Fix scoping for nimbleMCMC (#1554)

* Add missing newline in warning message.

* Fix roxygen for buildMCMC.

* Remove one of the refs to MCMCsuite/compareMCMCs as redundant.

* Reword some text related to compareMCMCs in manual.

* Fix scoping for user-def objects with nimbleMCMC (issue 1545).

Author: paciorek

packages/nimble/R/MCMC_run.R

@@ -313,7 +313,8 @@ nimbleMCMC <- function(code,
                        samples = TRUE,
                        samplesAsCodaMCMC = FALSE,
                        summary = FALSE,
-                       WAIC = FALSE) {
+                       WAIC = FALSE,
+                       userEnv = parent.frame()) {
     #### process 'code' argument, to accept a filename, or a function
     ##if(is.character(code) || is.function(code)) {
     ##    if(is.function(code)) modelText <- mergeMultiLineStatements(deparse(body(code)))
@@ -327,7 +328,7 @@ nimbleMCMC <- function(code,
     if(missing(code) && missing(model)) stop('must provide either code or model argument')
     if(!samples && !summary && !WAIC) stop('no output specified, use samples = TRUE, summary = TRUE, or WAIC = TRUE')
     if(!missing(code) && inherits(code, 'modelBaseClass')) model <- code   ## let's handle it, if model object is provided as un-named first argument to nimbleMCMC
-    Rmodel <- mcmc_createModelObject(model, inits, nchains, setSeed, code, constants, data, dimensions, check)
+    Rmodel <- mcmc_createModelObject(model, inits, nchains, setSeed, code, constants, data, dimensions, check, userEnv = userEnv)
     conf <- configureMCMC(Rmodel, monitors = monitors, thin = thin, enableWAIC = WAIC, print = FALSE)
     Rmcmc <- buildMCMC(conf)
     compiledList <- compileNimble(Rmodel, Rmcmc)    ## only one compileNimble() call

packages/nimble/R/MCMC_utils.R

@@ -422,7 +422,7 @@ mcmc_checkWAICmonitors <- function(model, monitors, dataNodes) {
 }
 
 
-mcmc_createModelObject <- function(model, inits, nchains, setSeed, code, constants, data, dimensions, check, buildDerivs = FALSE) {
+mcmc_createModelObject <- function(model, inits, nchains, setSeed, code, constants, data, dimensions, check, buildDerivs = FALSE, userEnv) {
     ## create the Rmodel object using arguments provided to nimbleMCMC
     if(missing(model)) {  ## model object not provided
         if(!missing(inits)) {
@@ -434,8 +434,8 @@ mcmc_createModelObject <- function(model, inits, nchains, setSeed, code, constan
             } else if(is.list(inits) && (length(inits) > 0) && is.list(inits[[1]])) {
                 theseInits <- inits[[1]]
             } else theseInits <- inits
-            Rmodel    <- nimbleModel(code, constants, data, theseInits, dimensions = dimensions, check = check, buildDerivs = buildDerivs)    ## inits provided
-        } else Rmodel <- nimbleModel(code, constants, data,             dimensions = dimensions, check = check, buildDerivs = buildDerivs)    ## inits not provided
+            Rmodel    <- nimbleModel(code, constants, data, theseInits, dimensions = dimensions, check = check, buildDerivs = buildDerivs, userEnv = userEnv)    ## inits provided
+        } else Rmodel <- nimbleModel(code, constants, data,             dimensions = dimensions, check = check, buildDerivs = buildDerivs, userEnv = userEnv)    ## inits not provided
     } else {              ## model object provided
         if(!is.model(model)) stop('model argument must be a NIMBLE model object')
         Rmodel <- if(is.Rmodel(model)) model else model$Rmodel