From 3c3e7c81a4ce1a6be18462f3c878c9d1bbae1962 Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Sat, 15 Aug 2026 13:14:47 -0700 Subject: [PATCH 01/14] Try self=TRUE in setupMargNodes. --- packages/nimble/R/setupMargNodes.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/nimble/R/setupMargNodes.R b/packages/nimble/R/setupMargNodes.R index ecb92c536..b8696d560 100644 --- a/packages/nimble/R/setupMargNodes.R +++ b/packages/nimble/R/setupMargNodes.R @@ -283,7 +283,7 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes, tempDataNodesDefault <- model$getNodeNames(dataOnly = TRUE) if(paramsHandled) tempDataNodesDefault <- setdiff(tempDataNodesDefault, paramNodes) - tempDataNodesDefaultParents <- model$getParents(tempDataNodesDefault, upstream = TRUE, stochOnly = TRUE) + tempDataNodesDefaultParents <- model$getParents(tempDataNodesDefault, upstream = TRUE, stochOnly = TRUE, self = TRUE) # See comment above about why this is necessary: tempDataNodesDefaultParents <- setdiff(tempDataNodesDefaultParents, tempDataNodesDefault) reNodesDefault <- intersect(reNodesDefault, tempDataNodesDefaultParents) @@ -292,12 +292,12 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes, if(paramsHandled) { # This means reProvided OR paramsProvided. Including parents allows checking # of potentially missing REs. reNodesDefault <- intersect(reNodesDefault, - model$getParents(calcNodes, upstream=TRUE, stochOnly = TRUE)) + model$getParents(calcNodes, upstream=TRUE, stochOnly = TRUE, self = TRUE)) } else { # This means !paramsHandled and hence !reProvided AND !paramsProvided reNodesDefault <- intersect(reNodesDefault, calcNodes) reNodesDefault <- intersect(reNodesDefault, - model$getParents(calcNodes, upstream=TRUE, stochOnly = TRUE)) + model$getParents(calcNodes, upstream=TRUE, stochOnly = TRUE, self = TRUE)) } } } From d2c84a7639bd859f109d6b3f7c7da9f67da0d19a Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Sun, 16 Aug 2026 09:00:14 -0700 Subject: [PATCH 02/14] Update test to seemingly fix randomEffectsNodes. --- packages/nimble/tests/testthat/test-setupMargNodes.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/nimble/tests/testthat/test-setupMargNodes.R b/packages/nimble/tests/testthat/test-setupMargNodes.R index 9eea48df8..e844aa369 100644 --- a/packages/nimble/tests/testthat/test-setupMargNodes.R +++ b/packages/nimble/tests/testthat/test-setupMargNodes.R @@ -436,7 +436,7 @@ test_that("setupMargNodes finds correct randomEffectsNodes based on calcNodes in }) m <- nimbleModel(code, data = list(y = c(1, 2))) SMN <- setupMargNodes(m, calcNodes = c("r", "s")) - expect_identical(SMN$randomEffectsNodes, c("r[1]","r[2]")) + expect_identical(SMN$randomEffectsNodes, c("r[1]","r[2]","s[1]","s[2]")) expect_identical(SMN$paramNodes, c("p[1]","p[2]")) }) From 32079acf168df18bac1edb0ac4e55548dd5d0359 Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Sun, 16 Aug 2026 11:47:40 -0700 Subject: [PATCH 03/14] Test full exclusion of input nodes when self=F in getParents. --- packages/nimble/R/BUGS_model.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/packages/nimble/R/BUGS_model.R b/packages/nimble/R/BUGS_model.R index 2cf6e609b..27c9083cd 100644 --- a/packages/nimble/R/BUGS_model.R +++ b/packages/nimble/R/BUGS_model.R @@ -959,7 +959,9 @@ Details: The upward search for dependent nodes propagates through deterministic if(self) { # The C++ call does *not* return self nodes nodeFunIDs <- unique(modelDef$maps$vertexID_2_nodeID[ nodeIDs ]) parentIDs <- sort(c(parentIDs, nodeFunIDs)) - } + } else parentIDs <- setdiff(parentIDs, nodeIDs) + + if(!includeRHSonly) parentIDs <- parentIDs[modelDef$maps$types[parentIDs] != 'RHSonly'] if(determOnly) parentIDs <- parentIDs[modelDef$maps$types[parentIDs] == 'determ'] if(stochOnly) parentIDs <- parentIDs[modelDef$maps$types[parentIDs] == 'stoch'] From 809207a8e3b9093bacae8f399ceedcbd2099d7fa Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Sun, 16 Aug 2026 13:35:03 -0700 Subject: [PATCH 04/14] Set self=TRUE in setupMargNodes when not specified. --- packages/nimble/R/setupMargNodes.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/nimble/R/setupMargNodes.R b/packages/nimble/R/setupMargNodes.R index ecb92c536..b8696d560 100644 --- a/packages/nimble/R/setupMargNodes.R +++ b/packages/nimble/R/setupMargNodes.R @@ -283,7 +283,7 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes, tempDataNodesDefault <- model$getNodeNames(dataOnly = TRUE) if(paramsHandled) tempDataNodesDefault <- setdiff(tempDataNodesDefault, paramNodes) - tempDataNodesDefaultParents <- model$getParents(tempDataNodesDefault, upstream = TRUE, stochOnly = TRUE) + tempDataNodesDefaultParents <- model$getParents(tempDataNodesDefault, upstream = TRUE, stochOnly = TRUE, self = TRUE) # See comment above about why this is necessary: tempDataNodesDefaultParents <- setdiff(tempDataNodesDefaultParents, tempDataNodesDefault) reNodesDefault <- intersect(reNodesDefault, tempDataNodesDefaultParents) @@ -292,12 +292,12 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes, if(paramsHandled) { # This means reProvided OR paramsProvided. Including parents allows checking # of potentially missing REs. reNodesDefault <- intersect(reNodesDefault, - model$getParents(calcNodes, upstream=TRUE, stochOnly = TRUE)) + model$getParents(calcNodes, upstream=TRUE, stochOnly = TRUE, self = TRUE)) } else { # This means !paramsHandled and hence !reProvided AND !paramsProvided reNodesDefault <- intersect(reNodesDefault, calcNodes) reNodesDefault <- intersect(reNodesDefault, - model$getParents(calcNodes, upstream=TRUE, stochOnly = TRUE)) + model$getParents(calcNodes, upstream=TRUE, stochOnly = TRUE, self = TRUE)) } } } From b85795afa45536aabed649c17b72dfea2448217c Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Sun, 16 Aug 2026 13:50:58 -0700 Subject: [PATCH 05/14] Fix tests to exclude inputs when self=F. --- packages/nimble/tests/testthat/test-getDependencies.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/packages/nimble/tests/testthat/test-getDependencies.R b/packages/nimble/tests/testthat/test-getDependencies.R index 028a5c545..acd75a7bf 100644 --- a/packages/nimble/tests/testthat/test-getDependencies.R +++ b/packages/nimble/tests/testthat/test-getDependencies.R @@ -154,12 +154,12 @@ test_that("getParents works in model with no criss-crossing dependencies", { expect_identical(m1$getParents("f1"), c("a1", "a2", "c2", "c4", "c3")) expect_identical(m1$getParents("f1", immediateOnly = TRUE), c("c4", "c3")) - expect_identical(m1$getParents(c("f1", "g1"), stochOnly = TRUE), c("a1", "a2", "f1")) - expect_identical(m1$getParents(c("f1", "g1"), immediateOnly = TRUE), c("c4", "c3", "f1")) - expect_identical(m1$getParents(c("g1", "f1"), stochOnly = TRUE), c("a1", "a2", "f1")) + expect_identical(m1$getParents(c("f1", "g1"), stochOnly = TRUE), c("a1", "a2")) + expect_identical(m1$getParents(c("f1", "g1"), immediateOnly = TRUE), c("c4", "c3")) + expect_identical(m1$getParents(c("g1", "f1"), stochOnly = TRUE), c("a1", "a2")) expect_identical(m1$getParents(c("f1", "g1"), stochOnly = TRUE, self = TRUE), c("a1", "a2", "f1", "g1")) - expect_identical(m1$getParents(c("c3", "c2", "e1"), stochOnly = FALSE), c("a1", "c2", "c3")) - expect_identical(m1$getParents(c("c3", "c2", "e1"), immediateOnly = TRUE, stochOnly = FALSE), c("a1", "c2", "c3")) + expect_identical(m1$getParents(c("c3", "c2", "e1"), stochOnly = FALSE), c("a1")) + expect_identical(m1$getParents(c("c3", "c2", "e1"), immediateOnly = TRUE, stochOnly = FALSE), c("a1")) expect_identical(m1$getParents("h1", includeRHSonly = TRUE, stochOnly = FALSE), c("lho")) }) From adc4abeb009446295cf021370ace1234a528121d Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Tue, 18 Aug 2026 18:10:50 -0700 Subject: [PATCH 06/14] Remove now-redundant `setdiff` in setupMargNodes(). --- packages/nimble/R/setupMargNodes.R | 6 ------ 1 file changed, 6 deletions(-) diff --git a/packages/nimble/R/setupMargNodes.R b/packages/nimble/R/setupMargNodes.R index b8696d560..7311b4bba 100644 --- a/packages/nimble/R/setupMargNodes.R +++ b/packages/nimble/R/setupMargNodes.R @@ -234,8 +234,6 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes, } else { nodesToFindParentsFrom <- randomEffectsNodes paramNodes <- model$getParents(nodesToFindParentsFrom, self=FALSE, stochOnly=TRUE) - # self=FALSE doesn't omit if one RE node is a parent of another, so we have to do the next step - paramNodes <- setdiff(paramNodes, nodesToFindParentsFrom) } if(paramsHandled) { if(calcProvided) paramNodes <- setdiff(paramNodes, calcNodes) @@ -306,8 +304,6 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes, # and are now ready to create default paramNodes if(!paramsHandled) { paramNodes <- model$getParents(reNodesDefault, self=FALSE, stochOnly=TRUE) - # See comment above about why this is necessary: - paramNodes <- setdiff(paramNodes, reNodesDefault) if(calcOtherProvided) paramNodes <- setdiff(paramNodes, calcNodesOther) } @@ -414,8 +410,6 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes, if(!paramProvided) { possibleNewParamNodes <- model$getParents(calcNodes, self=FALSE, stochOnly=TRUE, includeData=FALSE) # includeData=FALSE as data nodes cannot be parameters - # self=FALSE doesn't omit if one node is a parent of another, so we have to do the next step - possibleNewParamNodes <- setdiff(possibleNewParamNodes, calcNodesDefault) paramNodes <- unique(c(paramNodes, possibleNewParamNodes)) } From 00c690d3f133aa5e42f1ac3ac5d90419e299e3bf Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Thu, 20 Aug 2026 17:02:57 -0700 Subject: [PATCH 07/14] Update help for setupMargNodes related to missing randomEffectsNodes. --- packages/nimble/R/setupMargNodes.R | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/packages/nimble/R/setupMargNodes.R b/packages/nimble/R/setupMargNodes.R index 7311b4bba..821902a2a 100644 --- a/packages/nimble/R/setupMargNodes.R +++ b/packages/nimble/R/setupMargNodes.R @@ -91,15 +91,18 @@ #' \code{calcNodes}. Such deterministic nodes will be included in #' calculations automatically when needed. #' -#' If \code{randomEffectsNodes} is missing, the default is a bit complicated: it -#' includes all latent nodes that are descendants (or "downstream") of -#' \code{paramNodes} (if provided) and are either (i) ancestors (or -#' "upstream") of data nodes (if \code{calcNodes} is missing), or (ii) -#' ancestors or elements of \code{calcNodes} (if \code{calcNodes} and -#' \code{paramNodes} are provided), or (iii) elements of \code{calcNodes} (if -#' \code{calcNodes} is provided but \code{paramNodes} is missing). In all -#' cases, discrete nodes (with warning if \code{check=TRUE}), posterior -#' predictive nodes and \code{paramNodes} are excluded. +#' If \code{randomEffectsNodes} is missing, the default is a bit complicated. +#' It starts by considering all latent nodes as potential \code{randomEffectsNodes}. +#' If \code{paramNodes} is provided, only latent nodes that are downstream of +#' \code{paramNodes} are included. Then the set of potential nodes is filtered to +#' include only nodes that satisfy one of the following conditions +#' (only one of which will be applicable): (i) parents of data nodes +#' (applies only if calcNodes is missing), (ii) parents or elements of +#' \code{calcNodes} (applies only if \code{calcNodes} and \code{paramNodes} +#' are both provided), (iii) elements of calcNodes (applies if \code{calcNodes} +#' is provided but \code{paramNodes} is missing). In all +#' cases, discrete nodes (with warning if \code{check=TRUE}), posterior +#' predictive nodes and \code{paramNodes} are excluded. #' #' \code{randomEffectsNodes} should only include stochastic nodes. #' From f84c097cdbc70e407f30bb013f6be80c4fee2ad4 Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Thu, 20 Aug 2026 17:27:55 -0700 Subject: [PATCH 08/14] Make small further revision to help text. --- packages/nimble/R/setupMargNodes.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/packages/nimble/R/setupMargNodes.R b/packages/nimble/R/setupMargNodes.R index 821902a2a..b3a9eede9 100644 --- a/packages/nimble/R/setupMargNodes.R +++ b/packages/nimble/R/setupMargNodes.R @@ -94,7 +94,8 @@ #' If \code{randomEffectsNodes} is missing, the default is a bit complicated. #' It starts by considering all latent nodes as potential \code{randomEffectsNodes}. #' If \code{paramNodes} is provided, only latent nodes that are downstream of -#' \code{paramNodes} are included. Then the set of potential nodes is filtered to +#' \code{paramNodes} are included in the potential nodes. +#' Then the set of potential nodes is filtered to #' include only nodes that satisfy one of the following conditions #' (only one of which will be applicable): (i) parents of data nodes #' (applies only if calcNodes is missing), (ii) parents or elements of From d43cc3db67352793bbe27d511e53622cea6107f0 Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Fri, 21 Aug 2026 08:30:17 -0700 Subject: [PATCH 09/14] Remove strange handling in setupMargNodes.R. --- packages/nimble/R/setupMargNodes.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/packages/nimble/R/setupMargNodes.R b/packages/nimble/R/setupMargNodes.R index b3a9eede9..d16c33d87 100644 --- a/packages/nimble/R/setupMargNodes.R +++ b/packages/nimble/R/setupMargNodes.R @@ -298,8 +298,6 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes, } else { # This means !paramsHandled and hence !reProvided AND !paramsProvided reNodesDefault <- intersect(reNodesDefault, calcNodes) - reNodesDefault <- intersect(reNodesDefault, - model$getParents(calcNodes, upstream=TRUE, stochOnly = TRUE, self = TRUE)) } } } From 0e2e8cad9ac5e436973901fe0092c1682b6e766c Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Fri, 21 Aug 2026 08:48:35 -0700 Subject: [PATCH 10/14] Clean up handling of corner case in setupMargNodes per PR 1630 discussion. --- packages/nimble/R/setupMargNodes.R | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/packages/nimble/R/setupMargNodes.R b/packages/nimble/R/setupMargNodes.R index d16c33d87..38872fc7e 100644 --- a/packages/nimble/R/setupMargNodes.R +++ b/packages/nimble/R/setupMargNodes.R @@ -285,9 +285,8 @@ setupMargNodes <- function(model, paramNodes, randomEffectsNodes, calcNodes, tempDataNodesDefault <- model$getNodeNames(dataOnly = TRUE) if(paramsHandled) tempDataNodesDefault <- setdiff(tempDataNodesDefault, paramNodes) - tempDataNodesDefaultParents <- model$getParents(tempDataNodesDefault, upstream = TRUE, stochOnly = TRUE, self = TRUE) - # See comment above about why this is necessary: - tempDataNodesDefaultParents <- setdiff(tempDataNodesDefaultParents, tempDataNodesDefault) + tempDataNodesDefaultParents <- model$getParents(tempDataNodesDefault, upstream = TRUE, stochOnly = TRUE, + self = FALSE) reNodesDefault <- intersect(reNodesDefault, tempDataNodesDefaultParents) } else { # Update reNodesDefault to exclude nodes that lack downstream connection to a calcNode From 46e1147f01077fb6747e4daf754e1a49ef43c7e8 Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Fri, 21 Aug 2026 09:01:31 -0700 Subject: [PATCH 11/14] Clean up some spacing in MCMC chapter related to derived quantities. --- UserManual/src/chapter_MCMC.Rmd | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/UserManual/src/chapter_MCMC.Rmd b/UserManual/src/chapter_MCMC.Rmd index 60234d1e7..3092f1779 100644 --- a/UserManual/src/chapter_MCMC.Rmd +++ b/UserManual/src/chapter_MCMC.Rmd @@ -758,9 +758,8 @@ derived_name <- nimbleFunction( ## ## run fuction has one argument: ## timesRan, which is the number of times this method has executed during - ## the present MCMC chain, - ## including the present time. This can be used as an index for a matrix - ## of results. + ## the present MCMC chain, including the present time. This can be used + ## as an index for a matrix of results. ## }, methods = list( @@ -768,7 +767,7 @@ derived_name <- nimbleFunction( ## ## REQUIRED `set_interval` method, which matches the definition below ## exactly. - ## this method is necessary, to allow the default value of 'interval' to + ## This method is necessary, to allow the default value of 'interval' to ## match the thinning interval of the MCMC. ## interval <<- newInterval @@ -777,7 +776,7 @@ derived_name <- nimbleFunction( before_chain = function(niter = double(), nburnin = double(), thin = double(1), chain = double()) { ## - ## (optional) `before_chain` method, + ## (optional) `before_chain` method: ## must have must have these arguments specifications: ## - niter (total number of *post-burnin* MCMC iterations) ## - nburnin (number of burnin iterations for this MCMC chain) @@ -788,7 +787,7 @@ derived_name <- nimbleFunction( }, after_chain = function() { ## - ## (optional) `after_chain` method, + ## (optional) `after_chain` method: ## no arguments and no return value ## }, @@ -808,7 +807,7 @@ derived_name <- nimbleFunction( }, reset = function() { ## - ## (optional) `reset` method + ## (optional) `reset` method: ## no arguments and no return value ## } From e0108e97d9e0cbab87a5b9c502eaa15610fd17d8 Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Fri, 21 Aug 2026 09:16:07 -0700 Subject: [PATCH 12/14] Prepare for release: - fix some roxygen issues flagged by CRAN - update version number in metadata --- UserManual/src/_output.yml | 2 +- UserManual/src/title.tex | 2 +- packages/nimble/DESCRIPTION | 2 +- packages/nimble/INSTALL | 6 +++--- packages/nimble/R/cppDefs_ADtools.R | 2 ++ packages/nimble/R/nimbleFunction_Rexecution.R | 2 ++ packages/nimble/R/nimbleList_core.R | 2 ++ packages/nimble/man/setupOutputs.Rd | 3 --- 8 files changed, 12 insertions(+), 9 deletions(-) diff --git a/UserManual/src/_output.yml b/UserManual/src/_output.yml index 5515f8b9d..64eaa0258 100644 --- a/UserManual/src/_output.yml +++ b/UserManual/src/_output.yml @@ -5,7 +5,7 @@ bookdown::gitbook: before: | -
  • NIMBLE User Manual, Version 1.4.2
    • +
  • NIMBLE User Manual, Version 1.4.3
  • NIMBLE Development Team
  • https://R-nimble.org
    • after: | diff --git a/UserManual/src/title.tex b/UserManual/src/title.tex index 19690522a..6b0c7e5eb 100644 --- a/UserManual/src/title.tex +++ b/UserManual/src/title.tex @@ -4,7 +4,7 @@ \vspace{0.2in} {\large NIMBLE Development Team}\\ \vspace{0.2in} -{\large Version 1.4.2}\\ +{\large Version 1.4.3}\\ \vspace{3in} \includegraphics[width=1.5in]{../nimble-icon.png}\\ {\large diff --git a/packages/nimble/DESCRIPTION b/packages/nimble/DESCRIPTION index 8c9d46484..e833efe4a 100644 --- a/packages/nimble/DESCRIPTION +++ b/packages/nimble/DESCRIPTION @@ -16,7 +16,7 @@ Description: A system for writing hierarchical statistical models largely one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at . Version: 1.4.3 -Date: 2026-05-01 +Date: 2026-08-21 Maintainer: Christopher Paciorek Authors@R: c( person("Perry", "de Valpine", role = "aut"), diff --git a/packages/nimble/INSTALL b/packages/nimble/INSTALL index e04a7fe3f..cc9fe9d9a 100644 --- a/packages/nimble/INSTALL +++ b/packages/nimble/INSTALL @@ -1,9 +1,9 @@ You can install NIMBLE as an R package from CRAN in the usual way. You can install from the source file using - R CMD INSTALL nimble_1.4.2.tar.gz + R CMD INSTALL nimble_1.4.3.tar.gz or - install.packages("nimble_1.4.2.tar.gz", repos = NULL) + install.packages("nimble_1.4.3.tar.gz", repos = NULL) You can also install the package directly from the NIMBLE repository install.packages("nimble", repos = "https://r-nimble.org") @@ -21,7 +21,7 @@ i.e. not Windows. By default, we will use the Eigen distribution included with the package. We can specify any or all of these with - R CMD INSTALL nimble_1.4.2.tar.gz --configure-args="--enable-dylib=true --with-eigen=/Users/duncan/local" + R CMD INSTALL nimble_1.4.3.tar.gz --configure-args="--enable-dylib=true --with-eigen=/Users/duncan/local" or install.packages("nimble", configure.args = "--enable-dylib=true --with-eigen=/Users/duncan/local") diff --git a/packages/nimble/R/cppDefs_ADtools.R b/packages/nimble/R/cppDefs_ADtools.R index 1392efe5b..a2b3338c8 100644 --- a/packages/nimble/R/cppDefs_ADtools.R +++ b/packages/nimble/R/cppDefs_ADtools.R @@ -2,6 +2,8 @@ #' #' create an ADproxyModelClass object. For internal use. #' +#' @usage \code{ADproxyModelClass(Rmodel)} +#' #' @param Rmodel The name of an uncompiled model #' #' @author NIMBLE development team diff --git a/packages/nimble/R/nimbleFunction_Rexecution.R b/packages/nimble/R/nimbleFunction_Rexecution.R index c6e6958c9..3186c448e 100644 --- a/packages/nimble/R/nimbleFunction_Rexecution.R +++ b/packages/nimble/R/nimbleFunction_Rexecution.R @@ -107,6 +107,8 @@ nimSeq <- function(from, to, by, length.out) { ## this creates default arguments #' #' @name setupOutputs #' +#' @usage \code{setupOutputs(...)} +#' #' @param ... An arbitrary set of names #' #' @details diff --git a/packages/nimble/R/nimbleList_core.R b/packages/nimble/R/nimbleList_core.R index 692afcea4..58ac1eca4 100644 --- a/packages/nimble/R/nimbleList_core.R +++ b/packages/nimble/R/nimbleList_core.R @@ -27,6 +27,8 @@ nimbleListBase <- setRefClass(Class = 'nimbleListBase', #' #' Create a nimbleType object, with information on the name, type, and dimension of an object to be placed in a \code{\link{nimbleList}}. #' +#' @usage \code{nimbleType(name, type, dim = NA)} +#' #' @param name The name of the object, given as a character string. #' @param type The type of the object, given as a character string. #' @param dim The dimension of the object, given as an integer. This can be left blank if the object is a nimbleList. diff --git a/packages/nimble/man/setupOutputs.Rd b/packages/nimble/man/setupOutputs.Rd index 9870a9b2d..73fb8fc47 100644 --- a/packages/nimble/man/setupOutputs.Rd +++ b/packages/nimble/man/setupOutputs.Rd @@ -3,9 +3,6 @@ \name{setupOutputs} \alias{setupOutputs} \title{Explicitly declare objects created in setup code to be preserved and compiled as member data} -\arguments{ -\item{...}{An arbitrary set of names} -} \description{ Normally a nimbleFunction determines what objects from setup code need to be preserved for run code or other member functions. \code{setupOutputs} allows explicit declaration for cases when an object created in setup code is not used in member functions. } From 3db0cd7a5d75508fcee6fc725ab09952e0cd6504 Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Fri, 21 Aug 2026 10:44:53 -0700 Subject: [PATCH 13/14] Fix roxygen. --- packages/nimble/DESCRIPTION | 2 +- packages/nimble/R/cppDefs_ADtools.R | 4 ++-- packages/nimble/R/nimbleFunction_Rexecution.R | 2 +- packages/nimble/R/nimbleList_core.R | 2 +- .../nimble/man/ADproxyModelClass-class.Rd | 3 +++ packages/nimble/man/nimbleType-class.Rd | 3 +++ packages/nimble/man/samplers.Rd | 11 ++++------ packages/nimble/man/setupMargNodes.Rd | 22 +++++++++++-------- packages/nimble/man/setupOutputs.Rd | 6 +++++ 9 files changed, 34 insertions(+), 21 deletions(-) diff --git a/packages/nimble/DESCRIPTION b/packages/nimble/DESCRIPTION index e833efe4a..73a27fc99 100644 --- a/packages/nimble/DESCRIPTION +++ b/packages/nimble/DESCRIPTION @@ -153,4 +153,4 @@ Collate: registration.R nimble-package.r zzz.R -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 diff --git a/packages/nimble/R/cppDefs_ADtools.R b/packages/nimble/R/cppDefs_ADtools.R index a2b3338c8..9b85e2994 100644 --- a/packages/nimble/R/cppDefs_ADtools.R +++ b/packages/nimble/R/cppDefs_ADtools.R @@ -2,8 +2,8 @@ #' #' create an ADproxyModelClass object. For internal use. #' -#' @usage \code{ADproxyModelClass(Rmodel)} -#' +#' @usage ADproxyModelClass(Rmodel) +#' #' @param Rmodel The name of an uncompiled model #' #' @author NIMBLE development team diff --git a/packages/nimble/R/nimbleFunction_Rexecution.R b/packages/nimble/R/nimbleFunction_Rexecution.R index 3186c448e..ef83b3226 100644 --- a/packages/nimble/R/nimbleFunction_Rexecution.R +++ b/packages/nimble/R/nimbleFunction_Rexecution.R @@ -107,7 +107,7 @@ nimSeq <- function(from, to, by, length.out) { ## this creates default arguments #' #' @name setupOutputs #' -#' @usage \code{setupOutputs(...)} +#' @usage setupOutputs(...) #' #' @param ... An arbitrary set of names #' diff --git a/packages/nimble/R/nimbleList_core.R b/packages/nimble/R/nimbleList_core.R index 58ac1eca4..5fb7c30cc 100644 --- a/packages/nimble/R/nimbleList_core.R +++ b/packages/nimble/R/nimbleList_core.R @@ -27,7 +27,7 @@ nimbleListBase <- setRefClass(Class = 'nimbleListBase', #' #' Create a nimbleType object, with information on the name, type, and dimension of an object to be placed in a \code{\link{nimbleList}}. #' -#' @usage \code{nimbleType(name, type, dim = NA)} +#' @usage nimbleType(name, type, dim = NA) #' #' @param name The name of the object, given as a character string. #' @param type The type of the object, given as a character string. diff --git a/packages/nimble/man/ADproxyModelClass-class.Rd b/packages/nimble/man/ADproxyModelClass-class.Rd index 6309bcea4..a38efa1b7 100644 --- a/packages/nimble/man/ADproxyModelClass-class.Rd +++ b/packages/nimble/man/ADproxyModelClass-class.Rd @@ -5,6 +5,9 @@ \alias{ADproxyModelClass-class} \alias{ADproxyModelClass} \title{create an ADproxyModelClass object} +\usage{ +\code{ADproxyModelClass(Rmodel)} +} \arguments{ \item{Rmodel}{The name of an uncompiled model} } diff --git a/packages/nimble/man/nimbleType-class.Rd b/packages/nimble/man/nimbleType-class.Rd index f9cf25943..6be5efc19 100644 --- a/packages/nimble/man/nimbleType-class.Rd +++ b/packages/nimble/man/nimbleType-class.Rd @@ -5,6 +5,9 @@ \alias{nimbleType-class} \alias{nimbleType} \title{create a nimbleType object} +\usage{ +\code{nimbleType(name, type, dim = NA)} +} \arguments{ \item{name}{The name of the object, given as a character string.} diff --git a/packages/nimble/man/samplers.Rd b/packages/nimble/man/samplers.Rd index 9ffd1b96c..26e21222d 100644 --- a/packages/nimble/man/samplers.Rd +++ b/packages/nimble/man/samplers.Rd @@ -570,20 +570,17 @@ The CRP_concentration sampler is designed for Bayesian nonparametric mixture mod \section{prior_samples sampler}{ -The prior_samples sampler uses a provided set of numeric values (\code{samples}) to define the prior distribution of one or more model nodes. One every MCMC iteration, the prior_samples sampler takes value(s) from the numeric values provided, and stores these value(s) into the target model node(s). This allows one to define the prior distribution of model parameters empirically, using a set of numeric \code{samples}, presumably obtained previously using MCMC. The \code{target} node may be either a single scalar node (scalar case), or a collection of model nodes. +The prior_samples sampler uses a provided set of numeric values (\code{samples}) to define the prior distribution of one or more model nodes. Once every MCMC iteration, the prior_samples sampler randomly selects new value(s) from the numeric values provided, and probabilistically accepts these as the new values for the specific target node(s) using a standard Metropolis-Hastings accept/reject step. This allows one to define the prior distribution of model parameters empirically, using a set of numeric \code{samples}, presumably obtained previously using MCMC. -The prior_samples sampler provides two options for selection of the value to use on each MCMC iteration. The default behaviour is to take sequential values from the \code{samples} vector (scalar case), or in the case of multiple dimensions, sequential rows of the \code{samples} matrix are used. The alternative behaviour, by setting the control argument \code{randomDraws = TRUE}, will instead use random draws from the \code{samples} vector (scalar case), or randomly selected rows of the \code{samples} matrix in the multidimensional case. - -If the default of sequential selection of values is used, and the number of MCMC iterations exceeds the length of the \code{samples} vector (scalar case) or the number of rows of the \code{samples} matrix, then \code{samples} will be recycled as necessary for the number of MCMC iterations. A message to this effect is also printed at the beginning of the MCMC chain. +The \code{target} node may be either a single scalar node (scalar case), or a collection of model nodes (multidimensional case). In the scalar case, a propsed value is randomely selected from the \code{samples} vector. In the multidimensional case, a randomly selected rows of the \code{samples} matrix is used as the proposed values. Logically, prior_samples samplers might want to operate first, in advance of other samplers, on every MCMC iteration. By default, at the time of MCMC building, all prior_samples samplers are re-ordered to appear first in the list of MCMC samplers. This behavior can be subverted, however, by setting \code{nimbleOptions(MCMCorderPriorSamplesSamplersFirst = FALSE)}. -The prior_samples sampler can be assigned to non-stochastic model nodes (nodes which are not assigned a prior distribution in the model). In fact, it is recommended that nodes being assigned a prior_samples are not provided with a prior distribution in the model, and rather, that these nodes only appear on the right-hand-side of model declaration lines. In such case that a prior_samples sampler is assigned to a nodes with a prior distribution, the prior distribution will be overridden by the sample values provided to the sampler; however, the node will still be a stochastic node for other purposes, and will contribute to the model joint-density (using the sample values provided relative to the prior distribution), will have an MCMC sampler assigned to it by default, and also may introduce potential for confusion. In this case, a message is issued at the time of MCMC building. +The prior_samples sampler can be assigned to non-stochastic model nodes (nodes which are not assigned a prior distribution in the model). In fact, it is recommended that nodes being assigned a prior_samples are not provided with a prior distribution in the model, and rather, that these nodes only appear on the right-hand-side of model declaration lines. In such case that a prior_samples sampler is assigned to a nodes with a prior distribution, the prior distribution will be overridden by the \code{samples} provided to the sampler; however, the node will still be a stochastic node for other purposes, and will contribute to the model joint-density (using the current values relative to the prior distribution), will have an MCMC sampler assigned to it by default, and also may introduce potential for confusion. In this case, a message is issued at the time of MCMC building. The prior_samples sampler accepts the following control list elements: \itemize{ -\item \code{samples}. A numeric vector or matrix. When the \code{target} node is a single scalar-valued node, \code{samples} should be a numeric vector. When the \code{target} node specifies d > 2 model dimensions, \code{samples} should be a matrix containing d columns. The \code{samples} control argument is required. -\item \code{randomDraws}. A logical argument, specifying whether to use a random draw from \code{samples} on each iteration. If \code{samples} is a matrix, then a randomly-selected row of the \code{samples} matrix is used. When \code{FALSE}, sequential values (or sequential matrix rows) are used (default = \code{FALSE}). +\item \code{samples}. A numeric vector or matrix. When the \code{target} node is a single scalar-valued node, \code{samples} should be a numeric vector. When the \code{target} node specifies more \code{d} > 2 dimensions, \code{samples} should be a matrix containing \code{d} columns. The \code{samples} control argument is required. } } diff --git a/packages/nimble/man/setupMargNodes.Rd b/packages/nimble/man/setupMargNodes.Rd index 7fc1e1683..cab6d7f45 100644 --- a/packages/nimble/man/setupMargNodes.Rd +++ b/packages/nimble/man/setupMargNodes.Rd @@ -134,15 +134,19 @@ For purposes of \code{buildLaplace}, \code{paramNodes} does not need to (but \code{calcNodes}. Such deterministic nodes will be included in calculations automatically when needed. -If \code{randomEffectsNodes} is missing, the default is a bit complicated: it - includes all latent nodes that are descendants (or "downstream") of - \code{paramNodes} (if provided) and are either (i) ancestors (or - "upstream") of data nodes (if \code{calcNodes} is missing), or (ii) - ancestors or elements of \code{calcNodes} (if \code{calcNodes} and - \code{paramNodes} are provided), or (iii) elements of \code{calcNodes} (if - \code{calcNodes} is provided but \code{paramNodes} is missing). In all - cases, discrete nodes (with warning if \code{check=TRUE}), posterior - predictive nodes and \code{paramNodes} are excluded. + If \code{randomEffectsNodes} is missing, the default is a bit complicated. + It starts by considering all latent nodes as potential \code{randomEffectsNodes}. + If \code{paramNodes} is provided, only latent nodes that are downstream of + \code{paramNodes} are included in the potential nodes. + Then the set of potential nodes is filtered to + include only nodes that satisfy one of the following conditions + (only one of which will be applicable): (i) parents of data nodes + (applies only if calcNodes is missing), (ii) parents or elements of + \code{calcNodes} (applies only if \code{calcNodes} and \code{paramNodes} + are both provided), (iii) elements of calcNodes (applies if \code{calcNodes} + is provided but \code{paramNodes} is missing). In all + cases, discrete nodes (with warning if \code{check=TRUE}), posterior + predictive nodes and \code{paramNodes} are excluded. \code{randomEffectsNodes} should only include stochastic nodes. diff --git a/packages/nimble/man/setupOutputs.Rd b/packages/nimble/man/setupOutputs.Rd index 73fb8fc47..395f8be8f 100644 --- a/packages/nimble/man/setupOutputs.Rd +++ b/packages/nimble/man/setupOutputs.Rd @@ -3,6 +3,12 @@ \name{setupOutputs} \alias{setupOutputs} \title{Explicitly declare objects created in setup code to be preserved and compiled as member data} +\usage{ +\code{setupOutputs(...)} +} +\arguments{ +\item{...}{An arbitrary set of names} +} \description{ Normally a nimbleFunction determines what objects from setup code need to be preserved for run code or other member functions. \code{setupOutputs} allows explicit declaration for cases when an object created in setup code is not used in member functions. } From 68be4561ea3e23a8f944a92e845c0d8db4451a97 Mon Sep 17 00:00:00 2001 From: Christopher Paciorek Date: Fri, 21 Aug 2026 11:19:17 -0700 Subject: [PATCH 14/14] Generate new Rd files. --- packages/nimble/man/ADproxyModelClass-class.Rd | 2 +- packages/nimble/man/nimbleType-class.Rd | 2 +- packages/nimble/man/setupOutputs.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/packages/nimble/man/ADproxyModelClass-class.Rd b/packages/nimble/man/ADproxyModelClass-class.Rd index a38efa1b7..03d37bb11 100644 --- a/packages/nimble/man/ADproxyModelClass-class.Rd +++ b/packages/nimble/man/ADproxyModelClass-class.Rd @@ -6,7 +6,7 @@ \alias{ADproxyModelClass} \title{create an ADproxyModelClass object} \usage{ -\code{ADproxyModelClass(Rmodel)} +ADproxyModelClass(Rmodel) } \arguments{ \item{Rmodel}{The name of an uncompiled model} diff --git a/packages/nimble/man/nimbleType-class.Rd b/packages/nimble/man/nimbleType-class.Rd index 6be5efc19..242e3d16c 100644 --- a/packages/nimble/man/nimbleType-class.Rd +++ b/packages/nimble/man/nimbleType-class.Rd @@ -6,7 +6,7 @@ \alias{nimbleType} \title{create a nimbleType object} \usage{ -\code{nimbleType(name, type, dim = NA)} +nimbleType(name, type, dim = NA) } \arguments{ \item{name}{The name of the object, given as a character string.} diff --git a/packages/nimble/man/setupOutputs.Rd b/packages/nimble/man/setupOutputs.Rd index 395f8be8f..5b4853508 100644 --- a/packages/nimble/man/setupOutputs.Rd +++ b/packages/nimble/man/setupOutputs.Rd @@ -4,7 +4,7 @@ \alias{setupOutputs} \title{Explicitly declare objects created in setup code to be preserved and compiled as member data} \usage{ -\code{setupOutputs(...)} +setupOutputs(...) } \arguments{ \item{...}{An arbitrary set of names}