update chainoutput

Project.toml

@@ -1,7 +1,7 @@
 name = "Baytes"
 uuid = "72ddfcfc-6e9d-43df-829b-7aed7c549d4f"
 authors = ["Patrick Aschermayr <p.aschermayr@gmail.com>"]
-version = "0.1.15"
+version = "0.1.16"
 
 [deps]
 ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"

src/sampling/chain.jl

@@ -128,8 +128,7 @@ end
 ############################################################################################
 """
 $(SIGNATURES)
-Return summary for trace parameter chains. `Model` defines flattening type of parameter,
-`sym` defines parameter to be flattened, `backend` may be Val(:text), or Val(:latex).
+Return summary for trace parameter chains. 'printdefault' defines quantiles and number of digits for printing.
 
 # Examples
 ```julia
@@ -139,10 +138,8 @@ Return summary for trace parameter chains. `Model` defines flattening type of pa
 function chainsummary(
     trace::Trace,
     transform::TraceTransform,
-    backend, #i.e., Val(:text), or Val(:latex)
-    printdefault::PrintDefault=PrintDefault();
-    kwargs...,
-) where {S<:Union{Symbol,NTuple{k,Symbol} where k}}
+    printdefault::PrintDefault=PrintDefault()
+)
     ## Assign utility values
     @unpack Ndigits, quantiles = printdefault
     @unpack progress = trace.info
@@ -155,11 +152,7 @@ function chainsummary(
     ## Check if any MCMC sampler was stuck in any chain, in which case chainsummary will be skipped
     stuck, paramchain = is_stuck(arr3D)
     if stuck
-        println(
-            "#####################################################################################",
-        )
-        println("Chain is first stuck in (Nparam, Nchain) = ", paramchain, " - skipping chainsummary.")
-        return nothing
+        return stuck, paramchain, nothing
     end
     ## Compute summary statistics
     #!NOTE If more than 1 chain used, can use cross-chain diagnostics
@@ -181,14 +174,75 @@ function chainsummary(
     _reconstruct = ModelWrappers.ReConstructor(diag)
     diag_flattened = flatten(_reconstruct, diag)
     table = round.(reshape(diag_flattened, Nstats, Nparams)'; digits=Ndigits)
-    ## Print table
-    PrettyTables.pretty_table(
-        table, backend=backend, header=tablenames, row_labels=paramnames, kwargs...
-    )
     ## Return table arguments
     return table, tablenames, paramnames
 end
 
+"""
+$(SIGNATURES)
+Print summary for trace parameter chains. `backend` may be Val(:text), or Val(:latex).
+
+# Examples
+```julia
+```
+
+"""
+function printchainsummary(
+    trace::Trace,
+    transform::TraceTransform,
+    backend, #i.e., Val(:text), or Val(:latex)
+    printdefault::PrintDefault=PrintDefault();
+    kwargs...,
+)
+    table, tablenames, paramnames = chainsummary(trace, transform, printdefault)
+    if table isa Bool
+        println(
+            "#####################################################################################",
+        )
+        println("Chain is first stuck in (Nparam, Nchain) = ", tablenames, " - skipping chainsummary.")
+        return nothing, nothing, nothing
+    ## Print table
+    else
+        PrettyTables.pretty_table(
+            table, backend=backend, header=tablenames, row_labels=paramnames, kwargs...
+        )
+    end
+end
+
+"""
+$(SIGNATURES)
+Add a ModelWrapper struct 'model' as a function argument to print model.val as "true" parameter in table.
+
+# Examples
+```julia
+```
+
+"""
+function printchainsummary(
+    model::ModelWrapper,
+    trace::Trace,
+    transform::TraceTransform,
+    backend, #i.e., Val(:text), or Val(:latex)
+    printdefault::PrintDefault=PrintDefault();
+    kwargs...,
+)
+    table, tablenames, paramnames = chainsummary(trace, transform, printdefault)
+    if table isa Bool
+        println(
+            "#####################################################################################",
+        )
+        println("Chain is first stuck in (Nparam, Nchain) = ", tablenames, " - skipping chainsummary.")
+        return nothing, nothing, nothing
+    ## Print table
+    else
+        #Obtain true parameter from model
+        θ_true = round.(flatten(model, transform.tagged); digits = printdefault.Ndigits)
+        PrettyTables.pretty_table(
+            hcat(θ_true, table), backend=backend, header=vcat("True", tablenames), row_labels=paramnames, kwargs...
+        )
+    end
+end
+
 ############################################################################################
 #export
-export chainsummary
+export chainsummary, printchainsummary

src/sampling/diagnostics.jl

@@ -8,7 +8,7 @@ Return summary for trace parameter diagnostics, `backend` may be Val(:text), or
 ```
 
 """
-function diagnosticssummary(
+function printdiagnosticssummary(
     trace::Trace,
     algorithmᵛ::SMC,
     transform::TraceTransform,
@@ -29,7 +29,7 @@ function diagnosticssummary(
     )
 end
 
-function diagnosticssummary(
+function printdiagnosticssummary(
     trace::Trace,
     algorithmᵛ::AbstractVector,
     transform::TraceTransform,
@@ -60,4 +60,4 @@ end
 
 ############################################################################################
 #export
-export diagnosticssummary
+export printdiagnosticssummary

src/sampling/sample.jl

@@ -15,9 +15,9 @@ function summary(
     printdefault::PrintDefault=PrintDefault(),
 ) where {S<:Union{Symbol,NTuple{k,Symbol} where k}}
     ## Print Diagnostics summary
-    diagnosticssummary(trace, algorithmᵛ, transform, nothing, printdefault)
+    printdiagnosticssummary(trace, algorithmᵛ, transform, nothing, printdefault)
     ## Print Chain summary
-    chainsummary(trace, transform, Val(:text), printdefault)
+    printchainsummary(trace, transform, Val(:text), printdefault)
     ## Return
     return nothing
 end

src/sampling/trace.jl

@@ -238,34 +238,34 @@ end
 ############################################################################################
 """
 $(SIGNATURES)
-Safe `trace`, `model` and `algorithm` to current working directory.
+Save `trace`, `model` and `algorithm` to current working directory with name 'name'.
 
 # Examples
 ```julia
 ```
 
 """
-function savetrace(trace::Trace, model::ModelWrapper, algorithm)
-    @unpack iterations, burnin, Nchains = trace.info.sampling
+function savetrace(trace::Trace, model::ModelWrapper, algorithm,
+    name = join((
+        Base.nameof(typeof(model.id)),
+        "_",
+        Base.nameof(typeof(algorithm)),
+        "_",
+        Dates.today(),
+        "_H",
+        Dates.hour(Dates.now()),
+        "M",
+        Dates.minute(Dates.now()),
+        "_Nchains",
+        trace.info.sampling.Nchains,
+        "_Iter",
+        trace.info.sampling.iterations,
+        "_Burnin",
+        trace.info.sampling.burnin,
+    ))
+)
     JLD2.jldsave(
-        join((
-            Base.nameof(typeof(model.id)),
-            "_",
-            Base.nameof(typeof(algorithm)),
-            "_",
-            Dates.today(),
-            "_H",
-            Dates.hour(Dates.now()),
-            "M",
-            Dates.minute(Dates.now()),
-            "_Nchains",
-            Nchains,
-            "_Iter",
-            iterations,
-            "_Burnin",
-            burnin,
-            ".jld2",
-        ));
+        join((name, ".jld2"));
         trace=trace,
         model=model,
         algorithm=algorithm,