Add auto-marginalization implementation to the main package

JuliaBUGS/.JuliaFormatter.toml

@@ -1,2 +1,3 @@
 style="blue"
 always_use_return=false
+short_to_long_function_def=false

JuliaBUGS/src/BUGSExamples/Volume_2/08_Cervix.jl

@@ -47,6 +47,7 @@ model
 }
 """
 
+#! format: off
 data = (N = 2044,
     d = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
         1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0,
@@ -442,6 +443,7 @@ data = (N = 2044,
 
 inits = (beta0C = 0, beta = 0, q = 0.5, phi = [0.5 0.5; 0.5 0.5])
 inits_alternative = (beta0C = 1.0, beta = 1.0, q = 0.75, phi = [0.15 0.15; 0.15 0.15])
+#! format: on
 
 reference_results = (
     var"beta" = (mean = 0.6156, std = 0.3406),

JuliaBUGS/src/BUGSExamples/Volume_2/11_Schools.jl

@@ -70,6 +70,7 @@ model
 }
 """
 
+#! format: off
 data = (N = 1978, M = 38, mn = [0, 0, 0],
     prec = [0.0001 0 0; 0 0.0001 0; 0 0 0.0001],
     R = [0.1 0.005 0.005; 0.005 0.1 0.005; 0.005 0.005 0.1],
@@ -1573,6 +1574,7 @@ inits_alternative = (theta = 0.1, phi = 0, gamma = [1.0, 1.0, 1.0],
              0 0 0
              0 0 0
              0 0 0])
+#! format: on
 
 reference_results = (
     var"beta[1]" = (mean = 2.589E-4, std = 9.8E-5),

JuliaBUGS/src/BUGSExamples/Volume_2/16_Stagnant.jl

@@ -52,4 +52,4 @@ reference_results = (
 )
 
 stagnant = Example(
-    name, model_def, original, data, inits, inits_alternative, reference_results)
+    name, model_def, original, data, inits, inits_alternative, reference_results)

JuliaBUGS/src/BUGSExamples/Volume_2/18_Pigs.jl

@@ -0,0 +1 @@
+

JuliaBUGS/src/BUGSExamples/Volume_2/19_Simulating_data.jl

@@ -0,0 +1 @@
+

JuliaBUGS/src/BUGSExamples/Volume_3/09_Hips4.jl

@@ -92,7 +92,7 @@ model_def = @bugs begin
             for t in 2:N
                 for s in 1:S
                     var"pi"[
-                        n, k, t, s] = inprod(
+                    n, k, t, s] = inprod(
                         var"pi"[n, k, t - 1, :], Lambda[n, k, t, :, s])
                 end
             end

JuliaBUGS/src/BUGSExamples/Volume_4/11_Methadone.jl

@@ -51,7 +51,8 @@ end
 data_dict = JSON.parsefile(joinpath(readdir(), "methadone_data.json"))
 data = NamedTuple{Tuple([Symbol(key) for key in keys(data_dict)])}(Tuple([map(identity,
                                                                               val)
-                                                                          for val in values(data_dict)]))
+                                                                          for val in
+                                                                              values(data_dict)]))
 
 inits = (
     lambda = 0,

JuliaBUGS/src/JuliaBUGS.jl

@@ -42,7 +42,8 @@ using .Model:
     BUGSModel,
     evaluate_with_values!!,
     UseGraph,
-    UseGeneratedLogDensityFunction
+    UseGeneratedLogDensityFunction,
+    UseAutoMarginalization
 
 include("independent_mh.jl")
 include("gibbs.jl")

JuliaBUGS/src/model/Model.jl

@@ -9,6 +9,7 @@ using Graphs
 using LinearAlgebra
 using JuliaBUGS: JuliaBUGS, BUGSGraph
 using JuliaBUGS.BUGSPrimitives
+using LogExpFunctions
 using MetaGraphsNext
 using Random
 
@@ -20,5 +21,8 @@ include("logdensityproblems.jl")
 
 export parameters, variables, initialize!, getparams, settrans, set_evaluation_mode
 export evaluate_with_rng!!, evaluate_with_env!!, evaluate_with_values!!
+export evaluate_with_marginalization_rng!!,
+    evaluate_with_marginalization_env!!, evaluate_with_marginalization_values!!
+export UseAutoMarginalization, enumerate_discrete_values
 
 end # Model