perrydv · Oct 16, 2026 · Oct 17, 2026 · Oct 17, 2026 · Oct 17, 2026
diff --git a/.gitignore b/.gitignore
@@ -37,4 +37,4 @@ vignettes/*.pdf
 **/.DS_Store
 
 # Symlink to inst/include for devtools::load_all()
-nimbleModel/include
+nimbleModel/include
diff --git a/nimbleModel/R/all_utils.R b/nimbleModel/R/all_utils.R
@@ -163,11 +163,12 @@ messageIfVerbose <- function(...) {
 
 
 # Temporarily here as need for initial testing of processing.
+# Mis-named now as it also allows for nFunctions.
 is.rcf <- function(x, inputIsName = FALSE, where = -1) {
   if (inputIsName) {
     x <- get(x, pos = where)
   }
-  if (inherits(x, "nfMethodRC")) {
+  if (inherits(x, "nfMethodRC") || inherits(x, "nFunction")) {
     return(TRUE)
   }
   if (is.function(x)) {
@@ -184,12 +185,6 @@ is.rcf <- function(x, inputIsName = FALSE, where = -1) {
 nimbleUniqueID <- labelFunctionCreator("UID")
 nimbleModelID <- labelFunctionCreator("MID")
 
-
-# temporary, as we have some tests of use of `c()` in indexing
-nimC <- function(...) {
-  c(...)
-}
-
 evalNumeric <- function(expr) {
   if (length(expr) == 1) {
     return(expr)
@@ -202,3 +197,14 @@ evalNumeric <- function(expr) {
   }
   return(expr)
 }
+
+# Placeholders while we sort out packaging.
+
+nC <- function(...) {
+  c(...)
+}
+
+nMul <- function(x, y) {
+  x %*% y
+}  
+
diff --git a/nimbleModel/R/context.R b/nimbleModel/R/context.R
@@ -206,8 +206,8 @@ expandContextAndReplacements <- function(allReplacements, allReplacementNameExpr
   innerLoopCode <- as.call(c(list(quote(`{`)), replacementRecordingCode, indexRecordingCode, quote(iAns <- iAns + 1)))
 
   innerLoopCode <- context$embedCodeInForLoop(innerLoopCode, useContext)
-  # This is a hacky way to deal with `nimC`, which is not in `constantsCopy`.
-  if (length(innerLoopCode[[3]]) > 1 && innerLoopCode[[3]][[1]] == "nimC") {
+  # This is a hacky way to deal with `nC`, which is not in `constantsCopy`.
+  if (length(innerLoopCode[[3]]) > 1 && innerLoopCode[[3]][[1]] == "nC") {
     innerLoopCode[[3]][[1]] <- quote(c)
   }
 
@@ -265,8 +265,8 @@ determineContextSize <- function(context, useContext = rep(TRUE, length(context$
   innerLoopCode <- quote(iAns <- iAns + 1)
   innerLoopCode <- context$embedCodeInForLoop(innerLoopCode, useContext)
 
-  # This is a hacky way to deal with `nimC`, which is not in `evalEnv`.
-  if (length(innerLoopCode[[3]]) > 1 && innerLoopCode[[3]][[1]] == "nimC") {
+  # This is a hacky way to deal with `nC`, which is not in `evalEnv`.
+  if (length(innerLoopCode[[3]]) > 1 && innerLoopCode[[3]][[1]] == "nC") {
     innerLoopCode[[3]][[1]] <- quote(c)
   }
 

diff --git a/nimbleModel/R/getSymbolicParentNodes.R b/nimbleModel/R/getSymbolicParentNodes.R
@@ -89,7 +89,7 @@ nimblePreevaluationFunctionNames <- c(
   # distribution functions
   paste0(c("d", "q", "p"), "t"),
   paste0(c("d", "q", "p"), "exp"),
-  "nimC", "nimRep", "nimSeq", "diag",
+  "nC", "nimRep", "nimSeq", "diag", "nMul",
   "nimNumeric", "nimMatrix", "nimArray",
   "length"
 )
@@ -143,7 +143,7 @@ nimbleOrRfunctionNames <- c(
   # distribution functions
   paste0(c("d", "r", "q", "p"), "t"),
   paste0(c("d", "r", "q", "p"), "exp"),
-  "nimC", "nimRep", "nimSeq",
+  "nimC", "nimRep", "nimSeq", "nC", "nMul",
   "diag",
   "length"
 )

diff --git a/nimbleModel/R/indexConstraint.R b/nimbleModel/R/indexConstraint.R
@@ -149,7 +149,7 @@ newIndexConstraint_fromSimple <- function(expr, slot, constants) {
       slot
     ))
   } else { # various other cases such as `x[2]`, `x[k+1]`, `x[c(2,3,5)]`, `x[c(2,3,k)]`.
-    if (expr[[1]] == "nimC") {
+    if (expr[[1]] == "nC") {
       expr[[1]] <- quote(c)
     }
     result <- eval(expr, envir = constants)

diff --git a/nimbleModel/R/indexRuleConstant.R b/nimbleModel/R/indexRuleConstant.R
@@ -56,8 +56,8 @@ indexRuleConstant_setup <- function(toIndexExprList,
         eval(toIndexExpr[[2]], envir = constants),
         eval(toIndexExpr[[3]], envir = constants)
       )
-    } else if (length(toIndexExpr) > 1 && toIndexExpr[[1]] == "nimC") {
-      toIndexExpr[[1]] <- quote(c) # `nimC` not readily available in series of environments.
+    } else if (length(toIndexExpr) > 1 && toIndexExpr[[1]] == "nC") {  # TODO: revisit handling of c().
+      toIndexExpr[[1]] <- quote(c) # `nC` not readily available in series of environments.
       toConstant <- indexRangeMatrixClass$new(as.matrix(eval(toIndexExpr, envir = constants)))
     } else {
       stop("input error in `", safeDeparse(toIndexExprList), "`.")

diff --git a/nimbleModel/R/miscFunctions.R b/nimbleModel/R/miscFunctions.R
@@ -1,7 +1,7 @@
 # This needs to be sourced after `nimbleFunction` is defined, so can't be done in `distributions_inputList.R`.
-calc_dmnormAltParams <- nimble::nimbleFunction(
+calc_dmnormAltParams <- nCompiler::nFunction(
   name = "calc_dmnormAltParams",
-  run = function(cholesky = double(2), prec_param = double(), return_prec = double()) {
+  fun = function(cholesky = double(2), prec_param = double(), return_prec = double()) {
     if (prec_param == return_prec) {
       ans <- t(cholesky) %*% cholesky
     } else {
@@ -16,9 +16,9 @@ calc_dmnormAltParams <- nimble::nimbleFunction(
   }
 )
 
-calc_dwishAltParams <- nimble::nimbleFunction(
+calc_dwishAltParams <- nCompiler::nFunction(
   name = "calc_dwishAltParams",
-  run = function(cholesky = double(2), scale_param = double(), return_scale = double()) {
+  fun = function(cholesky = double(2), scale_param = double(), return_scale = double()) {
     if (scale_param == return_scale) {
       ans <- t(cholesky) %*% cholesky
     } else {
@@ -31,4 +31,5 @@ calc_dwishAltParams <- nimble::nimbleFunction(
     returnType(double(2))
     return(ans)
   }
-)
+)
+
diff --git a/nimbleModel/R/modelBaseClass.R b/nimbleModel/R/modelBaseClass.R
@@ -395,7 +395,7 @@ modelBase_nClass <- nClass(
     getDependencies = function(nodes, omit = NULL, self = TRUE,
                                determOnly = FALSE, stochOnly = FALSE,
                                includeData = TRUE, dataOnly = FALSE,
-                               includePredictive = nimble::getNimbleOption('getDependenciesIncludesPredictiveNodes'),
+                               includePredictive = getNimbleModelOption('getDependenciesIncludesPredictiveNodes'),
                                predictiveOnly = FALSE, includeRHSonly = FALSE,
                                downstream = FALSE, immediateOnly = FALSE,
                                nodesAsChars = getNimbleModelOption("nodesAsChars"),

diff --git a/nimbleModel/R/modelDecl.R b/nimbleModel/R/modelDecl.R
@@ -102,7 +102,7 @@ modelDeclClass <- R6Class(
       if (!stoch) {
         return(NULL)
       }
-      types <- nimble:::distributions[[distributionName]]$types
+      types <- nimbleModel:::distributions[[distributionName]]$types
       if (is.null(types)) {
         return(NULL)
       }
@@ -352,7 +352,7 @@ modelDeclClass <- R6Class(
               }
             }
             if (is.c(origIndex)) { # Handles new cases like `y[c(2,3,5)] ~ dmnorm(...)`.
-              if (origIndex[[1]] == "nimC") {
+              if (origIndex[[1]] == "nC") {
                 logProbExpr[[i]] <- origIndex[[2]]
               } else {
                 stop("unexpected input in `", safeDeparse(origIndex), "`.")

diff --git a/nimbleModel/R/modelDef.R b/nimbleModel/R/modelDef.R
@@ -34,7 +34,11 @@ modelDefClass <- R6Class(
       checkAndAssignConstants(constants, code)
 
       modelCode <<- codeProcessIfThenElse(code, constants, userEnv)
-      modelCode <<- nimble:::nf_changeNimKeywords(modelCode) # Formerly in `assignBUGScode`.
+
+      # Switch keyword name transformations as a test while we determine what happens here vs in nimble2.
+      # We need to not use nimble anymore.
+      #
+      modelCode <<- nCompiler:::nf_changeKeywords(modelCode) # Formerly in `assignBUGScode`.
 
       # TODO: add this later.
       # setModelValuesClassName()
@@ -575,7 +579,7 @@ modelDefClass <- R6Class(
         if (decl$stoch) {
           params <- as.list(valueExpr[-1]) # Extract the original distribution parameters.
           paramNames <- names(valueExpr)[-1]
-          types <- nimble:::distributions[[decl$distributionName]]$types
+          types <- nimbleModel:::distributions[[decl$distributionName]]$types
           # `types` may be NULL if all are scalar.
 
           for (iParam in seq_along(params)) {

diff --git a/nimbleModel/R/modelFunctions.R b/nimbleModel/R/modelFunctions.R
@@ -219,7 +219,7 @@ taggedClass <- R6Class(
 getDependencies <- function(model, nodes, omit = NULL,
                             self = TRUE, determOnly = FALSE, stochOnly = FALSE,
                             includeData = TRUE, dataOnly = FALSE,
-                            includePredictive = nimble::getNimbleOption('getDependenciesIncludesPredictiveNodes'),
+                            includePredictive = getNimbleModelOption('getDependenciesIncludesPredictiveNodes'),
                             predictiveOnly = FALSE, includeRHSonly = FALSE,
                             downstream = FALSE, immediateOnly = FALSE,
                             nodesAsChars = getNimbleModelOption("nodesAsChars"),
@@ -722,7 +722,7 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes,
       if (length(reCheck)) {
         errorNodes <- head(reCheck, n = 4)
         if (length(reCheck) > 4) moreText <- ", .." else moreText <- ""
-        extraMsg <- if (isTRUE(nimble::getNimbleOption("includeUnneededLatents"))) "" else "            They will be omitted, but one can force inclusion with\n            `nimbleOptions(includeUnneededLatents=TRUE)`.\n"
+        extraMsg <- if (isTRUE(getNimbleModelOption("includeUnneededLatents"))) "" else "            They will be omitted, but one can force inclusion with\n            `nimbleOptions(includeUnneededLatents=TRUE)`.\n"
         messageIfVerbose(
           "  [Warning] There are some `randomEffectsNodes` provided that look like\n",
           "            they are not needed for the provided (or default) `paramNodes`:\n",
@@ -731,7 +731,7 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes,
           "            (potentially in the control list) for the algorithm or as\n",
           "            an argument to `setupMargNodes`."
         )
-        if (!isTRUE(nimble::getNimbleOption("includeUnneededLatents"))) {
+        if (!isTRUE(getNimbleModelOption("includeUnneededLatents"))) {
           randomEffectsNodes <- setdiff_nodes(randomEffectsNodes, reCheck)
         }
       }

diff --git a/nimbleModel/R/model_utils.R b/nimbleModel/R/model_utils.R
@@ -31,9 +31,9 @@ is.vectorized <- function(node) {
 
 is.c <- function(node) {
   if (is.character(node)) {
-    return(grepl("^nimC", node))
+    return(grepl("^nC", node))
   } else {
-    return("nimC" %in% all.names(node))
+    return("nC" %in% all.names(node))
   }
 }
 

diff --git a/nimbleModel/R/options.R b/nimbleModel/R/options.R
@@ -10,7 +10,9 @@
     disallowMultivariateArgumentExpressions = TRUE,
     legacy_nimble = FALSE, # TRUE means stricter use of original nimble behavior in some cases.
     nodesAsChars = FALSE,
-    verbose = TRUE
+    verbose = TRUE,
+    getDependenciesIncludesPredictiveNodes = TRUE,    ## may be toggled off during MCMC sampler building
+    includeUnneededLatents = FALSE
   )
 )
 

diff --git a/nimbleModel/tests/testthat/test-graphRules.R b/nimbleModel/tests/testthat/test-graphRules.R
@@ -2058,7 +2058,7 @@ test_that("non-sequential indexing in for loop or indexRule", {
         NULL
     )
 
-    rule <- graphRuleClass$new(toExpr = quote(y[nimC(2,3,5)]),
+    rule <- graphRuleClass$new(toExpr = quote(y[nC(2,3,5)]),
                                fromExpr = quote(x[1:3]),
                                context = context_0)
 

diff --git a/nimbleModel/tests/testthat/test-setupMargNodes.R b/nimbleModel/tests/testthat/test-setupMargNodes.R
@@ -496,13 +496,12 @@ test_that("`setupMargNodes` handling of missing/extra latents", {
     expect_identical(result$randomEffectsNodes[[1]]$toNodeChars(), c("b[1]", "b[2]"))
     expect_identical(result$paramNodes[[1]]$toNodeChars(), c("mu"))
 
-    # TODO: presumably rework how this option is handled in nimble 2.
-    nimble::nimbleOptions(includeUnneededLatents = TRUE)
+    setNimbleModelOption('includeUnneededLatents', TRUE)
     expect_message(result <- setupMargNodes(m, randomEffectsNodes = 'b'), "they are not needed for the provided")
     expect_identical(result$randomEffectsNodes[[1]]$toNodeChars(), c("b[1]", "b[2]", "b[3]"))
     expect_identical(result$paramNodes[[1]]$toNodeChars(), c("mu"))
     ## Note `b[3]` is not in `calcNodes` because `predictiveNodes` are excluded.
-    nimble::nimbleOptions(includeUnneededLatents = FALSE)
+    setNimbleModelOption('includeUnneededLatents', FALSE)
 })
 
 test_that("getConditionallyIndependentSets works with grouped data", {