Update trace

Project.toml

@@ -1,7 +1,7 @@
 name = "Baytes"
 uuid = "72ddfcfc-6e9d-43df-829b-7aed7c549d4f"
 authors = ["Patrick Aschermayr <p.aschermayr@gmail.com>"]
-version = "0.1.10"
+version = "0.1.11"
 
 [deps]
 ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"

src/sampling/chain.jl

@@ -148,6 +148,7 @@ function chainsummary(
     @unpack progress = trace.info
     @unpack tagged, paramnames = transform
     Nparams = length(tagged)
+    Nchains = length(transform.chains)
     ## Flatten parameter to 3D array
     computingtime = progress.enabled ? (progress.tlast - progress.tinit) : NaN
     arr3D = trace_to_3DArray(trace, transform)
@@ -162,7 +163,7 @@ function chainsummary(
     end
     ## Compute summary statistics
     #!NOTE If more than 1 chain used, can use cross-chain diagnostics
-    if trace.info.sampling.Nchains > 1
+    if Nchains > 1
         #NOTE: Most of the computing time of the function happens here
         chainparamdiagnostic = chainparamdiagnostics(arr3D, computingtime)
     else

src/sampling/inference.jl

@@ -143,7 +143,9 @@ function trace_to_3DArray(
     ## Preallocate array
     mcmcchain = zeros(length(effective_iterations), length(tagged), length(chains))
     ## Flatten corresponding parameter
-    Threads.@threads for (idx, chain) in collect(enumerate(chains))
+    #!NOTE: This is threadsave, but chain is not flattened in correct ordered, which might be troublesome for MCMC chain analysis.
+#    Threads.@threads for (idx, chain) in collect(enumerate(chains))
+    for (idx, chain) in collect(enumerate(chains))
         for (iter0, iterburnin) in enumerate(effective_iterations)
             mcmcchain[iter0, :, idx] .= flatten(tagged.info.reconstruct, subset(trace.val[chain][iterburnin], tagged.parameter))
         end
@@ -230,7 +232,9 @@ function flatten_chainvals(
     ## Preallocate array
     mcmcchain = [ [ zeros(tagged.info.reconstruct.default.output, length(tagged)) for _ in eachindex(effective_iterations) ] for _ in eachindex(chains) ]
     ## Flatten corresponding parameter
-    Threads.@threads for (idx, chain) in collect(enumerate(chains))
+    #!NOTE: This is threadsave, but chain is not flattened in correct ordered, which might be troublesome for MCMC chain analysis.
+#    Threads.@threads for (idx, chain) in collect(enumerate(chains))
+    for (idx, chain) in collect(enumerate(chains))
         for (iter0, iterburnin) in enumerate(effective_iterations)
             mcmcchain[idx][iter0] .= flatten(tagged.info.reconstruct, subset(trace.val[chain][iterburnin], tagged.parameter))
         end