Release 2.0.0 final

Author: goedman

Project.toml

@@ -17,6 +17,7 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 TransformVariables = "84d833dd-6860-57f9-a1a7-6da5db126cff"
 
 [compat]
@@ -30,6 +31,7 @@ MonteCarloMeasurements = "0.8"
 Parameters = "0.12"
 Reexport = "0.2"
 Requires = "1.0"
+StatsFuns = "0.9"
 TransformVariables = "0.3"
 julia = "1"
 

scripts/04/m4.5d1.jl

@@ -68,27 +68,8 @@ P = TransformedLogDensity(make_transformation(model), model)
 results = mcmc_with_warmup(Random.GLOBAL_RNG, ∇P, 1000)
 posterior = P.transformation.(results.chain)
 
-println()
-DynamicHMC.Diagnostics.EBFMI(results.tree_statistics) |> display
-println()
-
-DynamicHMC.Diagnostics.summarize_tree_statistics(results.tree_statistics) |> display
-println()
-
-a3d = Array{Float64, 3}(undef, 1000, 4, 1);
-for j in 1:1
-  for i in 1:1000
-    a3d[i, 1:3, j] = values(posterior[i].β)
-    a3d[i, 4, j] = values(posterior[i].σ)
-  end
-end
-
-pnames = ["β[1]", "β[2]", "β[3]", "σ"]
-sections =   Dict(
-  :parameters => pnames,
-)
-chns = create_mcmcchains(a3d, pnames, sections, start=1);
-chns = set_names(chns, Dict("β[1]" => "α", "β[2]" => "β[1]", "β[3]" => "β[2]"))
+p = as_particles(posterior)
+display(p)
 
 stan_result = "
 Iterations = 1:1000
@@ -111,6 +92,4 @@ Quantiles:
 sigma   4.76114350   4.9816850   5.10326000   5.2300450   5.51500975
 ";
 
-describe(chns)
-
 # end of m4.5d.jl

scripts/10/m10.2d.jl

@@ -1,4 +1,4 @@
-using DynamicHMCModels, StatsFuns
+using DynamicHMCModels, LinearAlgebra, StatsFuns
 
 ProjDir = @__DIR__
 cd(ProjDir)

scripts/12/m12.6d.jl

@@ -88,6 +88,3 @@ Empirical Posterior Estimates:
  a_society.10   -0.094149204  0.2846206232 0.00450024719 0.0080735022 1000.000000
 sigma_society    0.310352849  0.1374834682 0.00217380450 0.0057325226  575.187461
 ";
-
-describe(chns, sections=[:pooled])
-