version = "0.1.7"
-
-[[deps.ArrayInterfaceStaticArrays]]
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-[[deps.ArrayInterfaceStaticArraysCore]]
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-
[[deps.Artifacts]]
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
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-[[deps.AxisArrays]]
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-[[deps.BangBang]]
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[[deps.Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
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-[[deps.BitTwiddlingConvenienceFunctions]]
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-git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b"
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-
-[[deps.Bzip2_jll]]
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-git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2"
-uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
-version = "1.0.8+0"
-
-[[deps.CPUSummary]]
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-git-tree-sha1 = "a7157ab6bcda173f533db4c93fc8a27a48843757"
-uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
-version = "0.1.30"
-
[[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.Cairo_jll]]
-deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
-git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2"
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-[[deps.Calculus]]
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[[deps.CodecZlib]]
deps = ["TranscodingStreams", "Zlib_jll"]
git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da"
uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
version = "0.7.0"
-[[deps.ColorSchemes]]
-deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"]
-git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3"
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-[[deps.ColorTypes]]
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-version = "0.11.4"
-
-[[deps.ColorVectorSpace]]
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-git-tree-sha1 = "d08c20eef1f2cbc6e60fd3612ac4340b89fea322"
-uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4"
-version = "0.9.9"
-
-[[deps.Colors]]
-deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
-git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40"
-uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
-version = "0.12.8"
-
-[[deps.Combinatorics]]
-git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860"
-uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
-version = "1.0.2"
-
-[[deps.CommonSubexpressions]]
-deps = ["MacroTools", "Test"]
-git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7"
-uuid = "bbf7d656-a473-5ed7-a52c-81e309532950"
-version = "0.3.0"
-
[[deps.Compat]]
deps = ["Dates", "LinearAlgebra", "UUIDs"]
git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a"
@@ -336,34 +171,6 @@ deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
version = "1.0.1+0"
-[[deps.CompositionsBase]]
-git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769"
-uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b"
-version = "0.1.1"
-
-[[deps.ConsoleProgressMonitor]]
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-git-tree-sha1 = "3ab7b2136722890b9af903859afcf457fa3059e8"
-uuid = "88cd18e8-d9cc-4ea6-8889-5259c0d15c8b"
-version = "0.1.2"
-
-[[deps.ConstructionBase]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95"
-uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
-version = "1.4.1"
-
-[[deps.Contour]]
-git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781"
-uuid = "d38c429a-6771-53c6-b99e-75d170b6e991"
-version = "0.6.2"
-
-[[deps.CpuId]]
-deps = ["Markdown"]
-git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406"
-uuid = "adafc99b-e345-5852-983c-f28acb93d879"
-version = "0.3.1"
-
[[deps.Crayons]]
git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
@@ -391,67 +198,20 @@ git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464"
version = "1.0.0"
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-version = "0.4.13"
-
[[deps.Dates]]
deps = ["Printf"]
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
-[[deps.DefineSingletons]]
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-version = "0.1.2"
-
[[deps.DelimitedFiles]]
deps = ["Mmap"]
git-tree-sha1 = "19b1417ff479c07e523fcbf2fd735a3fde3d1ab3"
uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
version = "1.9.0"
-[[deps.DensityInterface]]
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[[deps.Distributed]]
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uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
-[[deps.Distributions]]
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[[deps.DocStringExtensions]]
deps = ["LibGit2"]
git-tree-sha1 = "c36550cb29cbe373e95b3f40486b9a4148f89ffd"
@@ -469,47 +229,6 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
version = "1.6.0"
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[[deps.FilePathsBase]]
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git-tree-sha1 = "e27c4ebe80e8699540f2d6c805cc12203b614f12"
@@ -519,210 +238,42 @@ version = "0.9.20"
[[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
-[[deps.FillArrays]]
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@@ -1172,84 +408,21 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
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@@ -1259,27 +432,6 @@ version = "1.3.16"
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-[[deps.StatisticalTraits]]
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-version = "3.2.0"
-
[[deps.Statistics]]
deps = ["LinearAlgebra", "SparseArrays"]
uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
version = "1.9.0"
-[[deps.StatsAPI]]
-deps = ["LinearAlgebra"]
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-
-[[deps.StatsBase]]
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-version = "0.33.21"
-
-[[deps.StatsFuns]]
-deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "ab6083f09b3e617e34a956b43e9d51b824206932"
-uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "1.1.1"
-
-[[deps.StatsPlots]]
-deps = ["AbstractFFTs", "Clustering", "DataStructures", "DataValues", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"]
-git-tree-sha1 = "e0d5bc26226ab1b7648278169858adcfbd861780"
-uuid = "f3b207a7-027a-5e70-b257-86293d7955fd"
-version = "0.15.4"
-
[[deps.StringManipulation]]
git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123"
uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e"
@@ -1415,10 +478,6 @@ git-tree-sha1 = "ca4bccb03acf9faaf4137a9abc1881ed1841aa70"
uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
version = "1.10.0"
-[[deps.SuiteSparse]]
-deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
-uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
-
[[deps.SuiteSparse_jll]]
deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"]
uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
@@ -1452,18 +511,6 @@ deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
version = "1.10.0"
-[[deps.TensorCore]]
-deps = ["LinearAlgebra"]
-git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6"
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-version = "0.1.1"
-
-[[deps.TerminalLoggers]]
-deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"]
-git-tree-sha1 = "f53e34e784ae771eb9ccde4d72e578aa453d0554"
-uuid = "5d786b92-1e48-4d6f-9151-6b4477ca9bed"
-version = "0.1.6"
-
[[deps.Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
@@ -1474,17 +521,6 @@ git-tree-sha1 = "e4bdc63f5c6d62e80eb1c0043fcc0360d5950ff7"
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
version = "0.9.10"
-[[deps.Transducers]]
-deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"]
-git-tree-sha1 = "c42fa452a60f022e9e087823b47e5a5f8adc53d5"
-uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999"
-version = "0.4.75"
-
-[[deps.URIs]]
-git-tree-sha1 = "ac00576f90d8a259f2c9d823e91d1de3fd44d348"
-uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
-version = "1.4.1"
-
[[deps.UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
@@ -1497,191 +533,12 @@ version = "1.0.2"
[[deps.Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
-[[deps.UnicodeFun]]
-deps = ["REPL"]
-git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf"
-uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1"
-version = "0.4.1"
-
-[[deps.Unzip]]
-git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78"
-uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d"
-version = "0.2.0"
-
-[[deps.VectorizationBase]]
-deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"]
-git-tree-sha1 = "fc79d0f926592ecaeaee164f6a4ca81b51115c3b"
-uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
-version = "0.21.56"
-
-[[deps.Wayland_jll]]
-deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"]
-git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23"
-uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89"
-version = "1.19.0+0"
-
-[[deps.Wayland_protocols_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "4528479aa01ee1b3b4cd0e6faef0e04cf16466da"
-uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91"
-version = "1.25.0+0"
-
[[deps.WeakRefStrings]]
deps = ["DataAPI", "InlineStrings", "Parsers"]
git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23"
uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
version = "1.4.2"
-[[deps.Widgets]]
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-[[deps.WoodburyMatrices]]
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-git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3"
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-[[deps.XML2_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "58443b63fb7e465a8a7210828c91c08b92132dff"
-uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
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-[[deps.XSLT_jll]]
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-git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a"
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-version = "1.1.34+0"
-
-[[deps.Xorg_libX11_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"]
-git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527"
-uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc"
-version = "1.6.9+4"
-
-[[deps.Xorg_libXau_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e"
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-
-[[deps.Xorg_libXcursor_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"]
-git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd"
-uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724"
-version = "1.2.0+4"
-
-[[deps.Xorg_libXdmcp_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4"
-uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05"
-version = "1.1.3+4"
-
-[[deps.Xorg_libXext_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"]
-git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3"
-uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3"
-version = "1.3.4+4"
-
-[[deps.Xorg_libXfixes_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"]
-git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4"
-uuid = "d091e8ba-531a-589c-9de9-94069b037ed8"
-version = "5.0.3+4"
-
-[[deps.Xorg_libXi_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"]
-git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246"
-uuid = "a51aa0fd-4e3c-5386-b890-e753decda492"
-version = "1.7.10+4"
-
-[[deps.Xorg_libXinerama_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"]
-git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123"
-uuid = "d1454406-59df-5ea1-beac-c340f2130bc3"
-version = "1.1.4+4"
-
-[[deps.Xorg_libXrandr_jll]]
-deps = ["Artifacts", "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_libxkbfile_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"]
-git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2"
-uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a"
-version = "1.1.0+4"
-
-[[deps.Xorg_xcb_util_image_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"]
-git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97"
-uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b"
-version = "0.4.0+1"
-
-[[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"
+
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+"""
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+deps = ["Dates"]
+uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+version = "1.0.3"
+
+[[deps.TableOperations]]
+deps = ["SentinelArrays", "Tables", "Test"]
+git-tree-sha1 = "e383c87cf2a1dc41fa30c093b2a19877c83e1bc1"
+uuid = "ab02a1b2-a7df-11e8-156e-fb1833f50b87"
+version = "1.2.0"
+
+[[deps.TableTraits]]
+deps = ["IteratorInterfaceExtensions"]
+git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
+uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
+version = "1.0.1"
+
+[[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