perrydv · Oct 27, 2026 · Oct 26, 2026 · Oct 26, 2026 · Oct 27, 2026
diff --git a/nimbleModel/R/indexRuleBlock.R b/nimbleModel/R/indexRuleBlock.R
@@ -46,11 +46,11 @@ indexRuleBlockClass <- R6Class(
     getIDs = function(indexRange) {
       init <- as.integer(setupResults$fromMin + setupResults$offset)
       switch(class(indexRange)[1],
-             indexRangeScalarClass = as.integer(indexRange$value) - init + 1L,
-             indexRangeSequenceClass = (indexRange$start - init + 1):(indexRange$end - init + 1),
-             indexRangeMatrixClass = as.integer(c(indexRange$values)) - init + 1L,
-             stop("invalid type of indexRange provided for creating IDs")
-             )
+        indexRangeScalarClass = as.integer(indexRange$value) - init + 1L,
+        indexRangeSequenceClass = (indexRange$start - init + 1):(indexRange$end - init + 1),
+        indexRangeMatrixClass = as.integer(c(indexRange$values)) - init + 1L,
+        stop("invalid type of indexRange provided for creating IDs")
+      )
     },
     invertIDs = function(relativeNodeIDs) {
       if (setupResults$fromMin + setupResults$offset != 1) {

diff --git a/nimbleModel/R/modelValues.R b/nimbleModel/R/modelValues.R
@@ -226,7 +226,9 @@ make_modelValues_nClass <- function(varInfo,
   if (is.null(defaultSizes)) defaultSizes <- list()
   for (v in names(varInfo$vars)) {
     if (is.null(defaultSizes[[v]]) || length(defaultSizes[[v]]) == 0) {
-      defaultSizes[[v]] <- rep(0, max(varInfo$vars[[v]]$nDim, 1))
+      nDim <- varInfo$vars[[v]]$nDim
+      # Scalars get size 1 so uncompiled rows are numeric(1). C++ ignores sizes for nDim 0.
+      defaultSizes[[v]] <- if (nDim == 0) 1 else rep(0, nDim)
     }
   }
 
@@ -468,10 +470,11 @@ as.list.modelValues <- function(x, varNames, stack = TRUE, flatten = FALSE, iter
   if (length(varNames)) {
     ans <- vector("list", length(varNames)) |> setNames(varNames)
     for (var in varNames) {
-      res <- as.list(nCompiler::value(x, var)) # converts nList to list; compiled or uncompiled.
+      nl <- nCompiler::value(x, var)
+      res <- as.list(nl) # converts nList to list; compiled or uncompiled.
       if (flatten) {
         rawDims <- dimOrLength(res[[1]])
-        this_colnames <- dims_2_colnames(rawDims, var = var)
+        this_colnames <- nList_2_colnames(nl, rawDims, var = var)
       }
       if (stack) {
         res <- simplify2array(res, higher = !flatten)
@@ -567,6 +570,18 @@ dims_2_colnames <- function(dims, var = "x") {
   colnames <- paste0(var, "[", dim_strings, "]")
 }
 
+# Column names for the variable held in nList nl.
+# A true scalar (nDim 0) is named by the variable name alone, as in nimble,
+# whereas a length-1 vector is named with "[1]".
+# R values do not distinguish these cases, so we use the nList's element type.
+nList_2_colnames <- function(nl, dims, var) {
+  if (isTRUE(nl$get_nDim() == 0L)) {
+    var
+  } else {
+    dims_2_colnames(dims, var = var)
+  }
+}
+
 #' @exportS3Method
 #' @method as.matrix modelValues
 as.matrix.modelValues <- function(x) {
@@ -579,7 +594,7 @@ as.matrix.modelValues <- function(x) {
     if (length(this_list) == 0) next
     dim_x <- dimOrLength(this_list[[1]])
     tot_len <- prod(dim_x)
-    this_colnames <- dims_2_colnames(dim_x, var = vn)
+    this_colnames <- nList_2_colnames(this_list, dim_x, var = vn)
     # Possibly add check that all elements have the same dim
     this_matrix <- this_list |>
       lapply(\(x) {

diff --git a/nimbleModel/inst/generate_predefined.R b/nimbleModel/inst/generate_predefined.R
@@ -1,43 +1,43 @@
 ## # To update the set of predefined nClasses:
 ##
 ## # generate new predef/instr_nC. Move that directly to package code inst/nimbleModel/predef/instr_nC (i.e. move to package)
-nCompiler::nCompile(instr_nClass = nimbleModel:::instr_nClass, control=list(generate_predefined=TRUE))
+nCompiler::nCompile(instr_nClass = nimbleModel:::instr_nClass, control = list(generate_predefined = TRUE))
 test <- nCompiler::nCompile(instr_nClass = nimbleModel:::instr_nClass)
 ## #
 ## # generate new predef/declFunBase_nC. Move to package.
 ## # You should see "#include <nimbleModel/predef/declFunClass_/declFunClass_.h>" in the hContent
 ## # after declaration of declFunBase_nClass
 ## # and "// [[Rcpp::depends(nimbleModel)]]" in the cppContent
-nCompiler::nCompile(nimbleModel:::declFunBase_nClass, control=list(generate_predefined=TRUE))
+nCompiler::nCompile(nimbleModel:::declFunBase_nClass, control = list(generate_predefined = TRUE))
 test <- nCompiler::nCompile(nimbleModel:::declFunBase_nClass)
 ## #
 ## # generate new predef/modelBase_nC. Move to package.
 ## # You should see "#include <nimbleModel/predef/modelClass_/modelClass_.h>" in the hContent
 ## # after the declaration of modelBase_nClass.
 ## # and "// [[Rcpp::depends(nimbleModel)]]" in the cppContent
-nCompiler::nCompile(modelBase_nClass = nimbleModel:::modelBase_nClass, control=list(generate_predefined=TRUE))
+nCompiler::nCompile(modelBase_nClass = nimbleModel:::modelBase_nClass, control = list(generate_predefined = TRUE))
 test <- nCompiler::nCompile(nimbleModel:::modelBase_nClass)
 
 ## # generate new predef/copier_nClass. Move to package.
 ## # You should see "#include <nimbleModel/predef/copier_nC_base/copier_nC_base.h>" in the hContent BEFORE the class declaration
 ## # and "// [[Rcpp::depends(nimbleModel)]]" in the cppContent
-nCompiler::nCompile(copier_nClass = nimbleModel:::copier_nClass, control=list(generate_predefined=TRUE))
+nCompiler::nCompile(copier_nClass = nimbleModel:::copier_nClass, control = list(generate_predefined = TRUE))
 test <- nCompiler::nCompile(nimbleModel:::copier_nClass)
 
 ## # generate new predef/mCopy_nC Move to package.
 ## # You should see "#include <nimbleModel/predef/mCopy_nC_base/mCopy_model_nC_base.h>" in the hContent BEFORE the class declaration
 ## # and "// [[Rcpp::depends(nimbleModel)]]" in the cppContent
-nCompiler::nCompile(multiCopier_nClass = nimbleModel:::multiCopier_nClass, control=list(generate_predefined=TRUE))
+nCompiler::nCompile(multiCopier_nClass = nimbleModel:::multiCopier_nClass, control = list(generate_predefined = TRUE))
 test <- nCompiler::nCompile(nimbleModel:::multiCopier_nClass)
 
 ## # generate new predef/mCopyMV_nC. Move to package.
 ## # You should see "#include <nimbleModel/predef/mCopy_nC_base/mCopy_modelValues_nC_base.h>" in the hContent BEFORE the class declaration
 ## # and "// [[Rcpp::depends(nimbleModel)]]" in the cppContent
-nCompiler::nCompile(multiCopierMV_nClass = nimbleModel:::multiCopierMV_nClass, control=list(generate_predefined=TRUE))
+nCompiler::nCompile(multiCopierMV_nClass = nimbleModel:::multiCopierMV_nClass, control = list(generate_predefined = TRUE))
 test <- nCompiler::nCompile(nimbleModel:::multiCopierMV_nClass)
 
 ## # generate new predef/MVBase_nC Move to package.
 ## # You should see "#include <nimbleModel/predef/modelValuesClass_/modelValuesClass_.h>" in the hContent
 ## # and "// [[Rcpp::depends(nimbleModel)]]" in the cppContent
-nCompiler::nCompile(modelValuesBase_nClass = nimbleModel:::modelValuesBase_nClass, control=list(generate_predefined=TRUE))
+nCompiler::nCompile(modelValuesBase_nClass = nimbleModel:::modelValuesBase_nClass, control = list(generate_predefined = TRUE))
 test <- nCompiler::nCompile(nimbleModel:::modelValuesBase_nClass)
diff --git a/nimbleModel/inst/include/nimbleModel/predef/MVBase_nC/MVBase_nC_manifest.txt b/nimbleModel/inst/include/nimbleModel/predef/MVBase_nC/MVBase_nC_manifest.txt
@@ -1,4 +1,4 @@
-list(saved_at = structure(1792534431.59537, class = c("POSIXct", 
+list(saved_at = structure(1793056666.55996, class = c("POSIXct", 
 "POSIXt")), packet_name = "MVBase_nC", elements = c("preamble", 
 "cppContent", "hContent", "filebase", "post_cpp_compiler", "copyFiles", 
 "depends"), files = list(preamble = "MVBase_nC_preamble.cpp", 

diff --git a/nimbleModel/inst/include/nimbleModel/predef/copier_nClass/copier_nClass_manifest.txt b/nimbleModel/inst/include/nimbleModel/predef/copier_nClass/copier_nClass_manifest.txt
@@ -1,4 +1,4 @@
-list(saved_at = structure(1792534392.88472, class = c("POSIXct", 
+list(saved_at = structure(1793056472.33843, class = c("POSIXct", 
 "POSIXt")), packet_name = "copier_nClass", elements = c("preamble", 
 "cppContent", "hContent", "filebase", "post_cpp_compiler", "copyFiles", 
 "depends"), files = list(preamble = "copier_nClass_preamble.cpp", 

diff --git a/nimbleModel/inst/include/nimbleModel/predef/declFunBase_nC/declFunBase_nClass_manifest.txt b/nimbleModel/inst/include/nimbleModel/predef/declFunBase_nC/declFunBase_nClass_manifest.txt
@@ -1,4 +1,4 @@
-list(saved_at = structure(1792534340.26498, class = c("POSIXct", 
+list(saved_at = structure(1793056375.6661, class = c("POSIXct", 
 "POSIXt")), packet_name = "declFunBase_nClass", elements = c("preamble", 
 "cppContent", "hContent", "filebase", "post_cpp_compiler", "copyFiles", 
 "depends"), files = list(preamble = "declFunBase_nClass_preamble.cpp", 

diff --git a/nimbleModel/inst/include/nimbleModel/predef/instr_nClass/instr_nClass_manifest.txt b/nimbleModel/inst/include/nimbleModel/predef/instr_nClass/instr_nClass_manifest.txt
@@ -1,4 +1,4 @@
-list(saved_at = structure(1792534327.40934, class = c("POSIXct", 
+list(saved_at = structure(1793056317.67685, class = c("POSIXct", 
 "POSIXt")), packet_name = "instr_nClass", elements = c("preamble", 
 "cppContent", "hContent", "filebase", "post_cpp_compiler", "copyFiles", 
 "depends"), files = list(preamble = "instr_nClass_preamble.cpp", 

diff --git a/nimbleModel/inst/include/nimbleModel/predef/mCopyMV_nC/multiCopierMV_nClass_manifest.txt b/nimbleModel/inst/include/nimbleModel/predef/mCopyMV_nC/multiCopierMV_nClass_manifest.txt
@@ -1,4 +1,4 @@
-list(saved_at = structure(1792534418.86996, class = c("POSIXct", 
+list(saved_at = structure(1793056640.44678, class = c("POSIXct", 
 "POSIXt")), packet_name = "multiCopierMV_nClass", elements = c("preamble", 
 "cppContent", "hContent", "filebase", "post_cpp_compiler", "copyFiles", 
 "depends"), files = list(preamble = "multiCopierMV_nClass_preamble.cpp", 

diff --git a/nimbleModel/inst/include/nimbleModel/predef/mCopy_nC/mCopy_nC_manifest.txt b/nimbleModel/inst/include/nimbleModel/predef/mCopy_nC/mCopy_nC_manifest.txt
@@ -1,4 +1,4 @@
-list(saved_at = structure(1792534403.251, class = c("POSIXct", 
+list(saved_at = structure(1793056548.82963, class = c("POSIXct", 
 "POSIXt")), packet_name = "mCopy_nC", elements = c("preamble", 
 "cppContent", "hContent", "filebase", "post_cpp_compiler", "copyFiles", 
 "depends"), files = list(preamble = "mCopy_nC_preamble.cpp", 

diff --git a/nimbleModel/inst/include/nimbleModel/predef/modelBase_nC/modelBase_nClass_manifest.txt b/nimbleModel/inst/include/nimbleModel/predef/modelBase_nC/modelBase_nClass_manifest.txt
@@ -1,4 +1,4 @@
-list(saved_at = structure(1792534353.3121, class = c("POSIXct", 
+list(saved_at = structure(1793056441.24624, class = c("POSIXct", 
 "POSIXt")), packet_name = "modelBase_nClass", elements = c("preamble", 
 "cppContent", "hContent", "filebase", "post_cpp_compiler", "copyFiles", 
 "depends"), files = list(preamble = "modelBase_nClass_preamble.cpp",