Nothing
R/nimbleFunction_keywordProcessing.R
In nimble: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Defines functions
nimDerivsInfoClass_update_init_impl
makeModelDerivsInfo_impl
getImmediateParentNodes
makeModelDerivsInfo
nimDerivsInfoClass_output_init_impl
makeOutputNodes
nimDerivsInfoClass_init_impl
handleScaleAndRateForExpNimble
handleScaleAndRateForGamma
makeSingleIndexAccessCodeNames
makeMapSetupCodeNames
varAndIndices2flatIndex
getVarAndIndices
varAndIndices2mapParts
determineNdimFromOneCase
makeMapAccessExpr
makeSingleIndexAccessExpr
matchKeywords_recurse
matchKeywordCode
matchKeywordCodeMemberFun
determineNdimsFromNfproc
matchAndFill.call
isSymbolType
symTypeFromSymTab
getSymObj_recurse
addNecessarySetupCode
addNewCode
addBlockFromCppName
addSetupCodeNames
isSetupCodeGenerated
isCodeArgBlank
code2Name_fromArgList
processKeywords_recurse
processKeywordCodeMemberFun
processKeyword
addDistList2matchFunctions
stripArgs
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Documented in
makeModelDerivsInfo
###### KEYWORD PROCESSING OBJECTS
### CLASSES
# keywordInfoClass is a class which contains the processor for each keyword
keywordInfoClass <- setRefClass('keywordInfoClass',
fields = list(
keyword = 'ANY',
processor = 'ANY'))
# setupCodeTemplateClass is a class that contains the template for generating
# new setupCode. Objects of this class are used by the function addNecessarySetupCode
setupCodeTemplateClass <- setRefClass('setupCodeTemplateClass',
fields = list(
makeName = 'ANY',
codeTemplate = 'ANY',
makeCodeSubList = 'ANY',
makeOtherNames = 'ANY'),
methods = list(
initialize = function(...){
makeOtherNames <<- function(name, argList) return(character(0))
callSuper(...)
}
) )
### KEYWORD INFO OBJECTS
d_gamma_keywordInfo <- keywordInfoClass(
keyword = 'dgamma',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForGamma(code)
return(code)
})
pq_gamma_keywordInfo <- keywordInfoClass(
keyword = 'pq_gamma',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForGamma(code)
return(code)
})
rgamma_keywordInfo <- keywordInfoClass(
keyword = 'rgamma',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForGamma(code)
return(code)
}
)
d_exp_nimble_keywordInfo <- keywordInfoClass(
keyword = 'dexp_nimble',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForExpNimble(code)
return(code)
})
pq_exp_nimble_keywordInfo <- keywordInfoClass(
keyword = 'pq_exp_nimble',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForExpNimble(code)
return(code)
})
rexp_nimble_keywordInfo <- keywordInfoClass(
keyword = 'rexp_nimble',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForExpNimble(code)
return(code)
}
)
besselK_keywordInfo <- keywordInfoClass(
keyword = 'besselK',
processor = function(code, nfProc, RCfunProc) {
expon.scaledArg <- code$expon.scaled
if(is.null(expon.scaledArg))
expon.scaledArg <- FALSE
if(is.numeric(expon.scaledArg) || is.logical(expon.scaledArg)) {
code$expon.scaled <- 1 + as.logical(expon.scaledArg)
} else code$expon.scaled <- substitute(1 + A, list(A = expon.scaledArg))
return(code)
}
)
nimSeq_keywordInfo <- keywordInfoClass(
keyword = 'nimSeq',
processor = function(code, nfProc, RCfunProc) {
useBy <- !isCodeArgBlank(code, 'by')
useLen <- !isCodeArgBlank(code, 'length.out')
if(useBy && useLen)
newRunCode <- substitute(nimSeqByLen(FROM, 0, BY, LEN), list(FROM = code$from, BY = code$by, LEN = code$length.out))
else {
if(useLen) {
newRunCode <- substitute(nimSeqLen(FROM, TO, 0, LEN), list(FROM = code$from, TO = code$to, LEN = code$length.out))
} else {
byVal <- if(useBy) code$by else 1 ## default by = 1
newRunCode <- substitute(nimSeqBy(FROM, TO, BY, 0), list(FROM = code$from, TO = code$to, BY = byVal))
}
}
return(newRunCode)
}
)
values_keywordInfo <- keywordInfoClass(
keyword = 'values',
processor = function(code, nfProc, RCfunProc){
if(!isCodeArgBlank(code, 'accessor'))
return(code)
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from values call, with no accessor argument supplied')
accessArgList <- list(model = code$model, nodes = code$nodes, logProb = FALSE, logProbOnly = FALSE)
useAccessorVectorByIndex <- FALSE
if(hasBracket(accessArgList$nodes)) {
useAccessorVectorByIndex <- TRUE
if(length(accessArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- accessArgList$nodes[[3]]
accessArgList$nodes <- accessArgList$nodes[[2]]
accessArgList$sortUnique <- FALSE
}
accessName <- modelVariableAccessorVector_setupCodeTemplate$makeName(accessArgList)
addNecessarySetupCode(accessName, accessArgList, modelVariableAccessorVector_setupCodeTemplate, nfProc)
if(!useAccessorVectorByIndex)
newRunCode <- substitute(values(accessor = ACCESS_NAME),
list(ACCESS_NAME = as.name(accessName)))
else
newRunCode <- substitute(values(accessor = ACCESS_NAME, accessorIndex = ACCESSVECINDEX),
list(ACCESS_NAME = as.name(accessName), ACCESSVECINDEX = nodesIndexExpr))
return(newRunCode)
})
getParam_keywordInfo <- keywordInfoClass(
keyword = 'getParam',
processor = function(code, nfProc, RCfunProc) {
if(!isCodeArgBlank(code, 'nodeFunction'))
return(code)
errorContext <- deparse(code)
nodeFunVec_ArgList <- list(model = code$model, nodes = code$node, includeData = TRUE, sortUnique = TRUE, errorContext = errorContext)
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to getParam if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from getParam, with no accessor argument supplied')
if(isCodeArgBlank(code, 'node'))
stop('node argument missing from getParam, with no accessor argument supplied')
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE
}
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
if(isCodeArgBlank(code, 'param'))
stop("'param' argument missing from 'getParam', with no accessor argument supplied")
## Avoid situations where user has syntax from run code in `param` or of getting anything from global env (issue 1344).
paramVars <- all.vars(code$param)
wh <- which(!paramVars %in% nfProc$setupSymTab$getSymbolNames())
if(length(wh))
stop("`param` argument in `getParam` contains variables not found in setup code: ", paste(paramVars[wh], collapse = ", "), ".")
paramInfo_ArgList <- list(model = code$model, node = nodeFunVec_ArgList$nodes, param = code$param, hasIndex = useNodeFunctionVectorByIndex) ## use nodeFunVec_ArgList$nodes instead of code$node because nodeFunVec_ArgList$nodes may have been updated if code$nodes has a run-time index. In that case the paramID will be vector
paramInfoName <- paramInfo_SetupTemplate$makeName(paramInfo_ArgList)
paramIDname <- paramInfo_SetupTemplate$makeOtherNames(paramInfoName, paramInfo_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
addNecessarySetupCode(paramInfoName, paramInfo_ArgList, paramInfo_SetupTemplate, nfProc)
if(!useNodeFunctionVectorByIndex)
newRunCode <- substitute(getParam(nodeFunction = NODEFUNVEC_NAME, paramID = PARAMID_NAME, paramInfo = PARAMINFO_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName), PARAMID_NAME = as.name(paramIDname), PARAMINFO_NAME = as.name(paramInfoName)))
else
newRunCode <- substitute(getParam(nodeFunction = NODEFUNVEC_NAME, paramID = PARAMID_NAME, paramInfo = PARAMINFO_NAME, nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName), PARAMID_NAME = as.name(paramIDname), PARAMINFO_NAME = as.name(paramInfoName), NODEFUNVECINDEX = nodesIndexExpr))
return(newRunCode)
}
)
getBound_keywordInfo <- keywordInfoClass(
keyword = 'getBound',
processor = function(code, nfProc, RCfunProc) {
if(!isCodeArgBlank(code, 'nodeFunction'))
return(code)
errorContext <- deparse(code)
nodeFunVec_ArgList <- list(model = code$model, nodes = code$node, includeData = TRUE, sortUnique = TRUE, errorContext = errorContext)
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to getParam if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from getParam, with no accessor argument supplied')
if(isCodeArgBlank(code, 'node'))
stop('node argument missing from getParam, with no accessor argument supplied')
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE
}
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
if(isCodeArgBlank(code, 'bound'))
stop("'bound' argument missing from 'getBound', with no accessor argument supplied")
boundInfo_ArgList <- list(model = code$model, node = nodeFunVec_ArgList$nodes, bound = code$bound) ## use nodeFunVec_ArgList$nodes instead of code$node because nodeFunVec_ArgList$nodes may have been updated if code$nodes has a run-time index. In that case the boundID will be vector
boundInfoName <- boundInfo_SetupTemplate$makeName(boundInfo_ArgList)
boundIDname <- boundInfo_SetupTemplate$makeOtherNames(boundInfoName, boundInfo_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
addNecessarySetupCode(boundInfoName, boundInfo_ArgList, boundInfo_SetupTemplate, nfProc)
if(!useNodeFunctionVectorByIndex)
newRunCode <- substitute(getBound(nodeFunction = NODEFUNVEC_NAME, boundID = BOUNDID_NAME, boundInfo = BOUNDINFO_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName), BOUNDID_NAME = as.name(boundIDname), BOUNDINFO_NAME = as.name(boundInfoName)))
else
newRunCode <- substitute(getBound(nodeFunction = NODEFUNVEC_NAME, boundID = BOUNDID_NAME, boundInfo = BOUNDINFO_NAME, nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName), BOUNDID_NAME = as.name(boundIDname), BOUNDINFO_NAME = as.name(boundInfoName), NODEFUNVECINDEX = nodesIndexExpr))
return(newRunCode)
}
)
calculate_keywordInfo <- keywordInfoClass(
keyword = 'calculate',
processor = function(code, nfProc, RCfunProc){
if(!isCodeArgBlank(code, 'nodeFxnVector'))
return(code)
errorContext <- deparse(code)
buildDerivs <- FALSE
withDerivsOutputOnly <- FALSE
if(isTRUE(getNimbleOption("enableDerivs"))) {
derivControl <- environment(nfProc$nfGenerator)$buildDerivs[[RCfunProc$name]]
## There are two cases.
## If buildDerivs has an entry, then derivatives are enabled either
## explicitly or because of a nimDerivs(model$calculate), i.e. a direct line into derivs for just a model calculation.
##
## These need to be disambiguated for use below to choose the right setup template case
buildDerivs <- !is.null(derivControl) | !is.null(code$wrt)
withDerivsOutputOnly <- buildDerivs & is.null(code$wrt) ## This is the case of *not* nimDerivs(model$calculate)
}
nodeFunVec_ArgList <- list(model = code$model, nodes = code$nodes, wrtNodes = code$wrt,
includeData = TRUE, sortUnique = TRUE, errorContext = errorContext)
##
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to calculate if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from calculate, with no accessor argument supplied')
if(isCodeArgBlank(code, 'nodes')){
LHSnodes_ArgList <- list(model = code$model)
LHSnodes_name <- allLHSNodes_SetupTemplate$makeName(LHSnodes_ArgList)
addNecessarySetupCode(LHSnodes_name, LHSnodes_ArgList, allLHSNodes_SetupTemplate, nfProc, allowToCpp = FALSE)
nodeFunVec_ArgList$nodes = as.name(LHSnodes_name)
}
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
if(buildDerivs)
stop(paste0('Derivatives for an indexed node are not allowed.\n',
'Use nimDerivs(model$calculate(nodes), ...) instead of \n',
'nimDerivs(model$calculate(nodes[i]).\n'))
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3)
stop(paste0('Problem with ',
deparse(code),
'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE
}
if(!withDerivsOutputOnly) { ## This is regular mode, including without derivs at all and with buildDerivs but not nimDerivs(model$calculate...)
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
} else {
nodeFunName <- nodeFunctionVector_WithDerivsOutput_SetupTemplate$makeName(nodeFunVec_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_WithDerivsOutput_SetupTemplate, nfProc)
}
if(!useNodeFunctionVectorByIndex){
newRunCode <- substitute(calculate(nodeFxnVector = NODEFUNVEC_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName)))
}
else{
newRunCode <- substitute(
calculate(nodeFxnVector = NODEFUNVEC_NAME,
nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName),
NODEFUNVECINDEX = nodesIndexExpr))
}
return(newRunCode)
}
)
calculateDiff_keywordInfo <- keywordInfoClass(
keyword = 'calculateDiff',
processor = function(code, nfProc, RCfunProc){
if(!isCodeArgBlank(code, 'nodeFxnVector'))
return(code)
errorContext <- deparse(code)
nodeFunVec_ArgList <- list(model = code$model, nodes = code$nodes, includeData = TRUE, sortUnique = TRUE, errorContext = errorContext)
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to calculateDiff if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from calculateDiff, with no accessor argument supplied')
if(isCodeArgBlank(code, 'nodes')){
LHSnodes_ArgList <- list(model = code$model)
LHSnodes_name <- allLHSNodes_SetupTemplate$makeName(LHSnodes_ArgList)
addNecessarySetupCode(LHSnodes_name, LHSnodes_ArgList, allLHSNodes_SetupTemplate, nfProc, allowToCpp = FALSE)
nodeFunVec_ArgList$nodes = as.name(LHSnodes_name)
}
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE
}
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
if(!useNodeFunctionVectorByIndex)
newRunCode <- substitute(calculateDiff(nodeFxnVector = NODEFUNVEC_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName)))
else
newRunCode <- substitute(calculateDiff(nodeFxnVector = NODEFUNVEC_NAME, nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName), NODEFUNVECINDEX = nodesIndexExpr))
return(newRunCode)
}
)
simulate_keywordInfo <- keywordInfoClass(
keyword = 'simulate',
processor = function(code, nfProc, RCfunProc){
if(!isCodeArgBlank(code, 'nodeFxnVector')){
return(substitute(simulate(nodeFxnVector = NODEFXNVECTOR), list(NODEFXNVECTOR = code$nodeFxnVector) ) )
}
if(!isCodeArgBlank(code, 'INDEXEDNODEINFO_'))
return(code)
errorContext <- deparse(code)
nodeFunVec_ArgList <- list(model = code$model, nodes = code$nodes, includeData = code$includeData, sortUnique = TRUE, errorContext = errorContext)
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to simulate if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from simulate, with no accessor argument supplied')
if(isCodeArgBlank(code, 'nodes')){
LHSnodes_ArgList <- list(model = code$model)
LHSnodes_name <- allLHSNodes_SetupTemplate$makeName(LHSnodes_ArgList)
addNecessarySetupCode(LHSnodes_name, LHSnodes_ArgList, allLHSNodes_SetupTemplate, nfProc, allowToCpp = FALSE)
nodeFunVec_ArgList$nodes = as.name(LHSnodes_name)
}
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE # If includeData = FALSE, this can trigger error from nodeFunctionVector if nodes does contain data
}
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
if(!useNodeFunctionVectorByIndex)
newRunCode <- substitute(simulate(nodeFxnVector = NODEFUNVEC_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName)))
else
newRunCode <- substitute(simulate(nodeFxnVector = NODEFUNVEC_NAME, nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName), NODEFUNVECINDEX = nodesIndexExpr))
return(newRunCode)
}
)
getLogProb_keywordInfo <- keywordInfoClass(
keyword = 'getLogProb',
processor = function(code, nfProc, RCfunProc){
if(!isCodeArgBlank(code, 'nodeFxnVector'))
return(code)
errorContext <- deparse(code)
nodeFunVec_ArgList <- list(model = code$model, nodes = code$nodes, includeData = TRUE, sortUnique = TRUE, errorContext = errorContext)
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to getLogProb if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from getLogProb, with no accessor argument supplied')
if(isCodeArgBlank(code, 'nodes')){
LHSnodes_ArgList <- list(model = code$model)
LHSnodes_name <- allLHSNodes_SetupTemplate$makeName(LHSnodes_ArgList)
addNecessarySetupCode(LHSnodes_name, LHSnodes_ArgList, allLHSNodes_SetupTemplate, nfProc, allowToCpp = FALSE)
nodeFunVec_ArgList$nodes = as.name(LHSnodes_name)
}
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE
}
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
if(!useNodeFunctionVectorByIndex)
newRunCode <- substitute(getLogProb(nodeFxnVector = NODEFUNVEC_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName)))
else
newRunCode <- substitute(getLogProb(nodeFxnVector = NODEFUNVEC_NAME, nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName), NODEFUNVECINDEX = nodesIndexExpr))
return(newRunCode)
}
)
nimCopy_keywordInfo <- keywordInfoClass(
keyword = 'nimCopy',
processor = function(code, nfProc, RCfunProc){
if(is.null(nfProc)) stop("Can\'t call copy (nimCopy) from a nimbleFunction without setup code")
possibleObjects <- c('symbolModel', 'symbolModelValues', 'symbolModelVariableAccessorVector', 'symbolModelValuesAccessorVector')
modelValuesTypes <- c('symbolModelValues', 'symbolModelValuesAccessorVector')
accessTypes <- c('symbolModelVariableAccessorVector', 'symbolModelValuesAccessorVector')
from_ArgList <- list(name = code$from, class = symTypeFromSymTab(code$from, nfProc$setupSymTab, options = possibleObjects))
to_ArgList <- list(name = code$to, class = symTypeFromSymTab(code$to, nfProc$setupSymTab, options = possibleObjects))
if(is.null(from_ArgList$class))
stop("Error in nimCopy: '", code$from, "' is not a recognized model or modelValues object.")
if(is.null(to_ArgList$class))
stop("Error in nimCopy: '", code$to, "' is not a recognized model or modelValues object.")
if(from_ArgList$class %in% modelValuesTypes){
if(isCodeArgBlank(code, 'row')) stop('row argument missing in copy call')
from_ArgList$row = code$row
}
if(to_ArgList$class %in% modelValuesTypes){
if(isCodeArgBlank(code, 'rowTo')){
if(isCodeArgBlank(code, 'row')) stop('row argument missing in copy call')
else to_ArgList$row = code$row
}
else to_ArgList$row = code$rowTo
}
if(isCodeArgBlank(code, 'nodes')){
if(from_ArgList$class == 'symbolModel'){
node_ArgList <- list(model = from_ArgList$name)
allNodes_name <- allModelNodes_SetupTemplate$makeName( node_ArgList )
addNecessarySetupCode(allNodes_name, node_ArgList, allModelNodes_SetupTemplate, nfProc, allowToCpp = FALSE)
}
else if(from_ArgList$class == 'symbolModelValues'){
from_ArgList$row = code$row
mvVar_ArgList <- list(modelValues = from_ArgList$name)
allNodes_name <- allModelValuesVars_SetupTemplate$makeName(mvVar_ArgList)
addNecessarySetupCode(allNodes_name, mvVar_ArgList, allModelValuesVars_SetupTemplate, nfProc, allowToCpp = FALSE)
}
from_ArgList$nodes <- as.name(allNodes_name)
}
else from_ArgList$nodes <- code$nodes
if(isCodeArgBlank(code, 'nodesTo')) to_ArgList$nodes <- from_ArgList$nodes
else to_ArgList$nodes <- code$nodesTo
if(from_ArgList$class == 'symbolModel'){
isMVfrom <- 0
accessFrom_ArgList <- list(model = code$from, nodes = from_ArgList$nodes, logProb = code$logProb, logProbOnly = code$logProbOnly)
accessFrom_name <- modelVariableAccessorVector_setupCodeTemplate$makeName(accessFrom_ArgList)
addNecessarySetupCode(accessFrom_name, accessFrom_ArgList, modelVariableAccessorVector_setupCodeTemplate, nfProc)
}
else if(from_ArgList$class == 'symbolModelValues'){
isMVfrom <- 1
accessFrom_ArgList <- list(modelValues = code$from, nodes = from_ArgList$nodes, logProb = code$logProb, logProbOnly = code$logProbOnly, row = from_ArgList$row)
accessFrom_name <- modelValuesAccessorVector_setupCodeTemplate$makeName(accessFrom_ArgList)
addNecessarySetupCode(accessFrom_name, accessFrom_ArgList, modelValuesAccessorVector_setupCodeTemplate, nfProc)
}
else if(from_ArgList$class %in% accessTypes) {
isMVfrom <- as.integer(from_ArgList$class == 'symbolModelValuesAccessorVector')
accessFrom_name <- as.character(code$from)
}
if(to_ArgList$class == 'symbolModel'){
isMVto <- 0
accessTo_ArgList <- list(model = code$to, nodes = to_ArgList$nodes, logProb = code$logProb, logProbOnly = code$logProbOnly)
accessTo_name <- modelVariableAccessorVector_setupCodeTemplate$makeName(accessTo_ArgList)
addNecessarySetupCode(accessTo_name, accessTo_ArgList, modelVariableAccessorVector_setupCodeTemplate, nfProc)
}
else if(to_ArgList$class == 'symbolModelValues'){
isMVto <- 1
accessTo_ArgList <- list(modelValues = code$to, nodes = to_ArgList$nodes, logProb = code$logProb, logProbOnly = code$logProbOnly, row = to_ArgList$row)
accessTo_name <- modelValuesAccessorVector_setupCodeTemplate$makeName(accessTo_ArgList)
addNecessarySetupCode(accessTo_name, accessTo_ArgList, modelValuesAccessorVector_setupCodeTemplate, nfProc)
}
else if(to_ArgList$class %in% accessTypes) {
isMVto <- as.integer(to_ArgList$class == 'symbolModelValuesAccessorVector')
accessTo_name <- as.character(code$to)
}
if(getNimbleOption('useNewNimCopy')) {
copierVector_ArgList <- list(accessFrom_name = accessFrom_name, accessTo_name = accessTo_name, isMVto = isMVto, isMVfrom = isMVfrom)
copierVector_name <- copierVector_setupCodeTemplate$makeName(copierVector_ArgList)
addNecessarySetupCode(copierVector_name, copierVector_ArgList, copierVector_setupCodeTemplate, nfProc)
}
if(!getNimbleOption('useNewNimCopy')) {
##What happens below is a bit convoluted and really for backwards compatibility
runCode <- substitute(nimCopy(from = FROM_ACCESS, rowFrom = NA, to = TO_ACCESS, rowTo = NA),
list(FROM_ACCESS = as.name(accessFrom_name), TO_ACCESS = as.name(accessTo_name)))
if(from_ArgList$class %in% modelValuesTypes)
runCode$rowFrom = from_ArgList$row
if(to_ArgList$class %in% modelValuesTypes)
runCode$rowTo = to_ArgList$row
} else {
rowFromArg <- if(from_ArgList$class %in% modelValuesTypes) from_ArgList$row else NA
rowToArg <- if(to_ArgList$class %in% modelValuesTypes) {
if(identical(rowFromArg, NA)) {rowFromArg <- 0; unusedArg <- NA} else unusedArg <- 0
to_ArgList$row
} else {
unusedArg <- NA
NA
}
runCode <- substitute(nimCopy(copierVector = COPIER_VECTOR, rowFrom = ROWFROM, rowTo = ROWTO, unused = UNUSED),
list(COPIER_VECTOR = as.name(copierVector_name),
ROWFROM = rowFromArg, ROWTO = rowToArg, UNUSED = unusedArg))
}
runCode <- runCode[as.character(runCode) != 'NA']
return(runCode)
})
doubleBracket_keywordInfo <- keywordInfoClass(
keyword = '[[',
processor = function(code, nfProc, RCfunProc){
callerCode <- code[[2]]
if(is.null(nfProc)) stop("No allowed use of [[ in a nimbleFunction without setup code.")
possibleObjects <- c('symbolModel', 'symbolNimPtrList', 'symbolNimbleFunctionList', 'symbolNimbleList')
class = symTypeFromSymTab(code[[2]], nfProc$setupSymTab, options = possibleObjects)
if(is.null(class)){ ##assume that an element of a run-time provided nimbleList is being accessed
nl_charName <- as.character(callerCode)
nl_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfVar(NIMBLELIST, VARNAME), list(NIMBLELIST = as.name(nl_charName), VARNAME = nl_fieldName))
return(newRunCode)
}
if(class == 'symbolNimPtrList' || class == 'symbolNimbleFunctionList')
return(code)
if(class == 'symbolNimbleList'){
# Code is of the form
# myNimbleList[['myVar']]
nl_charName <- as.character(callerCode)
nl_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfVar(NIMBLELIST, VARNAME), list(NIMBLELIST = as.name(nl_charName), VARNAME = nl_fieldName))
return(newRunCode)
}
if(class == 'symbolModel'){
singleAccess_ArgList <- list(code = code, model = code[[2]], nodeExpr = code[[3]])
nodeArg <- code[[3]]
if(is.character(nodeArg)){
if(length(nodeArg) > 1)
stop(paste0("Problem in ",
deparse(code), ". ",
deparse(code[[3]]),
" is too long. It can only have one element."),
call. = FALSE)
varAndIndices <- nimbleInternalFunctions$getVarAndIndices(nodeArg)
allNDims <- lapply(nfProc$instances, function(x) {
model <- eval(singleAccess_ArgList$model,
envir = x)
if(length(nodeArg) != 1)
stop(paste0("Length of ",
nodeArg,
" requested from ",
deparse(singleAccess_ArgList$model),
" using '[[' is ",
length(nodeArg),
". It must be 1.")
, call. = FALSE)
determineNdimFromOneCase(model, varAndIndices)
} )
if(length(unique(allNDims)) > 1)
stop(paste0('Error for ', deparse(code),
'. Inconsistent numbers of dimensions for different instances.'),
call. = FALSE)
nDim <- allNDims[[1]]
useMap <- nDim > 0
## ##
## ## If input is of the form model[['a']]
## ## and a is non-scalar,
## ## we treat it like model$a, which handles either
if(useMap & length(varAndIndices$indices) == 0) {
return(
keywordList[['$']]$processor(code, nfProc, RCfunProc)
)
}
## ## Following line adds up 0 for each scalar index
## ## and 1 for each non-scalar index to determine if the
## ## accessed node is scalar
## nDim <- sum(1 - unlist(lapply(varAndIndices$indices, is.numeric) ) )
## useMap <- nDim > 0
}
else{
allNDims <- determineNdimsFromNfproc(singleAccess_ArgList$model, nodeArg, nfProc)
if(length(unique(allNDims)) > 1) stop(paste0('Error for ', deparse(code), '. Inconsistent numbers of dimensions for different instances.'), call. = FALSE)
nDim <- allNDims[[1]]
useMap <- nDim > 0
}
if(useMap){
accessName <- map_SetupTemplate$makeName(singleAccess_ArgList)
addNecessarySetupCode(accessName, singleAccess_ArgList, map_SetupTemplate, nfProc)
ans <- makeMapAccessExpr(accessName, as.name(accessName), nDim)
}
else{
accessName <- singleModelIndexAccess_SetupTemplate$makeName(singleAccess_ArgList)
addNecessarySetupCode(accessName, singleAccess_ArgList, singleModelIndexAccess_SetupTemplate, nfProc)
#ans <- substitute(ACCESSNAME[MFLATINDEX], list(ACCESSNAME = as.name(accessName), MFLATINDEX = as.name(paste0(accessName, '_flatIndex'))))
ans <- makeSingleIndexAccessExpr(accessName, as.name(accessName))
}
return(ans)
}
stop("Incorrect use of double brackets in: '", deparse(code), "'.")
})
modelMemberFun_keywordInfo <- keywordInfoClass(
keyword = 'multiple',
processor = function(code, nfProc, RCfunProc) {
## if we get here it must be model$member(args)
## We will turn it into member(model, args)
newRunCode <- do.call("call",
c(list(as.character(code[[1]][[3]]),
code[[1]][[2]]),
as.list(code[-1])),
quote = TRUE)
return(newRunCode)
})
dollarSign_keywordInfo <- keywordInfoClass(
keyword = '$',
processor = function(code, nfProc, RCfunProc){
callerCode <- code[[2]]
if(is.null(nfProc)) {
nl_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfVar(NIMBLELIST, VARNAME), list(NIMBLELIST = callerCode, VARNAME = nl_fieldName))
return(newRunCode)
}
doubleBracketCase <- FALSE
if(length(callerCode) > 1) {
if(deparse(callerCode[[1]] == '[[')) {
doubleBracketCase <- TRUE
symObj <- getSymObj_recurse(callerCode[[2]], nfProc$setupSymTab)
}
}
if(!doubleBracketCase)
symObj <- getSymObj_recurse(callerCode, nfProc$setupSymTab)
class <- class(symObj)[1] ## symObj is allowed to be NULL
# This extracts myNimbleFunction from the expression myNimbleFunction$foo()
if(length(callerCode) > 1){
if(callerCode[[1]] == '$'){ ## nested NL or NF case
callerCode <- processKeyword(callerCode, nfProc, RCfunProc)
}
}
# This extracts myNimbleFunctionList from the expression myNimbleFunctionList[[i]]
# May be a better way to do this
if(is.null(class) || class == 'NULL'){ ##assume that an element of a run-time provided nimbleList is being accessed
nl_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfVar(NIMBLELIST, VARNAME), list(NIMBLELIST = callerCode, VARNAME = nl_fieldName))
return(newRunCode)
}
if(class == 'symbolNimbleFunctionList'){
nf_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfMethod(NIMBLEFXN, METHODNAME), list(NIMBLEFXN = callerCode, METHODNAME = nf_fieldName))
return(newRunCode)
}
if(class == 'symbolModel'){
singleAccess_ArgList <- list(code = code, model = callerCode, var = as.character(code[[3]]) )
accessName <- singleVarAccess_SetupTemplate$makeName(singleAccess_ArgList)
addNecessarySetupCode(accessName, singleAccess_ArgList, singleVarAccess_SetupTemplate, nfProc)
return(as.name(accessName))
}
if(class == 'symbolNimbleFunction'){
# Code is of the form myNimbleFunction$myMethod
# or myNimbleFunction$myVar
# Note that we have cut off '()' in the case of myMethod, so we must inspect the
# nested symbol for myMethod to determine whether it is a method or variable
nf_fieldName <-as.character(code[[3]])
objectSymbol = symObj$nfProc$setupSymTab$getSymbolObject(nf_fieldName)
if(class(objectSymbol)[[1]] == 'symbolMemberFunction'){
newRunCode <- substitute(nfMethod(NIMBLEFXN, METHODNAME), list(NIMBLEFXN = callerCode, METHODNAME = nf_fieldName))
return(newRunCode)
}
else {
# We *assume* that if its not a member function, it should be treated with
# nfVar
newRunCode <- substitute(nfVar(NIMBLEFXN, VARNAME), list(NIMBLEFXN = callerCode, VARNAME = nf_fieldName))
return(newRunCode)
}
}
if(class == 'symbolNimbleList'){
# Code is of the form
# myNimbleList$myVar
nl_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfVar(NIMBLELIST, VARNAME), list(NIMBLELIST = callerCode, VARNAME = nl_fieldName))
return(newRunCode)
}
if(class == 'symbolNimbleFunctionList'){
# Code is of the form myNimbleFunctionList[[i]]$foo (foo should be a method)
# At this point, we cannot access variables of a nimble function list, ie
# myNimbleFunctionList[[i]]$myVariable is not allowed
# If we add this functionality, we will need to look up what foo as we do
# for the nimbleFunction case above
nf_name <-code[[2]]
nf_fieldName <- as.character(code[[3]])
newRunCode <- substitute(nfMethod(NIMBLEFXN, METHODNAME), list(NIMBLEFXN = nf_name, METHODNAME = nf_fieldName))
return(newRunCode)
}
}
)
singleBracket_keywordInfo <- keywordInfoClass(
keyword = '[',
processor = function(code, nfProc, RCfunProc){
if(is.null(nfProc)) return (code)
class <- symTypeFromSymTab(code[[2]], nfProc$setupSymTab)
if(class == 'symbolModelValues'){
if(length(code) < 4) {
stop(paste0("incorrect syntax for accessing element of modelValues: ", deparse(code)))
}
singleMVAccess_ArgList <- list(code = code, modelValues = code[[2]], var = code[[3]], row = code[[4]])
accessName <- singleModelValuesAccessor_SetupTemplate$makeName(singleMVAccess_ArgList)
addNecessarySetupCode(accessName, singleMVAccess_ArgList, singleModelValuesAccessor_SetupTemplate, nfProc)
if(length(code) == 4)
indexExpr = code[[4]]
else
indexExpr = substitute(1)
return(substitute(ACCESS[INDEX], list(ACCESS = as.name(accessName), INDEX = indexExpr) ) )
}
return(code)
}
)
length_char_keywordInfo <- keywordInfoClass(
keyword = 'length',
processor = function(code, nfProc, RCfunProc) {
if(is.null(nfProc)) return(code)
if(length(code) < 2) stop('length() used without an argument')
class <- symTypeFromSymTab(code[[2]], nfProc$setupSymTab)
if(class == "symbolString") {
length_char_ArgList <- list(code = code, string = code[[2]])
accessName <- length_char_SetupTemplate$makeName(length_char_ArgList)
addNecessarySetupCode(accessName, length_char_ArgList, length_char_SetupTemplate, nfProc)
return(substitute(LENGTHNAME, list(LENGTHNAME = as.name(accessName))))
}
return(code)
})
nimIntegrate_keywordInfo <- keywordInfoClass(
keyword = 'nimIntegrate',
processor = function(code, nfProc, RCfunProc) {
if(code$abs.tol == quote(rel.tol))
code$abs.tol = code$rel.tol
iTols <- which(names(code) %in% c('rel.tol','abs.tol'))
for(i in iTols) {
code_i <- code[[i]]
if(length(code_i) > 1) {
if(".Machine" %in% all.vars(code_i)) # Must be an expression using .Machine$double.eps or related
code[[i]] <- eval(code_i)
}
}
code
}
)
nimDerivs_keywordInfo <- keywordInfoClass(
keyword = 'nimDerivs',
processor = function(code, nfProc, RCfunProc) {
wrtArgs <- code[['wrt']]
## First check to see if nimFxn argument is a method.
fxnCall <- code[[2]][[1]]
order <- code[['order']]
calculateCase <- FALSE
if(deparse(fxnCall) == 'calculate'){
calculateCase <- TRUE
}
else if(length(fxnCall) == 3 &&
(deparse(fxnCall[[1]]) == '$' &&
deparse(fxnCall[[3]]) == 'calculate')){
## re-arrange nimDerivs(model$calculate(...), ...) to nimDerivs(calculate(model, ...), ...)
code[[2]] <- modelMemberFun_keywordInfo$processor(code[[2]], nfProc)
code[[2]] <- matchKeywordCode(code[[2]], nfProc)
calculateCase <- TRUE
}
if(calculateCase) {
innerCode <- code[[2]]
if(length(code$wrt)==1)
if(!is.name(code$wrt))
if(is.na(code$wrt[1]))
stop("Derivatives of a call to 'calculate()' must have 'wrt' argument specified.")
innerCode$wrt <- code$wrt
newCode <- calculate_keywordInfo$processor(innerCode, nfProc, RCfunProc)
newCode[[1]] <- as.name('nimDerivs_calculate')
newCode$orderVector <- code$order
newCode$update <- if(is.null(code[['update']])) TRUE else code[['update']]
newCode$reset <- if(is.null(code[['reset']])) FALSE else code[['reset']]
return(newCode)
}
## Not a calculate case:
if(!is.null(nfProc$origMethods[[deparse(fxnCall)]])) {
derivMethod <- nfProc$origMethods[[deparse(fxnCall)]]
derivMethodArgs <- derivMethod$getArgInfo()
## Only make the wrt substitution if the names are baked in as character
wrtArg <- code$wrt
doPreprocess <- FALSE
if(is.numeric(wrtArg) | is.logical(wrtArg)) {
if(any(is.na(wrtArg[1]))) { ## wrt = NULL (default), set to NA, which will become -1 by convertWrtArgToIndices and then c(-1, -1) in the setup code
doPreprocess <- TRUE
}
} else if(is.name(wrtArg)) { ## wrt = some_index_var_maybe_from_setup
## do nothing
} else if(deparse(wrtArg[[1]]) == 'nimC') { ## wrt = c('x', ...)
if(is.character(wrtArg[[2]]))
doPreprocess <- TRUE
} else if(is.character(wrtArg)) { ## wrt = 'x'
doPreprocess <- TRUE
} ## In any other setting, it must be an index vector and we leave it alone here.
##
if(doPreprocess) {
wrt_argList <- list(fxnCall = fxnCall,
wrt = code$wrt,
# vector = wrtArgIndices
derivMethodArgs = derivMethodArgs)
accessName <- wrtVector_setupCodeTemplate$makeName(wrt_argList)
addNecessarySetupCode(accessName, wrt_argList, wrtVector_setupCodeTemplate, nfProc)
code[['wrt']] <- substitute(VECNAME,
list(VECNAME = as.name(accessName)))
}
## Check if model and updateNodes are provided.
## If so, create a nodeFxnVector for them.
modelProvided <- is.name(code[['model']])
updateNodesProvided <- is.name(code[['updateNodes']])
if(!updateNodesProvided)
if(is.character(code[['updateNodes']]))
updateNodesProvided <- !is.na(code[['updateNodes']][1])
constantNodesProvided <- is.name(code[['constantNodes']])
if(!constantNodesProvided)
if(is.character(code[['constantNodes']]))
constantNodesProvided <- !is.na(code[['constantNodes']][1])
if(xor(modelProvided, updateNodesProvided || constantNodesProvided))
stop('nimDerivs arguments model and at least one of updateNodes or constantNodes must be provided together or not at all.')
if(modelProvided) { ## At this point that means both were provided
DMUNargList <- list(model = code$model,
updateNodes = if(updateNodesProvided) code[["updateNodes"]] else NULL,
constantNodes = if(constantNodesProvided) code[["constantNodes"]] else NULL)
accessName <- nodeFunctionVector_DerivsModelUpdateNodes_SetupTemplate$makeName(DMUNargList)
addNecessarySetupCode(accessName, DMUNargList, nodeFunctionVector_DerivsModelUpdateNodes_SetupTemplate, nfProc)
## code[['model']] <- NULL
## if(updateNodesProvided) code[['updateNodes']] <- NULL
## if(constantNodesProvided) code[['constantNodes']] <- NULL
code[['updateNodesName']] <- accessName
}
code[['model']] <- NULL
code[['updateNodes']] <- NULL
code[['constantNodes']] <- NULL
}
return(code)
}
)
derivInfo_keywordInfo <- keywordInfoClass(
keyword = 'derivInfo',
processor = function(code, nfProc, RCfunProc) {
fxnCall <- code[[2]][[1]]
calculateCase <- FALSE
if(deparse(fxnCall) == 'calculate'){
calculateCase <- TRUE
}
else if(length(fxnCall) == 3 &&
(deparse(fxnCall[[1]]) == '$' &&
deparse(fxnCall[[3]]) == 'calculate')){
## re-arrange nimDerivs(model$calculate(...), ...) to nimDerivs(calculate(model, ...), ...)
code[[2]] <- modelMemberFun_keywordInfo$processor(code[[2]], nfProc)
code[[2]] <- matchKeywordCode(code[[2]], nfProc)
calculateCase <- TRUE
}
if(!calculateCase) {
stop('The first argument to derivInfo must be a call to calculate(model, ...) or model$calculate(...)')
}
innerCode <- code[[2]]
if(is.null(code$wrt))
stop("derivInfo must provide 'wrt' argument.")
innerCode$wrt <- code$wrt
newCode <- calculate_keywordInfo$processor(innerCode, nfProc, RCfunProc)
return(newCode)
}
)
# KeywordList
keywordList <- new.env()
keywordList[['nimSeq']] <- nimSeq_keywordInfo
keywordList[['getParam']] <- getParam_keywordInfo
keywordList[['getBound']] <- getBound_keywordInfo
keywordList[['values']] <- values_keywordInfo
keywordList[['calculate']] <- calculate_keywordInfo
keywordList[['calculateDiff']] <- calculateDiff_keywordInfo
keywordList[['simulate']] <- simulate_keywordInfo
keywordList[['getLogProb']] <- getLogProb_keywordInfo
keywordList[['nimCopy']] <- nimCopy_keywordInfo
keywordList[['[[']] <- doubleBracket_keywordInfo
keywordList[['$']] <- dollarSign_keywordInfo
keywordList[['[']] <- singleBracket_keywordInfo
keywordList[['besselK']] <- besselK_keywordInfo
keywordList[['dgamma']] <- d_gamma_keywordInfo
keywordList[['pgamma']] <- pq_gamma_keywordInfo
keywordList[['qgamma']] <- pq_gamma_keywordInfo
keywordList[['rgamma']] <- rgamma_keywordInfo
keywordList[['dinvgamma']] <- d_gamma_keywordInfo
keywordList[['pinvgamma']] <- pq_gamma_keywordInfo
keywordList[['qinvgamma']] <- pq_gamma_keywordInfo
keywordList[['rinvgamma']] <- rgamma_keywordInfo
keywordList[['dsqrtinvgamma']] <- d_gamma_keywordInfo
keywordList[['psqrtinvgamma']] <- pq_gamma_keywordInfo
keywordList[['qsqrtinvgamma']] <- pq_gamma_keywordInfo
keywordList[['rsqrtinvgamma']] <- rgamma_keywordInfo
keywordList[['ddexp']] <- d_gamma_keywordInfo
keywordList[['pdexp']] <- pq_gamma_keywordInfo
keywordList[['qdexp']] <- pq_gamma_keywordInfo
keywordList[['rdexp']] <- rgamma_keywordInfo
# can be handled the same as gamma, so include although we have dexp_nimble too
keywordList[['dexp']] <- d_gamma_keywordInfo
keywordList[['pexp']] <- pq_gamma_keywordInfo
keywordList[['qexp']] <- pq_gamma_keywordInfo
keywordList[['rexp']] <- rgamma_keywordInfo
keywordList[['dexp_nimble']] <- d_exp_nimble_keywordInfo
keywordList[['pexp_nimble']] <- pq_exp_nimble_keywordInfo
keywordList[['qexp_nimble']] <- pq_exp_nimble_keywordInfo
keywordList[['rexp_nimble']] <- rexp_nimble_keywordInfo
keywordList[['length']] <- length_char_keywordInfo ## active only if argument has type character
keywordList[['nimIntegrate']] <- nimIntegrate_keywordInfo
keywordList[['nimDerivs']] <- nimDerivs_keywordInfo
keywordList[['derivInfo']] <- derivInfo_keywordInfo
keywordListModelMemberFuns <- new.env()
keywordListModelMemberFuns[['calculate']] <- modelMemberFun_keywordInfo
keywordListModelMemberFuns[['simulate']] <- modelMemberFun_keywordInfo
keywordListModelMemberFuns[['calculateDiff']] <- modelMemberFun_keywordInfo
keywordListModelMemberFuns[['getLogProb']] <- modelMemberFun_keywordInfo
keywordListModelMemberFuns[['getParam']] <- modelMemberFun_keywordInfo
keywordListModelMemberFuns[['getBound']] <- modelMemberFun_keywordInfo
matchFunctions <- new.env()
matchFunctions[['setSize']] <- function(var, ..., copy = TRUE, fillZeros = TRUE){}
matchFunctions[['nimC']] <- nimC
matchFunctions[['nimRep']] <- function(x, times = 1, length.out, each = 1) {}
matchFunctions[['nimSeq']] <- nimSeq
matchFunctions[['nimNumeric']] <- nimNumeric
matchFunctions[['nimInteger']] <- nimInteger
matchFunctions[['nimLogical']] <- nimLogical
matchFunctions[['nimMatrix']] <- nimMatrix
matchFunctions[['nimArray']] <- nimArray
matchFunctions[['values']] <- function(model, nodes, accessor){}
matchFunctions[['getParam']] <- getParam
matchFunctions[['getBound']] <- getBound
matchFunctions[['calculate']] <- calculate
matchFunctions[['calculateDiff']] <- calculateDiff
matchFunctions[['simulate']] <- simulate
matchFunctions[['getLogProb']] <- getLogProb
matchFunctions[['nimCopy']] <- function(from, to, nodes, nodesTo, row, rowTo, logProb = FALSE, logProbOnly = FALSE){}
matchFunctions[['double']] <- function(nDim, dim, default, ...){}
matchFunctions[['int']] <- function(nDim, dim, default, ...){}
matchFunctions[['nimOptim']] <- nimOptim
matchFunctions[['nimIntegrate']] <- nimIntegrate
matchFunctions[['nimOptimDefaultControl']] <- nimOptimDefaultControl
matchFunctions[['nimEigen']] <- function(squareMat, symmetric = FALSE, only.values = FALSE){}
matchFunctions[['nimSvd']] <- function(mat, vectors = 'full'){}
matchFunctions[['nimDerivs']] <- function(call = NA,
order = nimC(0,1,2),
wrt = NA,
model = NA, updateNodes = NA, constantNodes = NA,
do_update = TRUE, reset = FALSE) {}
matchFunctions[['derivInfo']] <- derivInfo
matchFunctions[['besselK']] <- function(x, nu, expon.scaled = FALSE){}
matchFunctions[['dgamma']] <- function(x, shape, rate = 1, scale, log = FALSE){}
matchFunctions[['rgamma']] <- function(n, shape, rate = 1, scale){}
matchFunctions[['qgamma']] <- function(p, shape, rate = 1, scale, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['pgamma']] <- function(q, shape, rate = 1, scale, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['dinvgamma']] <- matchFunctions[['dsqrtinvgamma']] <- function(x, shape, scale = 1, rate, log = FALSE){}
matchFunctions[['rinvgamma']] <- matchFunctions[['rsqrtinvgamma']] <- function(n, shape, scale = 1, rate){}
matchFunctions[['qinvgamma']] <- matchFunctions[['qsqrtinvgamma']] <- function(p, shape, scale = 1, rate, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['pinvgamma']] <- matchFunctions[['psqrtinvgamma']] <- function(q, shape, scale = 1, rate, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['dexp']] <- function(x, rate = 1, log = FALSE){}
matchFunctions[['rexp']] <- function(n, rate = 1){}
matchFunctions[['qexp']] <- function(p, rate = 1, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['pexp']] <- function(q, rate = 1, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['dexp_nimble']] <- function(x, rate, scale = 1, log = FALSE){}
matchFunctions[['rexp_nimble']] <- function(n, rate, scale = 1){}
matchFunctions[['qexp_nimble']] <- function(p, rate, scale = 1, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['pexp_nimble']] <- function(q, rate, scale = 1, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['ddexp']] <- function(x, location, scale = 1, rate, log = FALSE){}
matchFunctions[['rdexp']] <- function(n, location, scale = 1, rate){}
matchFunctions[['qdexp']] <- function(p, location, scale = 1, rate, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['pdexp']] <- function(q, location, scale = 1, rate, lower.tail = TRUE, log.p = FALSE){}
matchModelMemberFunctions <- new.env()
matchModelMemberFunctions[['calculate']] <- function(nodes) {}
matchModelMemberFunctions[['calculateDiff']] <- function(nodes) {}
matchModelMemberFunctions[['getLogProb']] <- function(nodes) {}
matchModelMemberFunctions[['simulate']] <- function(nodes, includeData = FALSE) {}
matchModelMemberFunctions[['getParam']] <- function(node, param) {}
matchModelMemberFunctions[['getBound']] <- function(node, bound) {}
# remove ncp from signatures
stripArgs <- function(fname, argNames) {
if(exists(fname)) {
args <- formals(eval(as.name(fname)))
args <- args[-which(names(args) %in% argNames)]
template <- function() {}
formals(template) <- args
return(template)
} else return(NULL)
}
for(distfun in paste0(c('d','p','q','r'), 'beta'))
matchFunctions[[distfun]] <- stripArgs(distfun, 'ncp')
for(distfun in paste0(c('d','p','q','r'), 'chisq'))
matchFunctions[[distfun]] <- stripArgs(distfun, 'ncp')
for(distfun in paste0(c('d','p','q','r'), 't'))
matchFunctions[[distfun]] <- stripArgs(distfun, 'ncp')
for(distfun in paste0(c('d','p','q','r'), 'nbinom'))
matchFunctions[[distfun]] <- stripArgs(distfun, 'mu')
# the following are standard in terms of both matchFunctions and keywordList
matchDistList <- list('binom', 'cat', 'dirch', 'interval', 'lnorm', 'logis', 'multi', 'mnorm_chol', 'mvt_chol', 'norm', 'pois', 't_nonstandard', 'unif', 'weibull', 'wish_chol', 'invwish_chol', 'car_normal', 'car_proper')
addDistList2matchFunctions <- function(distList, matchFunEnv){
for(thisDist in distList){
pFun <- paste0('p', thisDist)
qFun <- paste0('q', thisDist)
rFun <- paste0('r', thisDist)
dFun <- paste0('d', thisDist)
eval(substitute(matchFunctions[[dFun]] <- DFUN, list(DFUN = as.name(dFun))))
eval(substitute(matchFunctions[[rFun]] <- RFUN, list(RFUN = as.name(rFun))))
if(exists(qFun))
eval(substitute(matchFunctions[[qFun]] <- QFUN, list(QFUN = as.name(qFun))))
if(exists(pFun))
eval(substitute(matchFunctions[[pFun]] <- PFUN, list(PFUN = as.name(pFun))))
}
}
addDistList2matchFunctions(matchDistList, matchFunctions)
# processKeyword function to be called by nfProc
processKeyword <- function(code, nfProc, RCfunProc){
thisKeywordInfo <- keywordList[[ as.character(code[[1]]) ]]
if(!is.null(thisKeywordInfo))
return(thisKeywordInfo$processor(code, nfProc, RCfunProc))
return(code)
}
processKeywordCodeMemberFun <- function(code, nfProc, RCfunProc) { ## handle cases like a$b(c) as one unit
## this includes nf$method()
## nfList[[i]]$method
## model$calculate(nodes)
dollarSignPart <- code[[1]]
objectPart <- dollarSignPart[[2]]
isModel <- FALSE
if(length(objectPart) != 1) isModel <- FALSE ## a case like a[[i]]$b(), which can only be a nimbleFunction list
else {
symObj <- nfProc$setupSymTab$getSymbolObject(as.character(objectPart))
if(is.null(symObj)) stop(paste0("In processKeywordCodeMemberFun: not sure what to do with ", deparse(code)))
if(inherits(symObj, 'symbolModel'))
isModel <- TRUE
}
if(isModel) {
thisKeywordInfo <- keywordListModelMemberFuns[[ as.character(dollarSignPart[[3]]) ]]
if(is.null(thisKeywordInfo)) stop(paste0("In processKeywordCodeMemberFun, don't know what do with: ", deparse(code)))
rearrangedCode <- thisKeywordInfo$processor(code, nfProc)
rearrangedCode <- matchKeywordCode(rearrangedCode, nfProc)
return(processKeywords_recurse(rearrangedCode, nfProc, RCfunProc))
} else {
## same as processKeywords_recurse
## first line here creates something like nfMethod(model, method)(args)
## which is handled as a chainedCall in later processing
code[[1]] <- processKeywords_recurse(code[[1]], nfProc, RCfunProc)
cl <- length(code)
if(cl >= 2) {
for(i in 2:cl) {
code[[i]] <- processKeywords_recurse(code[[i]], nfProc, RCfunProc)
}
}
return(code)
}
}
processKeywords_recurse <- function(code, nfProc = NULL, RCfunProc) {
cl = length(code)
if(cl == 1) {
if(is.call(code)) {
if(length(code[[1]]) > 1)
if(deparse(code[[1]][[1]] == '$'))
code <- processKeywordCodeMemberFun(code, nfProc, RCfunProc)
else
code[[1]] <- processKeywords_recurse(code[[1]], nfProc, RCfunProc)
}
return(code)
}
if(length(code[[1]]) == 1) {
code <- processKeyword(code, nfProc, RCfunProc)
}
cl = length(code)
if(is.call(code)) {
if(length(code[[1]]) > 1) {
if(deparse(code[[1]][[1]] == '$')) {
code <- processKeywordCodeMemberFun(code, nfProc, RCfunProc) ## case like model$calculate(nodes)
return(code) ## don't recurse on arguments of anything in this category
}
code[[1]] <- processKeywords_recurse(code[[1]], nfProc, RCfunProc)
}
if(cl >= 2) {
for(i in 2:cl) {
code[[i]] <- processKeywords_recurse(code[[i]], nfProc, RCfunProc)
}
}
}
return(code)
}
##### SETUPCODE TEMPLATES
wrtVector_setupCodeTemplate <- setupCodeTemplateClass(
makeName = function(argList){Rname2CppName(paste0('wrtVec_',
deparse(argList$fxn),
paste(deparse(argList$wrt), sep='_'),
'_'))},
codeTemplate = quote(
{
WRTVEC <- nimble:::convertWrtArgToIndices(WRT, #code$wrt
DERIVMETHODARGS,
FXNNAME)
if(length(WRTVEC) == 1)
WRTVEC <- c(WRTVEC, -1)
}
),
makeCodeSubList = function(resultName, argList){
list(WRTVEC = as.name(resultName),
WRT = argList$wrt
,DERIVMETHODARGS = argList$derivMethodArgs
,FXNNAME = deparse(argList$fxnCall)
)##argList$vector)
}
)
length_char_SetupTemplate <- setupCodeTemplateClass(
makeName = function(argList) {Rname2CppName(paste0(paste("length", deparse(argList$string), sep='_'), '_KNOWN_'))},
codeTemplate = quote(LENGTHNAME <- CODE),
makeCodeSubList = function(resultName, argList) {
list(LENGTHNAME = as.name(resultName),
CODE = argList$code)
})
modelVariableAccessorVector_setupCodeTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model, nodes and logProb
makeName = function(argList) {Rname2CppName(paste(deparse(argList$model), deparse(argList$nodes), 'access_logProb', deparse(argList$logProb),'LPO', deparse(argList$logProbOnly), sep = '_'))},
codeTemplate = quote( ACCESSNAME <- nimble:::modelVariableAccessorVector(MODEL, NODES, logProb = LOGPROB, logProbOnly = LOGPROBONLY) ),
makeCodeSubList = function(resultName, argList) {
list(ACCESSNAME = as.name(resultName),
MODEL = argList$model,
NODES = argList$nodes,
LOGPROB = argList$logProb,
LOGPROBONLY = argList$logProbOnly)
})
copierVector_setupCodeTemplate <- setupCodeTemplateClass(
makeName = function(argList) {Rname2CppName(paste0(argList$accessFrom_name, '_', argList$accessTo_name))},
codeTemplate = quote( COPIERNAME <- nimble:::copierVector(ACCESS_FROM, ACCESS_TO, ISMVFROM, ISMVTO) ),
makeCodeSubList = function(resultName, argList) {
list(COPIERNAME = as.name(resultName),
ACCESS_FROM = as.name(argList$accessFrom_name),
ACCESS_TO = as.name(argList$accessTo_name),
ISMVFROM = as.integer(argList$isMVfrom),
ISMVTO = as.integer(argList$isMVto))
})
modelValuesAccessorVector_setupCodeTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are modelValues, nodes and logProb
makeName = function(argList) {Rname2CppName(paste(deparse(argList[['modelValues']]), deparse(argList$nodes), 'access_logProb', deparse(argList$logProb), 'LPO', deparse(argList$logProbOnly), deparse(argList$row), sep = '_'))},
codeTemplate = quote( ACCESSNAME <- nimble:::modelValuesAccessorVector(MODEL, NODES, logProb = LOGPROB, logProbOnly = LOGPROBONLY) ),
makeCodeSubList = function(resultName, argList) {
list(ACCESSNAME = as.name(resultName),
MODEL = argList[['modelValues']],
NODES = argList$nodes,
LOGPROB = argList$logProb,
LOGPROBONLY = argList$logProbOnly)
})
nodeFunctionVector_WithDerivsOutput_SetupTemplate <- setupCodeTemplateClass(
makeName = function(argList){
Rname2CppName(paste(deparse(argList$model),
deparse(argList$nodes),
'nodeFxnVector_WithDerivsOutput', ## The "_derivs_" tag is used later to determine the right class - klugey
deparse(argList$includeData),
if(argList$sortUnique) "SU" else "notSU",
'_derivs_',
sep = '_')
)
},
codeTemplate = quote(
NODEFXNVECNAME <- nimble:::nodeFunctionVector_WithDerivsOutputNodes(
model = MODEL,
calcNodes = CALCNODES,
excludeData = EXCLUDEDATA,
sortUnique = SORTUNIQUE)
),
makeCodeSubList = function(resultName, argList){
list(NODEFXNVECNAME = as.name(resultName),
MODEL = argList$model,
CALCNODES = argList$nodes,
EXCLUDEDATA = !argList$includeData,
SORTUNIQUE = argList$sortUnique
)
})
nodeFunctionVector_DerivsModelUpdateNodes_SetupTemplate <- setupCodeTemplateClass(
makeName = function(argList){
Rname2CppName(paste(deparse(argList$model),
deparse(argList[['updateNodes']]),
deparse(argList[['constantNodes']]),
'nodeFxnVector_DerivsModelUpdateNodes_derivs_', ## The "_derivs_" tag is used later to determine the right class - klugey
sep = '_')
)
},
codeTemplate = quote(
NODEFXNVECNAME <- nimble:::nodeFunctionVector_DerivsModelUpdateNodes(
model = MODEL,
updateNodes = UPDATENODES,
constantNodes = CONSTANTNODES)
),
makeCodeSubList = function(resultName, argList){
list(NODEFXNVECNAME = as.name(resultName),
MODEL = argList$model,
UPDATENODES = argList[["updateNodes"]],
CONSTANTNODES = argList[["constantNodes"]]
)
})
nodeFunctionVector_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model, nodes and includeData
makeName = function(argList){
Rname2CppName(paste(deparse(argList$model),
deparse(argList$nodes),
'nodeFxnVector_includeData',
deparse(argList$includeData),
if(argList$sortUnique) "SU" else "notSU",
if(is.null(argList$wrtNodes)) '' else '_derivs_', sep = '_')
)
},
codeTemplate = quote(
NODEFXNVECNAME <- nimble:::nodeFunctionVector(model = MODEL,
nodeNames = NODES,
wrtNodes = WRTNODES,
excludeData = EXCLUDEDATA,
sortUnique = SORTUNIQUE,
errorContext = ERRORCONTEXT)
),
makeCodeSubList = function(resultName, argList){
list(NODEFXNVECNAME = as.name(resultName),
MODEL = argList$model,
NODES = argList$nodes,
WRTNODES = argList$wrtNodes,
EXCLUDEDATA = !argList$includeData,
SORTUNIQUE = argList$sortUnique,
ERRORCONTEXT = argList$errorContext
)
})
paramInfo_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model, node and param
makeName = function(argList){Rname2CppName(paste(deparse(argList$model), deparse(argList$node), deparse(argList$param), 'paramInfo', sep='_'))},
makeOtherNames = function(name,argList) {Rname2CppName(paste0(name,'_ID'))},
codeTemplate = quote({
PARAMINFONAME <- nimble:::makeParamInfo(model = MODEL, nodes = NODE, param = PARAM, vector = HASINDEX )
PARAMIDNAME <- PARAMINFONAME$paramID
PARAMINFONAME$paramID <- NULL
}),
makeCodeSubList = function(resultName, argList){
list(PARAMINFONAME = as.name(resultName),
PARAMIDNAME = as.name(paste0(resultName,'_ID')),
MODEL = argList$model,
NODE = argList$node,
PARAM = argList$param,
HASINDEX = argList$hasIndex)
})
boundInfo_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model, node and param
makeName = function(argList){Rname2CppName(paste(deparse(argList$model), deparse(argList$node), deparse(argList$bound), 'boundInfo', sep='_'))},
makeOtherNames = function(name,argList) {Rname2CppName(paste0(name,'_ID'))},
codeTemplate = quote({
BOUNDINFONAME <- nimble:::makeBoundInfo(MODEL, NODE, BOUND)
BOUNDIDNAME <- BOUNDINFONAME$boundID
BOUNDINFONAME$boundID <- NULL
}),
makeCodeSubList = function(resultName, argList){
list(BOUNDINFONAME = as.name(resultName),
BOUNDIDNAME = as.name(paste0(resultName,'_ID')),
MODEL = argList$model,
NODE = argList$node,
BOUND = argList$bound)
})
allLHSNodes_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model
makeName = function(argList){
Rname2CppName(paste('allLHSnodes', deparse(argList$model), sep = '_'))
},
codeTemplate = quote(NODENAMES <- MODEL$getMaps('nodeNamesLHSall')),
makeCodeSubList = function(resultName, argList){
list(NODENAMES = as.name(resultName),
MODEL = argList$model)
})
allModelNodes_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model
makeName = function(argList){
Rname2CppName(paste('allModelNodes', deparse(argList$model), sep = '_'))
},
codeTemplate = quote(NODENAMES <- MODEL$getVarNames()),
makeCodeSubList = function(resultName, argList){
list(NODENAMES = as.name(resultName),
MODEL = argList$model)
})
allModelValuesVars_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are modelValues
makeName = function(argList){
Rname2CppName(paste('allMVVars', deparse(argList$modelValues), sep = '_'))
},
codeTemplate = quote(NODENAMES <- MODELVALUES$getVarNames(includeLogProb = FALSE)),
makeCodeSubList = function(resultName, argList){
list(NODENAMES = as.name(resultName),
MODELVALUES = argList$modelValues)
})
code2Name_fromArgList <- function(argList)
Rname2CppName(deparse(argList$code))
singleVarAccess_SetupTemplate <- setupCodeTemplateClass(
#Note to progammer: required fields of argList are 'code' (raw code to be processed), model and var
makeName = code2Name_fromArgList,
codeTemplate = quote(SINGLEACCESSOR <- nimble:::singleVarAccess(MODEL, VAR)),
makeCodeSubList = function(resultName, argList){
list(SINGLEACCESSOR = as.name(resultName),
MODEL = argList$model,
VAR = argList$var)
})
singleModelIndexAccess_SetupTemplate <- setupCodeTemplateClass(
#Note to progammer: required fields of argList are code, varAndIndices, node (character) and model(expression)
makeOtherNames = function(name, argList){ paste0(name, '_flatIndex')},
makeName = code2Name_fromArgList,
codeTemplate = quote({
VARANDINDICES <- nimble:::nimbleInternalFunctions$getVarAndIndices(NODEVARNAME)
NEWVARNAME <- as.character(VARANDINDICES$varName)
MFLATINDEX <- nimble:::varAndIndices2flatIndex(VARANDINDICES, MODELVAREXPR$getVarInfo(NEWVARNAME))
VARACCESSOR <- nimble:::singleVarAccess(MODELVAREXPR, NEWVARNAME, useSingleIndex = TRUE)
}),
makeCodeSubList = function(resultName, argList){
list(VARACCESSOR = as.name(resultName),
VARANDINDICES = as.name(paste0(resultName, '_varAndIndices') ),
NEWVARNAME = as.name(paste0(resultName, '_newVarName')),
NODEVARNAME = argList$nodeExpr,
MFLATINDEX = as.name(paste0(resultName, '_flatIndex')),
MODELVAREXPR = argList$model)
})
map_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are code, model
makeName = code2Name_fromArgList,
makeOtherNames = function(name, argList){
output <- character()
output[1] = paste0(name, '_strides')
output[2] = paste0(name, '_offset')
output[3] = paste0(name, '_sizes')
return(output)
},
codeTemplate = quote({
VARANDINDICES <- nimble:::nimbleInternalFunctions$getVarAndIndices(NODEVARNAME)
NEWVARNAME <- as.character(VARANDINDICES$varName)
map_SetupTemplate_vi <- MODEL$getVarInfo(NEWVARNAME)
map_SetupTemplate_mapParts <- nimble:::varAndIndices2mapParts(VARANDINDICES, map_SetupTemplate_vi$maxs, map_SetupTemplate_vi$nDim)
MSTRIDES <- map_SetupTemplate_mapParts$strides
MOFFSET <- map_SetupTemplate_mapParts$offset
MSIZES <- map_SetupTemplate_mapParts$sizes
VARACCESSOR <- nimble:::singleVarAccess(model, NEWVARNAME)
}),
makeCodeSubList = function(resultName, argList){
list(VARACCESSOR = as.name(resultName),
NODEVARNAME = argList$nodeExpr,
NEWVARNAME = as.name(paste0(resultName, '_newVarName')),
VARANDINDICES = as.name(paste0(resultName, '_varAndIndices')),
MODEL = argList$model,
MSTRIDES = as.name(paste0(resultName, '_strides')),
MOFFSET = as.name(paste0(resultName, '_offset')),
MSIZES = as.name(paste0(resultName, '_sizes')))
})
singleModelValuesAccessor_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are modelValues, var, row, code
makeName = code2Name_fromArgList,
codeTemplate = quote({
MVACCESS <- nimble:::singleModelValuesAccess(MODELVALUES, VAR)
}),
makeCodeSubList = function(resultName, argList){
list(MVACCESS = as.name(resultName),
MODELVALUES = argList$modelValues,
VAR = argList$var)
}
)
#### KEYWORD PROCESSING UTILITIES
isCodeArgBlank <- function(code, arg){
#return(nchar(code[[arg]]) == 0)
return(is.null(code[[arg]]))
}
# Utility functions to make things a little neater
isSetupCodeGenerated <- function(name, nfProc)
name %in% nfProc$newSetupOutputNames
addSetupCodeNames <- function(name, otherNames, nfProc)
nfProc$newSetupOutputNames <- c(name, otherNames, nfProc$newSetupOutputNames)
addBlockFromCppName <- function(name, nfProc)
nfProc$blockFromCppNames <- c(name, nfProc$blockFromCppNames)
addNewCode <- function(name, subList, template, nfProc)
nfProc$newSetupCode[[name]] <- eval(substitute(substitute(TEMPLATE, subList), list(TEMPLATE = template$codeTemplate) ) )
addNecessarySetupCode <- function(name, argList, template, nfProc, allowToCpp = TRUE){
if(is.null(nfProc)) stop("Trying to add setup code for a nimbleFunction with no setup code.")
if(!isSetupCodeGenerated(name, nfProc)){
addSetupCodeNames(name, template$makeOtherNames(name, argList), nfProc)
subList <- template$makeCodeSubList(name, argList)
addNewCode(name, subList, template, nfProc)
if(!allowToCpp) addBlockFromCppName(name, nfProc) ## ignores makeOtherNames for now
}
}
getSymObj_recurse <- function(code, symTab, recurse = FALSE) { #code will be like a$b$c with expectation all are NF or NL
if(length(code) > 1) {
if(deparse(code[[1]]) != '$') return(NULL) ## This is valid if we have makeNewNimbleListObject(...)$member or foo()$member
firstArg <- code[[2]]
memberName <- deparse(code[[3]])
symTab <- getSymObj_recurse(firstArg, symTab, recurse = TRUE) ## when recursing, return the symTab
} else {
memberName <- deparse(code)
}
symObject <- if(is.null(symTab)) NULL else symTab$getSymbolObject(memberName)
if(recurse) {
if(inherits(symObject, 'symbolNimbleFunction')) return(symObject$nfProc$setupSymTab)
if(inherits(symObject, 'symbolNimbleList')) return(symObject$nlProc$symTab) ## can only be known if it was created in setup code
if(is.null(symObject)) return(NULL) ## will assume to be nimbleList, only kind of nested data structure that could be of unknown type right now
} else {
return(symObject)
}
stop(paste0('Problem (ii) working through ', deparse(code)), .call = FALSE)
}
symTypeFromSymTab <- function(codeName, symTab, options = character(0) ){
if(is.language(codeName))
codeName <- as.character(codeName)
if(length(codeName) > 1)
return('NULL')
class <- class(symTab$symbols[[codeName]])[1]
if(length(options) == 0)
return(class)
if(!(class %in% options))
return(NULL) ## nimbleList that was not constructed in setup code
return(class)
}
isSymbolType <- function(symTab, varName, symType)
inherits(symTab$symbols[[varName]], symType)
matchAndFill.call <- function(def, call){
## Note re: matchAndFill.call(function(a = 1, ..., b = 2){}, quote(foo(b = 1, 2, 3))): behavior on this is due to match.call
theseFormals <- formals(def)
formalNames <- names(theseFormals) # formalArgs are the arguments that are defined, i.e. does NOT include anything that is from the args "..."
theseFormals <- theseFormals[nchar(theseFormals) > 0]
matchedCall <- match.call(def, call) # problem with match.call for our needs is it omits formals that were not provided
missingArgs <- which(!(names(theseFormals) %in% names(matchedCall)))
for(ind in missingArgs){ ## this puts back in anything omitted, but order may become wrong
name <- names(theseFormals)[ind]
matchedCall[[name]] <- (if(is.null(theseFormals[[name]])) list(NULL) else theseFormals[[name]])
}
newCall <- matchedCall[1]
if(is.null(names(matchedCall))) names(matchedCall) <- c("CALL_", rep("", length(matchedCall) - 1)) ## strangely assigning all "" values results in NULL
indexAdditionalArgs <- which(!(names(matchedCall)[-1] %in% formalNames))
for(thisArgName in formalNames){ # This is to get the order of the arguments correctly and to insert unmatched arguemnts to ... location if appropriate
if(thisArgName == '...') {
for(thisIndex in indexAdditionalArgs) {
thisName <- names(matchedCall)[thisIndex+1]
if(thisName=="")
newCall[[length(newCall) + 1]] <- matchedCall[[thisIndex + 1]]
else {
newCall[[thisName]] <- matchedCall[[thisName]]
}
}
} else {
thisArg <- matchedCall[[thisArgName]]
if(!is.null(thisArg))
newCall[[thisArgName]] <- thisArg
}
}
return(newCall)
}
determineNdimsFromNfproc <- function(modelExpr, varOrNodeExpr, nfProc) {
allNDims <- lapply(nfProc$instances, function(x) {
model <- eval(modelExpr, envir = x)
if(length(varOrNodeExpr) > 1)
stop("One must request a node from a model using syntax like `model[[node]]` and not syntax such as `model[[nodes[i]]]`. For the latter case use `values()` instead.")
if(!exists(as.character(varOrNodeExpr), x, inherits = FALSE) ) {
stop(paste0('Problem accessing node or variable ', deparse(varOrNodeExpr), '.'), call. = FALSE)
}
lab <- eval(varOrNodeExpr, envir = x)
if(length(lab) != 1)
stop(paste0("Length of ",
deparse(varOrNodeExpr),
" requested from ",
deparse(modelExpr),
" using '[[' is ",
length(lab),
". It must be 1." )
, call. = FALSE)
varAndIndices <- nimbleInternalFunctions$getVarAndIndices(lab)
determineNdimFromOneCase(model, varAndIndices)
} )
return(allNDims)
}
## from a$b(), goal is to get symbolObject for a
## from a$b$c(), goal is to get symbolObject for b
matchKeywordCodeMemberFun <- function(code, nfProc) { ## handles cases like a$b(c) as one unit so the member function template for b can be looked up
dollarSignPart <- code[[1]] ## we already checked that code[[1]][[1]] is '$' before calling this function
leftSide <- dollarSignPart[[2]] ## could have further recursing needed. at the moment, nimbleFunction list can only appear at the end of nesting (member data are not part of inheritance)
rightSide <- dollarSignPart[[3]]
memFunName <- deparse(rightSide)
nestedLeftSide <- FALSE
## Step 1: Find the symbol object for whatever is on left-hand side of $
## This may involve recursion
## Only case where the symbol object can be missing (NULL) is nimbleListDef$new() if nimbleListDef if from global env
if(!is.null(nfProc)) { ## If nfProc is null, we are in an RCfunction and the only valid case is nimbleListDef$new()
if(length(leftSide) != 1) {
if(deparse(leftSide[[1]])=='$') {
symObj <- getSymObj_recurse(leftSide, nfProc$setupSymTab)
nestedLeftSide <- TRUE
} else {
nfNestedCall <- leftSide[[1]]
if(length(nfNestedCall) != 1) stop(paste0("Cannot handle this expression: ", deparse(code)))
if(deparse(nfNestedCall) != '[[') stop(paste0("Cannot handle this expression: ", deparse(code)))
leftLeftSide <- leftSide[[2]]
if(length(leftLeftSide) != 1) {
if(deparse(leftLeftSide[[1]]) == '$') { ##a$b[[i]]$foo()
symObj <- getSymObj_recurse(leftLeftSide, nfProc$setupSymTab)
nestedLeftSide <- TRUE
} else stop('Problem processing something like a$b[[i]]$foo()')
} else {
nfListName <- deparse(leftSide[[2]])
if(nfProc$setupSymTab$symbolExists(nfListName)) { ## look in symbol table
symObj <- nfProc$setupSymTab$getSymbolObject(nfListName)
}
}
}
} else {
symTab <- nfProc$setupSymTab
symObj <- symTab$getSymbolObject(deparse(leftSide))
}
} else {
symTab <- symObj <- NULL
}
if(memFunName=='new') { ## this is unique because in non-nested mode, this can be looking for a nlDef in global environment (or possibly elsewhere, but not dealt with)
## symObj can be null here
if(is.null(symObj)) {
if(nestedLeftSide) stop('Cannot find nested nimbleList definition')
nlGenName <- deparse(leftSide)
if(exists(nlGenName, where = globalenv())) {
possibleNLgen <- get(nlGenName, envir = globalenv())
if(is.nlGenerator(possibleNLgen)) {
thisFunctionMatch <- makeNimbleListTemplateWithBlankFirstArg(nl.getListDef(possibleNLgen))
} else {
stop(paste0('problem with ', deparse(code)))
}
} else {
stop(paste0('problem with ', deparse(code)))
}
} else {
thisFunctionMatch <- makeNimbleListTemplateWithBlankFirstArg(nl.getListDef(symObj$nlProc$nlGenerator))
}
for(i in seq_along(code[-1])) code[[i+1]] <- matchKeywords_recurse(code[[i+1]], nfProc)
code[[ length(code) + 1]] <- leftSide ## add '.LEFTSIDE = leftSide' arg to code
names(code)[length(code)] <- '.LEFTSIDE'
code[[1]] <- as.name('makeNewNimbleListObject') ## modify first arg of code to be desired name of call
return(matchAndFill.call(thisFunctionMatch, code ) ) ## should create makeNewNimbleListObject( nimbleListCallMaybeNested, var1, var2, etc.)
}
if(is.null(symObj)) stop('Problem looking up object')
if(symObj$type == 'nimbleFunction') {
thisRCfunProc <- symObj$nfProc$RCfunProcs[[memFunName]]
if(is.null(thisRCfunProc)) stop(paste0("Cannot handle this expression (member function may not exist): ", deparse(code)), call. = FALSE)
thisFunctionMatch <- thisRCfunProc$RCfun$template
return(matchAndFill.call(thisFunctionMatch, code ) )
}
if(inherits(symObj, 'symbolModel')) {
if(nestedLeftSide) stop('Access to a model cannot be nested.')
thisFunctionMatch <- matchModelMemberFunctions[[ memFunName ]]
if(is.null(thisFunctionMatch)) stop(paste0("Cannot handle this expression (looks like a model with an invalid member function call?): ", deparse(code)))
return(matchAndFill.call(thisFunctionMatch, code) )
}
if(inherits(symObj, 'symbolNimbleFunctionList')) {
thisBaseClass <- symObj$baseClass
thisFunctionMatch <- environment(symObj$baseClass)$methodList[[memFunName]]$template
return(matchAndFill.call(thisFunctionMatch, code ) )
}
stop(paste0("Cannot handle this expression: ", deparse(code)))
}
matchKeywordCode <- function(code, nfProc){
callName <- as.character(code[[1]])
thisFunctionMatch <- matchFunctions[[ callName ]]
## see if this is a member function of an nf object
if(!is.null(nfProc)) {
modCallName <- callName
if(nfProc$setupSymTab$symbolExists(modCallName)) {
symObj <- nfProc$setupSymTab$getSymbolObject(modCallName)
if(inherits(symObj, "symbolMemberFunction")) {
thisRCfunProc <- nfProc$RCfunProcs[[modCallName]]
if(is.null(thisRCfunProc)) stop(paste0("Cannot handle this expression (looks like a member function but something is wrong): ", deparse(code)), call. = FALSE)
thisFunctionMatch <- thisRCfunProc$RCfun$template
return(matchAndFill.call(thisFunctionMatch, code ) )
}
}
}
## see if this is a call to an RCfunction
if(is.null(thisFunctionMatch)) {
if(exists(callName)) {
callObj <- get(callName)
if(is.rcf(callObj)) {
thisFunctionMatch <- callObj
}
}
}
if(!is.null(thisFunctionMatch))
return(matchAndFill.call(thisFunctionMatch, code ) )
return(code)
}
matchKeywords_recurse <- function(code, nfProc = NULL) {
cl = length(code)
if(cl == 1){ ## There are no arguments
if(is.call(code)){
if(length(code[[1]]) > 1) {
if(deparse(code[[1]][[1]]) == '$') code <- matchKeywordCodeMemberFun(code, nfProc)
else
code[[1]] <- matchKeywords_recurse(code[[1]], nfProc) ## recurse on the "a$b" part of a$b() (or the "a(b)" part of a(b)()), etc
} else
code <- matchKeywordCode(code, nfProc)
}
return(code)
}
if(length(code[[1]]) == 1) ## a simple call like a(b,c), not a$b(c)
code <- matchKeywordCode(code, nfProc)
if(is.call(code)) {
if(length(code[[1]]) > 1) {
if(deparse(code[[1]][[1]]) == '$') code <- matchKeywordCodeMemberFun(code, nfProc) ## handle a$b(c) as one unit
else code[[1]] <- matchKeywords_recurse(code[[1]], nfProc) ## handle "a(b)" part of a(b)(c), which is probably *never* triggered
}
if(cl >= 2) { ## recurse through arguments
for(i in 2:cl) {
code[[i]] <- matchKeywords_recurse(code[[i]], nfProc)
}
}
}
return(code)
}
makeSingleIndexAccessExpr <- function(newName, newNameExpr) {
codeNames <- makeSingleIndexAccessCodeNames(newName)
subList <- lapply(codeNames, as.name)
ans <- substitute( name[MflatIndex], c(list(name = newNameExpr), subList))
ans
}
## want map(name, nDim, offset, sizelist, stridelist)
## this is a unique case, where sizelist and stridelist are just lists
## stuck in there
makeMapAccessExpr <- function(newName, newNameExpr, nDim) { ## newNameExpr not used any more!
codeNames <- makeMapSetupCodeNames(newName)
subList <- lapply(codeNames, as.name)
if(nDim == 0) { ## not sure this can happen
sizeExprList <- strideExprList <- list()
}
if(nDim == 1) {
sizeExprList <- list(substitute(Msizes, subList))
strideExprList <- list(substitute(Mstrides, subList))
}
if(nDim >= 2) {
sizeExprList <- rep(list( substitute(Msizes[1], subList)), nDim)
for(i in 1:nDim) sizeExprList[[i]][[3]] <- i
strideExprList <- rep(list( substitute(Mstrides[1], subList)), nDim)
for(i in 1:nDim) strideExprList[[i]][[3]] <- i
}
ans <- substitute(map( name, nDim, Moffset, sizes, strides),
c(subList, list(nDim = nDim, name = newName, sizes = sizeExprList, strides = strideExprList)))
ans
}
determineNdimFromOneCase <- function(model, varAndIndices) {
varInfo <- try(model$getVarInfo(as.character(varAndIndices$varName)))
if(inherits(varInfo, 'try-error')) stop(paste0('In determineNdimFromOneCase: error in extracting varInfo for ', varAndIndices$varName), call. = FALSE)
varNdim <- varInfo$nDim
if(length(varAndIndices$indices) == 0) return(varNdim)
if(length(varAndIndices$indices) != varNdim) {
stop(paste0('Error, wrong number of dimensions in a node label for ', varAndIndices$varName, '. Expected ',varNdim,' indices but got ', length(varAndIndices$indices),'.'))
}
dropNdim <- sum(unlist(lapply(varAndIndices$indices, is.numeric)))
return(varNdim - dropNdim)
}
## steps here are similar to makeMapExprFromBrackets, but that uses exprClasses
varAndIndices2mapParts <- function(varAndIndices, sizes, nDim) {
indices <- varAndIndices$indices
## put together offsetExpr, sizeExprs, strideExprs
## need sizes to get strides
if(length(sizes) == 0) sizes <- 1
if(nDim > 0 & length(indices)==0) {
blockBool <- rep(TRUE, nDim)
firstIndexRexprs <- rep(list(1), nDim)
targetSizes <- sizes
} else {
nDim <- length(indices) ## may be redundant/moot
firstIndexRexprs <- vector('list', nDim)
targetSizes <- integer(nDim)
blockBool <- rep(FALSE, nDim)
for(i in seq_along(indices)) {
if(is.blank(indices[[i]])) {
blockBool[i] <- TRUE
firstIndexRexprs[[i]] <- 1
targetSizes[i] <- sizes[i]
}
else if(is.numeric(indices[[i]])) {
firstIndexRexprs[[i]] <- indices[[i]]
} else {
## better be :
if(indices[[i]][[1]] != ":") stop("error, expecting : here")
blockBool[i] <- TRUE
firstIndexRexprs[[i]] <- indices[[i]][[2]]
targetSizes[i] <- indices[[i]][[3]] - indices[[i]][[2]] + 1
}
}
}
strides <- c(1, cumprod(sizes[-length(sizes)]))
sourceStrideRexprs <- as.list(strides)
targetOffsetRexpr <- makeOffsetRexpr(firstIndexRexprs, sourceStrideRexprs)
targetStrides <- strides[blockBool]
targetSizes <- targetSizes[blockBool]
list(offset = eval(targetOffsetRexpr),
sizes = targetSizes,
strides = targetStrides)
}
getVarAndIndices <- function(code) {
if(is.character(code)) code <- parse(text = code, keep.source = FALSE)[[1]]
if(length(code) > 1) {
if(code[[1]] == '[') {
varName <- code[[2]]
indices <- as.list(code[-c(1,2)])
} else {
stop(paste('Error:', deparse(code), 'is a malformed node label.'))
}
} else {
varName <- code
indices <- list()
}
list(varName = varName, indices = indices)
}
## This takes the indices field returned by getVarAndIndices and turns it into a matrix
## e.g. from getVarAndIndices('x[1:3, 2:4]'), we have varName = 'x' and indices = list(quote(1:3), quote(2:4))
## indexExprs2matrix takes the indices and makes [1 3; 2 4]
varAndIndices2flatIndex <- function(varAndIndices, varInfo) {
if(length(varInfo$maxs) == 0) return(1) ## A -1 is done automatically, later, so here we should stay in R's 1-based indexing
sizes <- varInfo$maxs
strides <- c(1, cumprod(sizes[-length(sizes)]))
flatIndex <- 1 + sum((unlist(varAndIndices$indices)-1) * strides)
flatIndex
}
makeMapSetupCodeNames <- function(baseName) {
list(Mstrides = paste0(baseName, '_strides'),
Msizes = paste0(baseName, '_sizes'),
Moffset = paste0(baseName, '_offset'))
}
makeSingleIndexAccessCodeNames <- function(baseName) {
list(MflatIndex = paste0(baseName, '_flatIndex'))
}
handleScaleAndRateForGamma <- function(code){
## also handles core R dexp, as well as ddexp, and dinvgamma
scaleArg <- code$scale
rateArg <- code$rate
if(is.null(scaleArg) && is.null(rateArg)) stop('neither scale nor rate defined in dgamma, invgamma, dexp, or ddexp')
codeName <- deparse(code[[1]])
dist <- substring(codeName, 2, nchar(codeName))
if(dist == 'invgamma' || dist == 'sqrtinvgamma') { ## For [drpq]invgamma
if(is.null(rateArg)) {
rateArg <- substitute(1.0/(A), list(A = code$scale))
code$scale <- rateArg
names(code)[which(names(code) == 'scale')] <- 'rate' # to preserve correct order
}
code$scale <- NULL
} else if(dist == 'dexp') { ## This is for [drpq]dexp
## The logic here is trickier. scale has a default value and is canonical (what is needed for C).
## If rate was provided, then by the time we are here, matchFunctions has been used (matchAndFill.call),
## so there will also be a scale, since it has a default
setScaleArg <- FALSE
if(is.null(scaleArg)) setScaleArg <- TRUE ## scale is not expected to be null ever (see previous comment), but this is defensive.
if(!is.null(scaleArg) & !is.null(rateArg)) setScaleArg <- TRUE ## Both are there, so set scale from the provided rate
if(setScaleArg) {
code$scale <- NULL
scaleArg <- substitute(1.0/(A), list(A = code$rate))
code$rate <- scaleArg
names(code)[which(names(code) == 'rate')] <- 'scale' # to preserve correct order
}
code$rate <- NULL
} else { # dgamma
if(is.null(scaleArg)) {
scaleArg <- substitute(1.0/(A), list(A = code$rate))
code$rate <- scaleArg
names(code)[which(names(code) == 'rate')] <- 'scale' # to preserve correct order
}
code$rate <- NULL
}
return(code)
}
handleScaleAndRateForExpNimble <- function(code){
scaleArg <- code$scale
rateArg <- code$rate
if(is.null(scaleArg) && is.null(rateArg)) stop('neither scale nor rate defined in dexp_nimble')
if(is.null(rateArg)) {
rateArg <- substitute(1.0/(A), list(A = code$scale))
code$scale <- rateArg
names(code)[which(names(code) == 'scale')] <- 'rate' # to preserve correct order
}
code$scale <- NULL
return(code)
}
## wrtNodes are nodes with respect to which derivatives will be taken
## (i.e. denominator of dy/dx). wrtNodes may or may not be part of
## calcNodes
## extraInputNodes are nodes needed in calculation of derivatives but
## are not wrtNodes. They include two categories: (i) parents of
## any calcNodes that are not themselves calcNodes or wrtNodes;
## (ii) any stochastic calcNodes, because the node values are needed.
## However, stochastic calcNodes that are in constantNodes are not
## included in extraInputNodes.
## constantNodes are nodes that are assumed to be constant for all
## derivative calls throughout the life of the nimbleFunction.
## They will be baked in to the CppAD tape and cannot then be changed.
## They will typically be model data.
## modelOutputNodes are nodes whose values are calculated as part of the
## tape "forward-zero" stage (value calculation) and need to be stored
## in the model. It appears more efficient to copy them in to the model
## than to use the regular model$calculate() itself.
## modelOutputNodes will include all deterministic nodes in calcNodes
## as well as the logProb_ node for any stochastic nodes in calcNodes.
## calcNodes is the same as calcNodes for model$calculate(calcNodes). It is
## the ordered sequence of nodes to be calculated
nimDerivsInfoClass_init_impl <- function(.self
, wrtNodes
, calcNodes
, model) {
.self$model <- model
## wrt nodes
wrtNodes <- model$expandNodeNames(wrtNodes, returnScalarComponents = TRUE)
wrtNodesAccessor <- modelVariableAccessorVector(model,
wrtNodes,
logProb = FALSE)
.self$wrtMapInfo <- makeMapInfoFromAccessorVectorFaster(wrtNodesAccessor)
# See comment in makeModelDerivsInfo for explanation of why both of the next
# two lines are necessary.
calcNodes <- model$expandNodeNames(calcNodes)
calcNodes <- model$expandNodeNames(calcNodes, returnScalarComponents = TRUE)
derivsInfo <- makeModelDerivsInfo_impl(model,
wrtNodes,
calcNodes,
dataAsConstantNodes = TRUE)
constantNodes <- derivsInfo$constantNodes
updateNodes <- derivsInfo$updateNodes
extraInputNodesAccessor <- modelVariableAccessorVector(model,
updateNodes,
logProb = FALSE)
.self$extraInputMapInfo <-
makeMapInfoFromAccessorVectorFaster(extraInputNodesAccessor)
constantNodesAccessor <- modelVariableAccessorVector(model,
constantNodes,
logProb = FALSE)
.self$constantMapInfo <- makeMapInfoFromAccessorVectorFaster(constantNodesAccessor)
## output nodes: deterministic nodes in calcNodes plus logProb nodes
## but not the actual data nodes.
modelOutputNodes <- makeOutputNodes(model, calcNodes)
modelOutputNodesAccessor <- modelVariableAccessorVector(model,
modelOutputNodes,
logProb = FALSE)
.self$modelOutputMapInfo <-
makeMapInfoFromAccessorVectorFaster(modelOutputNodesAccessor)
NULL
}
makeOutputNodes <- function(model,
calcNodes) {
## Need to do `isDeterm` on nodes, not node components (issue 1431).
## Presuming (and based on a simple test) that by now,
## input `calcNodes` would include all encompassing nodes
## and that this next step would not introduce any additional components.
calcNodes <- model$expandNodeNames(calcNodes)
logProbCalcNodeNames <- model$modelDef$nodeName2LogProbName(calcNodes)
isDetermCalcNodes <- model$isDeterm(calcNodes, nodesAlreadyExpanded = TRUE)
modelOutputNodes <- c(model$expandNodeNames(calcNodes[isDetermCalcNodes], returnScalarComponents = TRUE),
logProbCalcNodeNames)
modelOutputNodes
}
nimDerivsInfoClass_output_init_impl <- function(.self,
calcNodes,
model) {
.self$model <- model
wrtNodesAccessor <- modelVariableAccessorVector(model,
character(),
logProb = FALSE)
.self$wrtMapInfo <- makeMapInfoFromAccessorVectorFaster(wrtNodesAccessor)
constantNodesAccessor <- modelVariableAccessorVector(model,
character(),
logProb = FALSE)
.self$constantMapInfo <- makeMapInfoFromAccessorVectorFaster(constantNodesAccessor)
extraInputNodesAccessor <- modelVariableAccessorVector(model,
character(),
logProb = FALSE)
.self$extraInputMapInfo <-
makeMapInfoFromAccessorVectorFaster(extraInputNodesAccessor)
modelOutputNodes <- makeOutputNodes(model, calcNodes)
modelOutputNodesAccessor <- modelVariableAccessorVector(model,
modelOutputNodes,
logProb = FALSE)
.self$modelOutputMapInfo <-
makeMapInfoFromAccessorVectorFaster(modelOutputNodesAccessor)
NULL
}
#' Information on model structure used for derivatives
#'
#' Inspect structure of a nimble model to determine nodes needed as "update"
#' and/or "constant" entries in usage of nimDerivs. This will typically be used
#' in the setup code of a nimbleFunction.
#'
#' @param model a nimble model object, such as returned from \code{nimbleModel}.
#' @param wrtNodes a character vector of node names in the model with respect to
#' which derivatives will be taken through a call to \code{nimDerivs} (same as
#' \code{derivs}).
#' @param calcNodes a character vector of node names in the model that will be
#' used in \code{model$calculate(calcNodes)} while derivatives are being
#' recorded.
#' @param dataAsConstantNodes logical indicating whether data nodes in the model
#' should automatically be treated as "constant" entries (TRUE) or "update"
#' entries (FALSE). Defaults to TRUE.
#'
#' @details In the compilable parts of a \code{nimbleFunction} (i.e. \code{run}
#' or other method code, not \code{setup} code), a call like
#' \code{nimDerivs(foo(x), ...)} records derivatives of \code{foo(x)}. If
#' \code{foo} contains any calls to \code{model$calculate(calcNodes)}, it may
#' be necessary to provide auxiliary information about the model in further
#' arguments to \code{nimDerivs}, specifically the \code{model},
#' \code{updateNodes} and \code{constantNodes} arguments.
#' `makeModelDerivsInfo` is a utility to set up that information for typical
#' use cases. It returns a list with elements \code{updateNodes} and
#' \code{constantNodes} to be passed as arguments of the same name to
#' \code{nimDerivs} (along with passing the \code{model} as the \code{model}
#' argument).
#'
#' The reason auxiliary information is needed is that recording of derivatives
#' uses a different model than for regular calculations. Together,
#' \code{updateNodes} and \code{constantNodes} should contain all nodes whose
#' values are needed for the model calculations being recorded and that are not
#' part of \code{wrtNodes}. These may include parents of nodes that are in
#' \code{calcNodes} but are not themselves in \code{calcNodes}, as well as the
#' values of stochastic nodes in \code{calcNodes}, which are needed to calculate
#' the corresponding log probabilities. \code{updateNodes} will have their
#' values updated from the regular model every time that recorded derivative
#' calculations are used. \code{constantNodes} will not be updated every time,
#' which means their values will be permanently fixed either the first time the
#' call to `nimDerivs` is invoked or on any subsequent call that has
#' \code{reset=TRUE}. Use of \code{constantNodes} can be slightly more
#' efficient, but one must be careful to be aware that values will not be
#' updated unless \code{reset=TRUE}. See the automatic differentiation section
#' of the User Manual for more information.
#'
#' In the above explanation, care must be taken to understand what should be
#' included in \code{wrtNodes}. In a typical use case, some arguments to
#' \code{foo} are put into the model using \code{values(model, nodes) <-
#' some_foo_arguments}. Next there is typically a call to
#' \code{model$calculate(calcNodes)}. Here the \code{nodes} are considered
#' "with-respect-to" nodes because derivative tracking will follow the arguments
#' of \code{foo}, including when they are put into a model and hence used in
#' \code{model$calculate}. Therefore these \code{nodes} should be the
#' \code{wrtNodes} for \code{makeModelDerivsInfo}.
#'
#' @return A list with elements \code{updateNodes} and \code{constantNodes}.
#' These shouls be provided as the same-named arguments to \code{nimDerivs}
#' (same as \code{derivs}).
#'
#' When using double-taping of derivatives (i.e. \code{foo} contains another
#' call to \code{nimDerivs}), both calls to \code{nimDerivs} should include the
#' \code{model}, \code{updateNodes}, and \code{constantNodes} arguments.
#'
#' @export
makeModelDerivsInfo <- function(model,
wrtNodes,
calcNodes,
dataAsConstantNodes = TRUE) {
wrtNodes <- model$expandNodeNames(wrtNodes, returnScalarComponents = TRUE)
# This ensures that elements of a non-scalar node become the entire non-scalar node.
calcNodes <- model$expandNodeNames(calcNodes)
# And then this splits into scalar components.
# E.g. if calcNodes is 'mu[1]' but 'mu[1:3]' is a vector node,
# the above call gets `mu[1:3]` and then the below call splits it.
calcNodes <- model$expandNodeNames(calcNodes, returnScalarComponents = TRUE)
makeModelDerivsInfo_impl(model,
wrtNodes,
calcNodes,
dataAsConstantNodes)
}
getImmediateParentNodes <- function(nodes, model) {
## adapted from BUGS_modelDef creation of edgesFrom2To
maps <- model$modelDef$maps
maxNodeID <- length(maps$vertexID_2_nodeID) ## should be same as length(maps$nodeNames)
edgesLevels <- if(maxNodeID > 0) 1:maxNodeID else numeric(0)
fedgesTo <- factor(maps$edgesTo, levels = edgesLevels) ## setting levels ensures blanks inserted into the splits correctly
edgesTo2From <- split(maps$edgesFrom, fedgesTo)
nodeIDs <- model$expandNodeNames(nodes, returnType = "ids")
fromIDs <- sort(unique(unlist(edgesTo2From[nodeIDs])))
fromNodes <- maps$graphID_2_nodeName[fromIDs]
fromNodes
}
makeModelDerivsInfo_impl <- function(model,
wrtNodes,
calcNodes,
dataAsConstantNodes = TRUE) {
## Gymnastics to convert to actual nodes for computational efficiency are needed because `setdiff` needs to
## operate on node components because `wrt` is in terms of components not nodes.
nonWrtCalcNodes <- setdiff(calcNodes, wrtNodes) # Node components here, since `calcNodes`, `wrtNodes` are as components upon input.
nonWrtCalcActualNodes <- model$expandNodeNames(nonWrtCalcNodes) # Nodes here. Can be costly for large multivar nodes (say 3 sec. for a 1m-element node).
nonWrtStochCalcNodes <- nonWrtCalcActualNodes[ model$isStoch(nonWrtCalcActualNodes,
nodesAlreadyExpanded = TRUE) ] # Run `isStoch` on nodes not components (issue #1431).
parentNodes <- getImmediateParentNodes(calcNodes, model)
parentNodes <- model$expandNodeNames(parentNodes, returnScalarComponents = TRUE)
neededParentNodes <- setdiff(parentNodes, c(wrtNodes, nonWrtCalcNodes))
extraInputNodes <- model$expandNodeNames(c(neededParentNodes,
nonWrtStochCalcNodes)) # Need as nodes so `isData` below run on nodes for efficiency.
constantNodes <- character()
if(dataAsConstantNodes) {
boolData <- model$isData(extraInputNodes)
constantNodes <- model$expandNodeNames(extraInputNodes[boolData], returnScalarComponents = TRUE, sort = TRUE)
extraInputNodes <- model$expandNodeNames(extraInputNodes[!boolData], returnScalarComponents = TRUE, sort = TRUE)
## `wrtNodes` components could have crept in when initializing `extraInputNodes` based on nodes.
extraInputNodes <- setdiff(extraInputNodes, wrtNodes)
constantNodes <- setdiff(constantNodes, wrtNodes)
} else {
extraInputNodes <- model$expandNodeNames(extraInputNodes, returnScalarComponents = TRUE, sort = TRUE)
## `wrtNodes` components could have crept in when initializing `extraInputNodes` based on nodes.
extraInputNodes <- setdiff(extraInputNodes, wrtNodes)
}
list(updateNodes = extraInputNodes,
constantNodes = constantNodes)
}
nimDerivsInfoClass_update_init_impl <- function(.self,
updateNodes = NULL,
constantNodes = NULL,
model) {
if(is.null(updateNodes)) updateNodes <- character()
if(is.null(constantNodes)) constantNodes <- character()
.self$model <- model
wrtNodesAccessor <- modelVariableAccessorVector(model,
character(),
logProb = FALSE)
.self$wrtMapInfo <- makeMapInfoFromAccessorVectorFaster(wrtNodesAccessor)
constantNodesAccessor <- modelVariableAccessorVector(model,
constantNodes,
logProb = FALSE)
.self$constantMapInfo <- makeMapInfoFromAccessorVectorFaster(constantNodesAccessor)
extraInputNodesAccessor <- modelVariableAccessorVector(model,
updateNodes,
logProb = FALSE)
.self$extraInputMapInfo <-
makeMapInfoFromAccessorVectorFaster(extraInputNodesAccessor)
modelOutputNodesAccessor <- modelVariableAccessorVector(model,
character(),
logProb = FALSE)
.self$modelOutputMapInfo <-
makeMapInfoFromAccessorVectorFaster(modelOutputNodesAccessor)
NULL
}
nimDerivsInfoClass <- setRefClass(
'nimDerivsInfoClass',
fields = list(
wrtMapInfo = 'ANY'
, extraInputMapInfo = 'ANY'
, modelOutputMapInfo = 'ANY'
, constantMapInfo = 'ANY'
, model = 'ANY'
),
methods = list(
initialize = function(wrtNodes = NULL,
calcNodes = NULL,
updateNodes = NULL,
constantNodes = NULL,
thisModel = NULL,
case = "nimDerivsCalculate",
...) {
if(!isTRUE(thisModel$modelDef$buildDerivs)) {
stop(paste0("To use automatic differentiation involving model calculations,\n",
"include 'buildDerivs = TRUE' in the call to 'nimbleModel' or set\n",
"'nimbleOptions(buildModelDerivs = TRUE)' before calling 'nimbleModel'."), call. = FALSE)
}
switch(case,
nimDerivsCalculate = nimDerivsInfoClass_init_impl(.self = .self,
wrtNodes = wrtNodes,
calcNodes = calcNodes,
model = thisModel),
updateOnly = nimDerivsInfoClass_update_init_impl(.self = .self,
updateNodes = updateNodes,
constantNodes = constantNodes,
model = thisModel),
outputOnly = nimDerivsInfoClass_output_init_impl(.self = .self,
calcNodes = calcNodes,
model = thisModel)
)
}
)
)
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nimble documentation built on June 22, 2024, 9:49 a.m.
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Defines functions nimDerivsInfoClass_update_init_impl makeModelDerivsInfo_impl getImmediateParentNodes makeModelDerivsInfo nimDerivsInfoClass_output_init_impl makeOutputNodes nimDerivsInfoClass_init_impl handleScaleAndRateForExpNimble handleScaleAndRateForGamma makeSingleIndexAccessCodeNames makeMapSetupCodeNames varAndIndices2flatIndex getVarAndIndices varAndIndices2mapParts determineNdimFromOneCase makeMapAccessExpr makeSingleIndexAccessExpr matchKeywords_recurse matchKeywordCode matchKeywordCodeMemberFun determineNdimsFromNfproc matchAndFill.call isSymbolType symTypeFromSymTab getSymObj_recurse addNecessarySetupCode addNewCode addBlockFromCppName addSetupCodeNames isSetupCodeGenerated isCodeArgBlank code2Name_fromArgList processKeywords_recurse processKeywordCodeMemberFun processKeyword addDistList2matchFunctions stripArgs ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ]
Documented in makeModelDerivsInfo
###### KEYWORD PROCESSING OBJECTS
### CLASSES
# keywordInfoClass is a class which contains the processor for each keyword
keywordInfoClass <- setRefClass('keywordInfoClass',
fields = list(
keyword = 'ANY',
processor = 'ANY'))
# setupCodeTemplateClass is a class that contains the template for generating
# new setupCode. Objects of this class are used by the function addNecessarySetupCode
setupCodeTemplateClass <- setRefClass('setupCodeTemplateClass',
fields = list(
makeName = 'ANY',
codeTemplate = 'ANY',
makeCodeSubList = 'ANY',
makeOtherNames = 'ANY'),
methods = list(
initialize = function(...){
makeOtherNames <<- function(name, argList) return(character(0))
callSuper(...)
}
) )
### KEYWORD INFO OBJECTS
d_gamma_keywordInfo <- keywordInfoClass(
keyword = 'dgamma',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForGamma(code)
return(code)
})
pq_gamma_keywordInfo <- keywordInfoClass(
keyword = 'pq_gamma',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForGamma(code)
return(code)
})
rgamma_keywordInfo <- keywordInfoClass(
keyword = 'rgamma',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForGamma(code)
return(code)
}
)
d_exp_nimble_keywordInfo <- keywordInfoClass(
keyword = 'dexp_nimble',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForExpNimble(code)
return(code)
})
pq_exp_nimble_keywordInfo <- keywordInfoClass(
keyword = 'pq_exp_nimble',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForExpNimble(code)
return(code)
})
rexp_nimble_keywordInfo <- keywordInfoClass(
keyword = 'rexp_nimble',
processor = function(code, nfProc, RCfunProc){
code <- handleScaleAndRateForExpNimble(code)
return(code)
}
)
besselK_keywordInfo <- keywordInfoClass(
keyword = 'besselK',
processor = function(code, nfProc, RCfunProc) {
expon.scaledArg <- code$expon.scaled
if(is.null(expon.scaledArg))
expon.scaledArg <- FALSE
if(is.numeric(expon.scaledArg) || is.logical(expon.scaledArg)) {
code$expon.scaled <- 1 + as.logical(expon.scaledArg)
} else code$expon.scaled <- substitute(1 + A, list(A = expon.scaledArg))
return(code)
}
)
nimSeq_keywordInfo <- keywordInfoClass(
keyword = 'nimSeq',
processor = function(code, nfProc, RCfunProc) {
useBy <- !isCodeArgBlank(code, 'by')
useLen <- !isCodeArgBlank(code, 'length.out')
if(useBy && useLen)
newRunCode <- substitute(nimSeqByLen(FROM, 0, BY, LEN), list(FROM = code$from, BY = code$by, LEN = code$length.out))
else {
if(useLen) {
newRunCode <- substitute(nimSeqLen(FROM, TO, 0, LEN), list(FROM = code$from, TO = code$to, LEN = code$length.out))
} else {
byVal <- if(useBy) code$by else 1 ## default by = 1
newRunCode <- substitute(nimSeqBy(FROM, TO, BY, 0), list(FROM = code$from, TO = code$to, BY = byVal))
}
}
return(newRunCode)
}
)
values_keywordInfo <- keywordInfoClass(
keyword = 'values',
processor = function(code, nfProc, RCfunProc){
if(!isCodeArgBlank(code, 'accessor'))
return(code)
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from values call, with no accessor argument supplied')
accessArgList <- list(model = code$model, nodes = code$nodes, logProb = FALSE, logProbOnly = FALSE)
useAccessorVectorByIndex <- FALSE
if(hasBracket(accessArgList$nodes)) {
useAccessorVectorByIndex <- TRUE
if(length(accessArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- accessArgList$nodes[[3]]
accessArgList$nodes <- accessArgList$nodes[[2]]
accessArgList$sortUnique <- FALSE
}
accessName <- modelVariableAccessorVector_setupCodeTemplate$makeName(accessArgList)
addNecessarySetupCode(accessName, accessArgList, modelVariableAccessorVector_setupCodeTemplate, nfProc)
if(!useAccessorVectorByIndex)
newRunCode <- substitute(values(accessor = ACCESS_NAME),
list(ACCESS_NAME = as.name(accessName)))
else
newRunCode <- substitute(values(accessor = ACCESS_NAME, accessorIndex = ACCESSVECINDEX),
list(ACCESS_NAME = as.name(accessName), ACCESSVECINDEX = nodesIndexExpr))
return(newRunCode)
})
getParam_keywordInfo <- keywordInfoClass(
keyword = 'getParam',
processor = function(code, nfProc, RCfunProc) {
if(!isCodeArgBlank(code, 'nodeFunction'))
return(code)
errorContext <- deparse(code)
nodeFunVec_ArgList <- list(model = code$model, nodes = code$node, includeData = TRUE, sortUnique = TRUE, errorContext = errorContext)
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to getParam if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from getParam, with no accessor argument supplied')
if(isCodeArgBlank(code, 'node'))
stop('node argument missing from getParam, with no accessor argument supplied')
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE
}
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
if(isCodeArgBlank(code, 'param'))
stop("'param' argument missing from 'getParam', with no accessor argument supplied")
## Avoid situations where user has syntax from run code in `param` or of getting anything from global env (issue 1344).
paramVars <- all.vars(code$param)
wh <- which(!paramVars %in% nfProc$setupSymTab$getSymbolNames())
if(length(wh))
stop("`param` argument in `getParam` contains variables not found in setup code: ", paste(paramVars[wh], collapse = ", "), ".")
paramInfo_ArgList <- list(model = code$model, node = nodeFunVec_ArgList$nodes, param = code$param, hasIndex = useNodeFunctionVectorByIndex) ## use nodeFunVec_ArgList$nodes instead of code$node because nodeFunVec_ArgList$nodes may have been updated if code$nodes has a run-time index. In that case the paramID will be vector
paramInfoName <- paramInfo_SetupTemplate$makeName(paramInfo_ArgList)
paramIDname <- paramInfo_SetupTemplate$makeOtherNames(paramInfoName, paramInfo_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
addNecessarySetupCode(paramInfoName, paramInfo_ArgList, paramInfo_SetupTemplate, nfProc)
if(!useNodeFunctionVectorByIndex)
newRunCode <- substitute(getParam(nodeFunction = NODEFUNVEC_NAME, paramID = PARAMID_NAME, paramInfo = PARAMINFO_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName), PARAMID_NAME = as.name(paramIDname), PARAMINFO_NAME = as.name(paramInfoName)))
else
newRunCode <- substitute(getParam(nodeFunction = NODEFUNVEC_NAME, paramID = PARAMID_NAME, paramInfo = PARAMINFO_NAME, nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName), PARAMID_NAME = as.name(paramIDname), PARAMINFO_NAME = as.name(paramInfoName), NODEFUNVECINDEX = nodesIndexExpr))
return(newRunCode)
}
)
getBound_keywordInfo <- keywordInfoClass(
keyword = 'getBound',
processor = function(code, nfProc, RCfunProc) {
if(!isCodeArgBlank(code, 'nodeFunction'))
return(code)
errorContext <- deparse(code)
nodeFunVec_ArgList <- list(model = code$model, nodes = code$node, includeData = TRUE, sortUnique = TRUE, errorContext = errorContext)
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to getParam if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from getParam, with no accessor argument supplied')
if(isCodeArgBlank(code, 'node'))
stop('node argument missing from getParam, with no accessor argument supplied')
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE
}
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
if(isCodeArgBlank(code, 'bound'))
stop("'bound' argument missing from 'getBound', with no accessor argument supplied")
boundInfo_ArgList <- list(model = code$model, node = nodeFunVec_ArgList$nodes, bound = code$bound) ## use nodeFunVec_ArgList$nodes instead of code$node because nodeFunVec_ArgList$nodes may have been updated if code$nodes has a run-time index. In that case the boundID will be vector
boundInfoName <- boundInfo_SetupTemplate$makeName(boundInfo_ArgList)
boundIDname <- boundInfo_SetupTemplate$makeOtherNames(boundInfoName, boundInfo_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
addNecessarySetupCode(boundInfoName, boundInfo_ArgList, boundInfo_SetupTemplate, nfProc)
if(!useNodeFunctionVectorByIndex)
newRunCode <- substitute(getBound(nodeFunction = NODEFUNVEC_NAME, boundID = BOUNDID_NAME, boundInfo = BOUNDINFO_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName), BOUNDID_NAME = as.name(boundIDname), BOUNDINFO_NAME = as.name(boundInfoName)))
else
newRunCode <- substitute(getBound(nodeFunction = NODEFUNVEC_NAME, boundID = BOUNDID_NAME, boundInfo = BOUNDINFO_NAME, nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName), BOUNDID_NAME = as.name(boundIDname), BOUNDINFO_NAME = as.name(boundInfoName), NODEFUNVECINDEX = nodesIndexExpr))
return(newRunCode)
}
)
calculate_keywordInfo <- keywordInfoClass(
keyword = 'calculate',
processor = function(code, nfProc, RCfunProc){
if(!isCodeArgBlank(code, 'nodeFxnVector'))
return(code)
errorContext <- deparse(code)
buildDerivs <- FALSE
withDerivsOutputOnly <- FALSE
if(isTRUE(getNimbleOption("enableDerivs"))) {
derivControl <- environment(nfProc$nfGenerator)$buildDerivs[[RCfunProc$name]]
## There are two cases.
## If buildDerivs has an entry, then derivatives are enabled either
## explicitly or because of a nimDerivs(model$calculate), i.e. a direct line into derivs for just a model calculation.
##
## These need to be disambiguated for use below to choose the right setup template case
buildDerivs <- !is.null(derivControl) | !is.null(code$wrt)
withDerivsOutputOnly <- buildDerivs & is.null(code$wrt) ## This is the case of *not* nimDerivs(model$calculate)
}
nodeFunVec_ArgList <- list(model = code$model, nodes = code$nodes, wrtNodes = code$wrt,
includeData = TRUE, sortUnique = TRUE, errorContext = errorContext)
##
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to calculate if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from calculate, with no accessor argument supplied')
if(isCodeArgBlank(code, 'nodes')){
LHSnodes_ArgList <- list(model = code$model)
LHSnodes_name <- allLHSNodes_SetupTemplate$makeName(LHSnodes_ArgList)
addNecessarySetupCode(LHSnodes_name, LHSnodes_ArgList, allLHSNodes_SetupTemplate, nfProc, allowToCpp = FALSE)
nodeFunVec_ArgList$nodes = as.name(LHSnodes_name)
}
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
if(buildDerivs)
stop(paste0('Derivatives for an indexed node are not allowed.\n',
'Use nimDerivs(model$calculate(nodes), ...) instead of \n',
'nimDerivs(model$calculate(nodes[i]).\n'))
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3)
stop(paste0('Problem with ',
deparse(code),
'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE
}
if(!withDerivsOutputOnly) { ## This is regular mode, including without derivs at all and with buildDerivs but not nimDerivs(model$calculate...)
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
} else {
nodeFunName <- nodeFunctionVector_WithDerivsOutput_SetupTemplate$makeName(nodeFunVec_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_WithDerivsOutput_SetupTemplate, nfProc)
}
if(!useNodeFunctionVectorByIndex){
newRunCode <- substitute(calculate(nodeFxnVector = NODEFUNVEC_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName)))
}
else{
newRunCode <- substitute(
calculate(nodeFxnVector = NODEFUNVEC_NAME,
nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName),
NODEFUNVECINDEX = nodesIndexExpr))
}
return(newRunCode)
}
)
calculateDiff_keywordInfo <- keywordInfoClass(
keyword = 'calculateDiff',
processor = function(code, nfProc, RCfunProc){
if(!isCodeArgBlank(code, 'nodeFxnVector'))
return(code)
errorContext <- deparse(code)
nodeFunVec_ArgList <- list(model = code$model, nodes = code$nodes, includeData = TRUE, sortUnique = TRUE, errorContext = errorContext)
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to calculateDiff if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from calculateDiff, with no accessor argument supplied')
if(isCodeArgBlank(code, 'nodes')){
LHSnodes_ArgList <- list(model = code$model)
LHSnodes_name <- allLHSNodes_SetupTemplate$makeName(LHSnodes_ArgList)
addNecessarySetupCode(LHSnodes_name, LHSnodes_ArgList, allLHSNodes_SetupTemplate, nfProc, allowToCpp = FALSE)
nodeFunVec_ArgList$nodes = as.name(LHSnodes_name)
}
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE
}
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
if(!useNodeFunctionVectorByIndex)
newRunCode <- substitute(calculateDiff(nodeFxnVector = NODEFUNVEC_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName)))
else
newRunCode <- substitute(calculateDiff(nodeFxnVector = NODEFUNVEC_NAME, nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName), NODEFUNVECINDEX = nodesIndexExpr))
return(newRunCode)
}
)
simulate_keywordInfo <- keywordInfoClass(
keyword = 'simulate',
processor = function(code, nfProc, RCfunProc){
if(!isCodeArgBlank(code, 'nodeFxnVector')){
return(substitute(simulate(nodeFxnVector = NODEFXNVECTOR), list(NODEFXNVECTOR = code$nodeFxnVector) ) )
}
if(!isCodeArgBlank(code, 'INDEXEDNODEINFO_'))
return(code)
errorContext <- deparse(code)
nodeFunVec_ArgList <- list(model = code$model, nodes = code$nodes, includeData = code$includeData, sortUnique = TRUE, errorContext = errorContext)
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to simulate if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from simulate, with no accessor argument supplied')
if(isCodeArgBlank(code, 'nodes')){
LHSnodes_ArgList <- list(model = code$model)
LHSnodes_name <- allLHSNodes_SetupTemplate$makeName(LHSnodes_ArgList)
addNecessarySetupCode(LHSnodes_name, LHSnodes_ArgList, allLHSNodes_SetupTemplate, nfProc, allowToCpp = FALSE)
nodeFunVec_ArgList$nodes = as.name(LHSnodes_name)
}
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE # If includeData = FALSE, this can trigger error from nodeFunctionVector if nodes does contain data
}
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
if(!useNodeFunctionVectorByIndex)
newRunCode <- substitute(simulate(nodeFxnVector = NODEFUNVEC_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName)))
else
newRunCode <- substitute(simulate(nodeFxnVector = NODEFUNVEC_NAME, nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName), NODEFUNVECINDEX = nodesIndexExpr))
return(newRunCode)
}
)
getLogProb_keywordInfo <- keywordInfoClass(
keyword = 'getLogProb',
processor = function(code, nfProc, RCfunProc){
if(!isCodeArgBlank(code, 'nodeFxnVector'))
return(code)
errorContext <- deparse(code)
nodeFunVec_ArgList <- list(model = code$model, nodes = code$nodes, includeData = TRUE, sortUnique = TRUE, errorContext = errorContext)
if(!isCodeArgBlank(code, 'nodeFunctionIndex')) { ## new case: calculate(myNodeFunctionVector, nodeFunctionIndex = i), if myNodeFunctionVector was hand-created in setup code
if(!isCodeArgBlank(code, 'nodes'))
stop('nodes argument cannot be provided to getLogProb if nodeFunctionIndex is specified')
return(code) ## no modification needed!
}
if(isCodeArgBlank(code, 'model'))
stop('model argument missing from getLogProb, with no accessor argument supplied')
if(isCodeArgBlank(code, 'nodes')){
LHSnodes_ArgList <- list(model = code$model)
LHSnodes_name <- allLHSNodes_SetupTemplate$makeName(LHSnodes_ArgList)
addNecessarySetupCode(LHSnodes_name, LHSnodes_ArgList, allLHSNodes_SetupTemplate, nfProc, allowToCpp = FALSE)
nodeFunVec_ArgList$nodes = as.name(LHSnodes_name)
}
useNodeFunctionVectorByIndex <- FALSE
if(hasBracket(nodeFunVec_ArgList$nodes)) { ## like calculate(model, nodes[i]), which could have started as model$calculate(nodes[i])
useNodeFunctionVectorByIndex <- TRUE
if(length(nodeFunVec_ArgList$nodes) != 3) stop(paste0('Problem with ', deparse(code),'. If you need to index on the nodes argument there should be only one index.'))
nodesIndexExpr <- nodeFunVec_ArgList$nodes[[3]]
nodeFunVec_ArgList$nodes <- nodeFunVec_ArgList$nodes[[2]]
nodeFunVec_ArgList$sortUnique <- FALSE
}
nodeFunName <- nodeFunctionVector_SetupTemplate$makeName(nodeFunVec_ArgList)
addNecessarySetupCode(nodeFunName, nodeFunVec_ArgList, nodeFunctionVector_SetupTemplate, nfProc)
if(!useNodeFunctionVectorByIndex)
newRunCode <- substitute(getLogProb(nodeFxnVector = NODEFUNVEC_NAME),
list(NODEFUNVEC_NAME = as.name(nodeFunName)))
else
newRunCode <- substitute(getLogProb(nodeFxnVector = NODEFUNVEC_NAME, nodeFunctionIndex = NODEFUNVECINDEX),
list(NODEFUNVEC_NAME = as.name(nodeFunName), NODEFUNVECINDEX = nodesIndexExpr))
return(newRunCode)
}
)
nimCopy_keywordInfo <- keywordInfoClass(
keyword = 'nimCopy',
processor = function(code, nfProc, RCfunProc){
if(is.null(nfProc)) stop("Can\'t call copy (nimCopy) from a nimbleFunction without setup code")
possibleObjects <- c('symbolModel', 'symbolModelValues', 'symbolModelVariableAccessorVector', 'symbolModelValuesAccessorVector')
modelValuesTypes <- c('symbolModelValues', 'symbolModelValuesAccessorVector')
accessTypes <- c('symbolModelVariableAccessorVector', 'symbolModelValuesAccessorVector')
from_ArgList <- list(name = code$from, class = symTypeFromSymTab(code$from, nfProc$setupSymTab, options = possibleObjects))
to_ArgList <- list(name = code$to, class = symTypeFromSymTab(code$to, nfProc$setupSymTab, options = possibleObjects))
if(is.null(from_ArgList$class))
stop("Error in nimCopy: '", code$from, "' is not a recognized model or modelValues object.")
if(is.null(to_ArgList$class))
stop("Error in nimCopy: '", code$to, "' is not a recognized model or modelValues object.")
if(from_ArgList$class %in% modelValuesTypes){
if(isCodeArgBlank(code, 'row')) stop('row argument missing in copy call')
from_ArgList$row = code$row
}
if(to_ArgList$class %in% modelValuesTypes){
if(isCodeArgBlank(code, 'rowTo')){
if(isCodeArgBlank(code, 'row')) stop('row argument missing in copy call')
else to_ArgList$row = code$row
}
else to_ArgList$row = code$rowTo
}
if(isCodeArgBlank(code, 'nodes')){
if(from_ArgList$class == 'symbolModel'){
node_ArgList <- list(model = from_ArgList$name)
allNodes_name <- allModelNodes_SetupTemplate$makeName( node_ArgList )
addNecessarySetupCode(allNodes_name, node_ArgList, allModelNodes_SetupTemplate, nfProc, allowToCpp = FALSE)
}
else if(from_ArgList$class == 'symbolModelValues'){
from_ArgList$row = code$row
mvVar_ArgList <- list(modelValues = from_ArgList$name)
allNodes_name <- allModelValuesVars_SetupTemplate$makeName(mvVar_ArgList)
addNecessarySetupCode(allNodes_name, mvVar_ArgList, allModelValuesVars_SetupTemplate, nfProc, allowToCpp = FALSE)
}
from_ArgList$nodes <- as.name(allNodes_name)
}
else from_ArgList$nodes <- code$nodes
if(isCodeArgBlank(code, 'nodesTo')) to_ArgList$nodes <- from_ArgList$nodes
else to_ArgList$nodes <- code$nodesTo
if(from_ArgList$class == 'symbolModel'){
isMVfrom <- 0
accessFrom_ArgList <- list(model = code$from, nodes = from_ArgList$nodes, logProb = code$logProb, logProbOnly = code$logProbOnly)
accessFrom_name <- modelVariableAccessorVector_setupCodeTemplate$makeName(accessFrom_ArgList)
addNecessarySetupCode(accessFrom_name, accessFrom_ArgList, modelVariableAccessorVector_setupCodeTemplate, nfProc)
}
else if(from_ArgList$class == 'symbolModelValues'){
isMVfrom <- 1
accessFrom_ArgList <- list(modelValues = code$from, nodes = from_ArgList$nodes, logProb = code$logProb, logProbOnly = code$logProbOnly, row = from_ArgList$row)
accessFrom_name <- modelValuesAccessorVector_setupCodeTemplate$makeName(accessFrom_ArgList)
addNecessarySetupCode(accessFrom_name, accessFrom_ArgList, modelValuesAccessorVector_setupCodeTemplate, nfProc)
}
else if(from_ArgList$class %in% accessTypes) {
isMVfrom <- as.integer(from_ArgList$class == 'symbolModelValuesAccessorVector')
accessFrom_name <- as.character(code$from)
}
if(to_ArgList$class == 'symbolModel'){
isMVto <- 0
accessTo_ArgList <- list(model = code$to, nodes = to_ArgList$nodes, logProb = code$logProb, logProbOnly = code$logProbOnly)
accessTo_name <- modelVariableAccessorVector_setupCodeTemplate$makeName(accessTo_ArgList)
addNecessarySetupCode(accessTo_name, accessTo_ArgList, modelVariableAccessorVector_setupCodeTemplate, nfProc)
}
else if(to_ArgList$class == 'symbolModelValues'){
isMVto <- 1
accessTo_ArgList <- list(modelValues = code$to, nodes = to_ArgList$nodes, logProb = code$logProb, logProbOnly = code$logProbOnly, row = to_ArgList$row)
accessTo_name <- modelValuesAccessorVector_setupCodeTemplate$makeName(accessTo_ArgList)
addNecessarySetupCode(accessTo_name, accessTo_ArgList, modelValuesAccessorVector_setupCodeTemplate, nfProc)
}
else if(to_ArgList$class %in% accessTypes) {
isMVto <- as.integer(to_ArgList$class == 'symbolModelValuesAccessorVector')
accessTo_name <- as.character(code$to)
}
if(getNimbleOption('useNewNimCopy')) {
copierVector_ArgList <- list(accessFrom_name = accessFrom_name, accessTo_name = accessTo_name, isMVto = isMVto, isMVfrom = isMVfrom)
copierVector_name <- copierVector_setupCodeTemplate$makeName(copierVector_ArgList)
addNecessarySetupCode(copierVector_name, copierVector_ArgList, copierVector_setupCodeTemplate, nfProc)
}
if(!getNimbleOption('useNewNimCopy')) {
##What happens below is a bit convoluted and really for backwards compatibility
runCode <- substitute(nimCopy(from = FROM_ACCESS, rowFrom = NA, to = TO_ACCESS, rowTo = NA),
list(FROM_ACCESS = as.name(accessFrom_name), TO_ACCESS = as.name(accessTo_name)))
if(from_ArgList$class %in% modelValuesTypes)
runCode$rowFrom = from_ArgList$row
if(to_ArgList$class %in% modelValuesTypes)
runCode$rowTo = to_ArgList$row
} else {
rowFromArg <- if(from_ArgList$class %in% modelValuesTypes) from_ArgList$row else NA
rowToArg <- if(to_ArgList$class %in% modelValuesTypes) {
if(identical(rowFromArg, NA)) {rowFromArg <- 0; unusedArg <- NA} else unusedArg <- 0
to_ArgList$row
} else {
unusedArg <- NA
NA
}
runCode <- substitute(nimCopy(copierVector = COPIER_VECTOR, rowFrom = ROWFROM, rowTo = ROWTO, unused = UNUSED),
list(COPIER_VECTOR = as.name(copierVector_name),
ROWFROM = rowFromArg, ROWTO = rowToArg, UNUSED = unusedArg))
}
runCode <- runCode[as.character(runCode) != 'NA']
return(runCode)
})
doubleBracket_keywordInfo <- keywordInfoClass(
keyword = '[[',
processor = function(code, nfProc, RCfunProc){
callerCode <- code[[2]]
if(is.null(nfProc)) stop("No allowed use of [[ in a nimbleFunction without setup code.")
possibleObjects <- c('symbolModel', 'symbolNimPtrList', 'symbolNimbleFunctionList', 'symbolNimbleList')
class = symTypeFromSymTab(code[[2]], nfProc$setupSymTab, options = possibleObjects)
if(is.null(class)){ ##assume that an element of a run-time provided nimbleList is being accessed
nl_charName <- as.character(callerCode)
nl_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfVar(NIMBLELIST, VARNAME), list(NIMBLELIST = as.name(nl_charName), VARNAME = nl_fieldName))
return(newRunCode)
}
if(class == 'symbolNimPtrList' || class == 'symbolNimbleFunctionList')
return(code)
if(class == 'symbolNimbleList'){
# Code is of the form
# myNimbleList[['myVar']]
nl_charName <- as.character(callerCode)
nl_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfVar(NIMBLELIST, VARNAME), list(NIMBLELIST = as.name(nl_charName), VARNAME = nl_fieldName))
return(newRunCode)
}
if(class == 'symbolModel'){
singleAccess_ArgList <- list(code = code, model = code[[2]], nodeExpr = code[[3]])
nodeArg <- code[[3]]
if(is.character(nodeArg)){
if(length(nodeArg) > 1)
stop(paste0("Problem in ",
deparse(code), ". ",
deparse(code[[3]]),
" is too long. It can only have one element."),
call. = FALSE)
varAndIndices <- nimbleInternalFunctions$getVarAndIndices(nodeArg)
allNDims <- lapply(nfProc$instances, function(x) {
model <- eval(singleAccess_ArgList$model,
envir = x)
if(length(nodeArg) != 1)
stop(paste0("Length of ",
nodeArg,
" requested from ",
deparse(singleAccess_ArgList$model),
" using '[[' is ",
length(nodeArg),
". It must be 1.")
, call. = FALSE)
determineNdimFromOneCase(model, varAndIndices)
} )
if(length(unique(allNDims)) > 1)
stop(paste0('Error for ', deparse(code),
'. Inconsistent numbers of dimensions for different instances.'),
call. = FALSE)
nDim <- allNDims[[1]]
useMap <- nDim > 0
## ##
## ## If input is of the form model[['a']]
## ## and a is non-scalar,
## ## we treat it like model$a, which handles either
if(useMap & length(varAndIndices$indices) == 0) {
return(
keywordList[['$']]$processor(code, nfProc, RCfunProc)
)
}
## ## Following line adds up 0 for each scalar index
## ## and 1 for each non-scalar index to determine if the
## ## accessed node is scalar
## nDim <- sum(1 - unlist(lapply(varAndIndices$indices, is.numeric) ) )
## useMap <- nDim > 0
}
else{
allNDims <- determineNdimsFromNfproc(singleAccess_ArgList$model, nodeArg, nfProc)
if(length(unique(allNDims)) > 1) stop(paste0('Error for ', deparse(code), '. Inconsistent numbers of dimensions for different instances.'), call. = FALSE)
nDim <- allNDims[[1]]
useMap <- nDim > 0
}
if(useMap){
accessName <- map_SetupTemplate$makeName(singleAccess_ArgList)
addNecessarySetupCode(accessName, singleAccess_ArgList, map_SetupTemplate, nfProc)
ans <- makeMapAccessExpr(accessName, as.name(accessName), nDim)
}
else{
accessName <- singleModelIndexAccess_SetupTemplate$makeName(singleAccess_ArgList)
addNecessarySetupCode(accessName, singleAccess_ArgList, singleModelIndexAccess_SetupTemplate, nfProc)
#ans <- substitute(ACCESSNAME[MFLATINDEX], list(ACCESSNAME = as.name(accessName), MFLATINDEX = as.name(paste0(accessName, '_flatIndex'))))
ans <- makeSingleIndexAccessExpr(accessName, as.name(accessName))
}
return(ans)
}
stop("Incorrect use of double brackets in: '", deparse(code), "'.")
})
modelMemberFun_keywordInfo <- keywordInfoClass(
keyword = 'multiple',
processor = function(code, nfProc, RCfunProc) {
## if we get here it must be model$member(args)
## We will turn it into member(model, args)
newRunCode <- do.call("call",
c(list(as.character(code[[1]][[3]]),
code[[1]][[2]]),
as.list(code[-1])),
quote = TRUE)
return(newRunCode)
})
dollarSign_keywordInfo <- keywordInfoClass(
keyword = '$',
processor = function(code, nfProc, RCfunProc){
callerCode <- code[[2]]
if(is.null(nfProc)) {
nl_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfVar(NIMBLELIST, VARNAME), list(NIMBLELIST = callerCode, VARNAME = nl_fieldName))
return(newRunCode)
}
doubleBracketCase <- FALSE
if(length(callerCode) > 1) {
if(deparse(callerCode[[1]] == '[[')) {
doubleBracketCase <- TRUE
symObj <- getSymObj_recurse(callerCode[[2]], nfProc$setupSymTab)
}
}
if(!doubleBracketCase)
symObj <- getSymObj_recurse(callerCode, nfProc$setupSymTab)
class <- class(symObj)[1] ## symObj is allowed to be NULL
# This extracts myNimbleFunction from the expression myNimbleFunction$foo()
if(length(callerCode) > 1){
if(callerCode[[1]] == '$'){ ## nested NL or NF case
callerCode <- processKeyword(callerCode, nfProc, RCfunProc)
}
}
# This extracts myNimbleFunctionList from the expression myNimbleFunctionList[[i]]
# May be a better way to do this
if(is.null(class) || class == 'NULL'){ ##assume that an element of a run-time provided nimbleList is being accessed
nl_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfVar(NIMBLELIST, VARNAME), list(NIMBLELIST = callerCode, VARNAME = nl_fieldName))
return(newRunCode)
}
if(class == 'symbolNimbleFunctionList'){
nf_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfMethod(NIMBLEFXN, METHODNAME), list(NIMBLEFXN = callerCode, METHODNAME = nf_fieldName))
return(newRunCode)
}
if(class == 'symbolModel'){
singleAccess_ArgList <- list(code = code, model = callerCode, var = as.character(code[[3]]) )
accessName <- singleVarAccess_SetupTemplate$makeName(singleAccess_ArgList)
addNecessarySetupCode(accessName, singleAccess_ArgList, singleVarAccess_SetupTemplate, nfProc)
return(as.name(accessName))
}
if(class == 'symbolNimbleFunction'){
# Code is of the form myNimbleFunction$myMethod
# or myNimbleFunction$myVar
# Note that we have cut off '()' in the case of myMethod, so we must inspect the
# nested symbol for myMethod to determine whether it is a method or variable
nf_fieldName <-as.character(code[[3]])
objectSymbol = symObj$nfProc$setupSymTab$getSymbolObject(nf_fieldName)
if(class(objectSymbol)[[1]] == 'symbolMemberFunction'){
newRunCode <- substitute(nfMethod(NIMBLEFXN, METHODNAME), list(NIMBLEFXN = callerCode, METHODNAME = nf_fieldName))
return(newRunCode)
}
else {
# We *assume* that if its not a member function, it should be treated with
# nfVar
newRunCode <- substitute(nfVar(NIMBLEFXN, VARNAME), list(NIMBLEFXN = callerCode, VARNAME = nf_fieldName))
return(newRunCode)
}
}
if(class == 'symbolNimbleList'){
# Code is of the form
# myNimbleList$myVar
nl_fieldName <-as.character(code[[3]])
newRunCode <- substitute(nfVar(NIMBLELIST, VARNAME), list(NIMBLELIST = callerCode, VARNAME = nl_fieldName))
return(newRunCode)
}
if(class == 'symbolNimbleFunctionList'){
# Code is of the form myNimbleFunctionList[[i]]$foo (foo should be a method)
# At this point, we cannot access variables of a nimble function list, ie
# myNimbleFunctionList[[i]]$myVariable is not allowed
# If we add this functionality, we will need to look up what foo as we do
# for the nimbleFunction case above
nf_name <-code[[2]]
nf_fieldName <- as.character(code[[3]])
newRunCode <- substitute(nfMethod(NIMBLEFXN, METHODNAME), list(NIMBLEFXN = nf_name, METHODNAME = nf_fieldName))
return(newRunCode)
}
}
)
singleBracket_keywordInfo <- keywordInfoClass(
keyword = '[',
processor = function(code, nfProc, RCfunProc){
if(is.null(nfProc)) return (code)
class <- symTypeFromSymTab(code[[2]], nfProc$setupSymTab)
if(class == 'symbolModelValues'){
if(length(code) < 4) {
stop(paste0("incorrect syntax for accessing element of modelValues: ", deparse(code)))
}
singleMVAccess_ArgList <- list(code = code, modelValues = code[[2]], var = code[[3]], row = code[[4]])
accessName <- singleModelValuesAccessor_SetupTemplate$makeName(singleMVAccess_ArgList)
addNecessarySetupCode(accessName, singleMVAccess_ArgList, singleModelValuesAccessor_SetupTemplate, nfProc)
if(length(code) == 4)
indexExpr = code[[4]]
else
indexExpr = substitute(1)
return(substitute(ACCESS[INDEX], list(ACCESS = as.name(accessName), INDEX = indexExpr) ) )
}
return(code)
}
)
length_char_keywordInfo <- keywordInfoClass(
keyword = 'length',
processor = function(code, nfProc, RCfunProc) {
if(is.null(nfProc)) return(code)
if(length(code) < 2) stop('length() used without an argument')
class <- symTypeFromSymTab(code[[2]], nfProc$setupSymTab)
if(class == "symbolString") {
length_char_ArgList <- list(code = code, string = code[[2]])
accessName <- length_char_SetupTemplate$makeName(length_char_ArgList)
addNecessarySetupCode(accessName, length_char_ArgList, length_char_SetupTemplate, nfProc)
return(substitute(LENGTHNAME, list(LENGTHNAME = as.name(accessName))))
}
return(code)
})
nimIntegrate_keywordInfo <- keywordInfoClass(
keyword = 'nimIntegrate',
processor = function(code, nfProc, RCfunProc) {
if(code$abs.tol == quote(rel.tol))
code$abs.tol = code$rel.tol
iTols <- which(names(code) %in% c('rel.tol','abs.tol'))
for(i in iTols) {
code_i <- code[[i]]
if(length(code_i) > 1) {
if(".Machine" %in% all.vars(code_i)) # Must be an expression using .Machine$double.eps or related
code[[i]] <- eval(code_i)
}
}
code
}
)
nimDerivs_keywordInfo <- keywordInfoClass(
keyword = 'nimDerivs',
processor = function(code, nfProc, RCfunProc) {
wrtArgs <- code[['wrt']]
## First check to see if nimFxn argument is a method.
fxnCall <- code[[2]][[1]]
order <- code[['order']]
calculateCase <- FALSE
if(deparse(fxnCall) == 'calculate'){
calculateCase <- TRUE
}
else if(length(fxnCall) == 3 &&
(deparse(fxnCall[[1]]) == '$' &&
deparse(fxnCall[[3]]) == 'calculate')){
## re-arrange nimDerivs(model$calculate(...), ...) to nimDerivs(calculate(model, ...), ...)
code[[2]] <- modelMemberFun_keywordInfo$processor(code[[2]], nfProc)
code[[2]] <- matchKeywordCode(code[[2]], nfProc)
calculateCase <- TRUE
}
if(calculateCase) {
innerCode <- code[[2]]
if(length(code$wrt)==1)
if(!is.name(code$wrt))
if(is.na(code$wrt[1]))
stop("Derivatives of a call to 'calculate()' must have 'wrt' argument specified.")
innerCode$wrt <- code$wrt
newCode <- calculate_keywordInfo$processor(innerCode, nfProc, RCfunProc)
newCode[[1]] <- as.name('nimDerivs_calculate')
newCode$orderVector <- code$order
newCode$update <- if(is.null(code[['update']])) TRUE else code[['update']]
newCode$reset <- if(is.null(code[['reset']])) FALSE else code[['reset']]
return(newCode)
}
## Not a calculate case:
if(!is.null(nfProc$origMethods[[deparse(fxnCall)]])) {
derivMethod <- nfProc$origMethods[[deparse(fxnCall)]]
derivMethodArgs <- derivMethod$getArgInfo()
## Only make the wrt substitution if the names are baked in as character
wrtArg <- code$wrt
doPreprocess <- FALSE
if(is.numeric(wrtArg) | is.logical(wrtArg)) {
if(any(is.na(wrtArg[1]))) { ## wrt = NULL (default), set to NA, which will become -1 by convertWrtArgToIndices and then c(-1, -1) in the setup code
doPreprocess <- TRUE
}
} else if(is.name(wrtArg)) { ## wrt = some_index_var_maybe_from_setup
## do nothing
} else if(deparse(wrtArg[[1]]) == 'nimC') { ## wrt = c('x', ...)
if(is.character(wrtArg[[2]]))
doPreprocess <- TRUE
} else if(is.character(wrtArg)) { ## wrt = 'x'
doPreprocess <- TRUE
} ## In any other setting, it must be an index vector and we leave it alone here.
##
if(doPreprocess) {
wrt_argList <- list(fxnCall = fxnCall,
wrt = code$wrt,
# vector = wrtArgIndices
derivMethodArgs = derivMethodArgs)
accessName <- wrtVector_setupCodeTemplate$makeName(wrt_argList)
addNecessarySetupCode(accessName, wrt_argList, wrtVector_setupCodeTemplate, nfProc)
code[['wrt']] <- substitute(VECNAME,
list(VECNAME = as.name(accessName)))
}
## Check if model and updateNodes are provided.
## If so, create a nodeFxnVector for them.
modelProvided <- is.name(code[['model']])
updateNodesProvided <- is.name(code[['updateNodes']])
if(!updateNodesProvided)
if(is.character(code[['updateNodes']]))
updateNodesProvided <- !is.na(code[['updateNodes']][1])
constantNodesProvided <- is.name(code[['constantNodes']])
if(!constantNodesProvided)
if(is.character(code[['constantNodes']]))
constantNodesProvided <- !is.na(code[['constantNodes']][1])
if(xor(modelProvided, updateNodesProvided || constantNodesProvided))
stop('nimDerivs arguments model and at least one of updateNodes or constantNodes must be provided together or not at all.')
if(modelProvided) { ## At this point that means both were provided
DMUNargList <- list(model = code$model,
updateNodes = if(updateNodesProvided) code[["updateNodes"]] else NULL,
constantNodes = if(constantNodesProvided) code[["constantNodes"]] else NULL)
accessName <- nodeFunctionVector_DerivsModelUpdateNodes_SetupTemplate$makeName(DMUNargList)
addNecessarySetupCode(accessName, DMUNargList, nodeFunctionVector_DerivsModelUpdateNodes_SetupTemplate, nfProc)
## code[['model']] <- NULL
## if(updateNodesProvided) code[['updateNodes']] <- NULL
## if(constantNodesProvided) code[['constantNodes']] <- NULL
code[['updateNodesName']] <- accessName
}
code[['model']] <- NULL
code[['updateNodes']] <- NULL
code[['constantNodes']] <- NULL
}
return(code)
}
)
derivInfo_keywordInfo <- keywordInfoClass(
keyword = 'derivInfo',
processor = function(code, nfProc, RCfunProc) {
fxnCall <- code[[2]][[1]]
calculateCase <- FALSE
if(deparse(fxnCall) == 'calculate'){
calculateCase <- TRUE
}
else if(length(fxnCall) == 3 &&
(deparse(fxnCall[[1]]) == '$' &&
deparse(fxnCall[[3]]) == 'calculate')){
## re-arrange nimDerivs(model$calculate(...), ...) to nimDerivs(calculate(model, ...), ...)
code[[2]] <- modelMemberFun_keywordInfo$processor(code[[2]], nfProc)
code[[2]] <- matchKeywordCode(code[[2]], nfProc)
calculateCase <- TRUE
}
if(!calculateCase) {
stop('The first argument to derivInfo must be a call to calculate(model, ...) or model$calculate(...)')
}
innerCode <- code[[2]]
if(is.null(code$wrt))
stop("derivInfo must provide 'wrt' argument.")
innerCode$wrt <- code$wrt
newCode <- calculate_keywordInfo$processor(innerCode, nfProc, RCfunProc)
return(newCode)
}
)
# KeywordList
keywordList <- new.env()
keywordList[['nimSeq']] <- nimSeq_keywordInfo
keywordList[['getParam']] <- getParam_keywordInfo
keywordList[['getBound']] <- getBound_keywordInfo
keywordList[['values']] <- values_keywordInfo
keywordList[['calculate']] <- calculate_keywordInfo
keywordList[['calculateDiff']] <- calculateDiff_keywordInfo
keywordList[['simulate']] <- simulate_keywordInfo
keywordList[['getLogProb']] <- getLogProb_keywordInfo
keywordList[['nimCopy']] <- nimCopy_keywordInfo
keywordList[['[[']] <- doubleBracket_keywordInfo
keywordList[['$']] <- dollarSign_keywordInfo
keywordList[['[']] <- singleBracket_keywordInfo
keywordList[['besselK']] <- besselK_keywordInfo
keywordList[['dgamma']] <- d_gamma_keywordInfo
keywordList[['pgamma']] <- pq_gamma_keywordInfo
keywordList[['qgamma']] <- pq_gamma_keywordInfo
keywordList[['rgamma']] <- rgamma_keywordInfo
keywordList[['dinvgamma']] <- d_gamma_keywordInfo
keywordList[['pinvgamma']] <- pq_gamma_keywordInfo
keywordList[['qinvgamma']] <- pq_gamma_keywordInfo
keywordList[['rinvgamma']] <- rgamma_keywordInfo
keywordList[['dsqrtinvgamma']] <- d_gamma_keywordInfo
keywordList[['psqrtinvgamma']] <- pq_gamma_keywordInfo
keywordList[['qsqrtinvgamma']] <- pq_gamma_keywordInfo
keywordList[['rsqrtinvgamma']] <- rgamma_keywordInfo
keywordList[['ddexp']] <- d_gamma_keywordInfo
keywordList[['pdexp']] <- pq_gamma_keywordInfo
keywordList[['qdexp']] <- pq_gamma_keywordInfo
keywordList[['rdexp']] <- rgamma_keywordInfo
# can be handled the same as gamma, so include although we have dexp_nimble too
keywordList[['dexp']] <- d_gamma_keywordInfo
keywordList[['pexp']] <- pq_gamma_keywordInfo
keywordList[['qexp']] <- pq_gamma_keywordInfo
keywordList[['rexp']] <- rgamma_keywordInfo
keywordList[['dexp_nimble']] <- d_exp_nimble_keywordInfo
keywordList[['pexp_nimble']] <- pq_exp_nimble_keywordInfo
keywordList[['qexp_nimble']] <- pq_exp_nimble_keywordInfo
keywordList[['rexp_nimble']] <- rexp_nimble_keywordInfo
keywordList[['length']] <- length_char_keywordInfo ## active only if argument has type character
keywordList[['nimIntegrate']] <- nimIntegrate_keywordInfo
keywordList[['nimDerivs']] <- nimDerivs_keywordInfo
keywordList[['derivInfo']] <- derivInfo_keywordInfo
keywordListModelMemberFuns <- new.env()
keywordListModelMemberFuns[['calculate']] <- modelMemberFun_keywordInfo
keywordListModelMemberFuns[['simulate']] <- modelMemberFun_keywordInfo
keywordListModelMemberFuns[['calculateDiff']] <- modelMemberFun_keywordInfo
keywordListModelMemberFuns[['getLogProb']] <- modelMemberFun_keywordInfo
keywordListModelMemberFuns[['getParam']] <- modelMemberFun_keywordInfo
keywordListModelMemberFuns[['getBound']] <- modelMemberFun_keywordInfo
matchFunctions <- new.env()
matchFunctions[['setSize']] <- function(var, ..., copy = TRUE, fillZeros = TRUE){}
matchFunctions[['nimC']] <- nimC
matchFunctions[['nimRep']] <- function(x, times = 1, length.out, each = 1) {}
matchFunctions[['nimSeq']] <- nimSeq
matchFunctions[['nimNumeric']] <- nimNumeric
matchFunctions[['nimInteger']] <- nimInteger
matchFunctions[['nimLogical']] <- nimLogical
matchFunctions[['nimMatrix']] <- nimMatrix
matchFunctions[['nimArray']] <- nimArray
matchFunctions[['values']] <- function(model, nodes, accessor){}
matchFunctions[['getParam']] <- getParam
matchFunctions[['getBound']] <- getBound
matchFunctions[['calculate']] <- calculate
matchFunctions[['calculateDiff']] <- calculateDiff
matchFunctions[['simulate']] <- simulate
matchFunctions[['getLogProb']] <- getLogProb
matchFunctions[['nimCopy']] <- function(from, to, nodes, nodesTo, row, rowTo, logProb = FALSE, logProbOnly = FALSE){}
matchFunctions[['double']] <- function(nDim, dim, default, ...){}
matchFunctions[['int']] <- function(nDim, dim, default, ...){}
matchFunctions[['nimOptim']] <- nimOptim
matchFunctions[['nimIntegrate']] <- nimIntegrate
matchFunctions[['nimOptimDefaultControl']] <- nimOptimDefaultControl
matchFunctions[['nimEigen']] <- function(squareMat, symmetric = FALSE, only.values = FALSE){}
matchFunctions[['nimSvd']] <- function(mat, vectors = 'full'){}
matchFunctions[['nimDerivs']] <- function(call = NA,
order = nimC(0,1,2),
wrt = NA,
model = NA, updateNodes = NA, constantNodes = NA,
do_update = TRUE, reset = FALSE) {}
matchFunctions[['derivInfo']] <- derivInfo
matchFunctions[['besselK']] <- function(x, nu, expon.scaled = FALSE){}
matchFunctions[['dgamma']] <- function(x, shape, rate = 1, scale, log = FALSE){}
matchFunctions[['rgamma']] <- function(n, shape, rate = 1, scale){}
matchFunctions[['qgamma']] <- function(p, shape, rate = 1, scale, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['pgamma']] <- function(q, shape, rate = 1, scale, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['dinvgamma']] <- matchFunctions[['dsqrtinvgamma']] <- function(x, shape, scale = 1, rate, log = FALSE){}
matchFunctions[['rinvgamma']] <- matchFunctions[['rsqrtinvgamma']] <- function(n, shape, scale = 1, rate){}
matchFunctions[['qinvgamma']] <- matchFunctions[['qsqrtinvgamma']] <- function(p, shape, scale = 1, rate, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['pinvgamma']] <- matchFunctions[['psqrtinvgamma']] <- function(q, shape, scale = 1, rate, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['dexp']] <- function(x, rate = 1, log = FALSE){}
matchFunctions[['rexp']] <- function(n, rate = 1){}
matchFunctions[['qexp']] <- function(p, rate = 1, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['pexp']] <- function(q, rate = 1, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['dexp_nimble']] <- function(x, rate, scale = 1, log = FALSE){}
matchFunctions[['rexp_nimble']] <- function(n, rate, scale = 1){}
matchFunctions[['qexp_nimble']] <- function(p, rate, scale = 1, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['pexp_nimble']] <- function(q, rate, scale = 1, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['ddexp']] <- function(x, location, scale = 1, rate, log = FALSE){}
matchFunctions[['rdexp']] <- function(n, location, scale = 1, rate){}
matchFunctions[['qdexp']] <- function(p, location, scale = 1, rate, lower.tail = TRUE, log.p = FALSE){}
matchFunctions[['pdexp']] <- function(q, location, scale = 1, rate, lower.tail = TRUE, log.p = FALSE){}
matchModelMemberFunctions <- new.env()
matchModelMemberFunctions[['calculate']] <- function(nodes) {}
matchModelMemberFunctions[['calculateDiff']] <- function(nodes) {}
matchModelMemberFunctions[['getLogProb']] <- function(nodes) {}
matchModelMemberFunctions[['simulate']] <- function(nodes, includeData = FALSE) {}
matchModelMemberFunctions[['getParam']] <- function(node, param) {}
matchModelMemberFunctions[['getBound']] <- function(node, bound) {}
# remove ncp from signatures
stripArgs <- function(fname, argNames) {
if(exists(fname)) {
args <- formals(eval(as.name(fname)))
args <- args[-which(names(args) %in% argNames)]
template <- function() {}
formals(template) <- args
return(template)
} else return(NULL)
}
for(distfun in paste0(c('d','p','q','r'), 'beta'))
matchFunctions[[distfun]] <- stripArgs(distfun, 'ncp')
for(distfun in paste0(c('d','p','q','r'), 'chisq'))
matchFunctions[[distfun]] <- stripArgs(distfun, 'ncp')
for(distfun in paste0(c('d','p','q','r'), 't'))
matchFunctions[[distfun]] <- stripArgs(distfun, 'ncp')
for(distfun in paste0(c('d','p','q','r'), 'nbinom'))
matchFunctions[[distfun]] <- stripArgs(distfun, 'mu')
# the following are standard in terms of both matchFunctions and keywordList
matchDistList <- list('binom', 'cat', 'dirch', 'interval', 'lnorm', 'logis', 'multi', 'mnorm_chol', 'mvt_chol', 'norm', 'pois', 't_nonstandard', 'unif', 'weibull', 'wish_chol', 'invwish_chol', 'car_normal', 'car_proper')
addDistList2matchFunctions <- function(distList, matchFunEnv){
for(thisDist in distList){
pFun <- paste0('p', thisDist)
qFun <- paste0('q', thisDist)
rFun <- paste0('r', thisDist)
dFun <- paste0('d', thisDist)
eval(substitute(matchFunctions[[dFun]] <- DFUN, list(DFUN = as.name(dFun))))
eval(substitute(matchFunctions[[rFun]] <- RFUN, list(RFUN = as.name(rFun))))
if(exists(qFun))
eval(substitute(matchFunctions[[qFun]] <- QFUN, list(QFUN = as.name(qFun))))
if(exists(pFun))
eval(substitute(matchFunctions[[pFun]] <- PFUN, list(PFUN = as.name(pFun))))
}
}
addDistList2matchFunctions(matchDistList, matchFunctions)
# processKeyword function to be called by nfProc
processKeyword <- function(code, nfProc, RCfunProc){
thisKeywordInfo <- keywordList[[ as.character(code[[1]]) ]]
if(!is.null(thisKeywordInfo))
return(thisKeywordInfo$processor(code, nfProc, RCfunProc))
return(code)
}
processKeywordCodeMemberFun <- function(code, nfProc, RCfunProc) { ## handle cases like a$b(c) as one unit
## this includes nf$method()
## nfList[[i]]$method
## model$calculate(nodes)
dollarSignPart <- code[[1]]
objectPart <- dollarSignPart[[2]]
isModel <- FALSE
if(length(objectPart) != 1) isModel <- FALSE ## a case like a[[i]]$b(), which can only be a nimbleFunction list
else {
symObj <- nfProc$setupSymTab$getSymbolObject(as.character(objectPart))
if(is.null(symObj)) stop(paste0("In processKeywordCodeMemberFun: not sure what to do with ", deparse(code)))
if(inherits(symObj, 'symbolModel'))
isModel <- TRUE
}
if(isModel) {
thisKeywordInfo <- keywordListModelMemberFuns[[ as.character(dollarSignPart[[3]]) ]]
if(is.null(thisKeywordInfo)) stop(paste0("In processKeywordCodeMemberFun, don't know what do with: ", deparse(code)))
rearrangedCode <- thisKeywordInfo$processor(code, nfProc)
rearrangedCode <- matchKeywordCode(rearrangedCode, nfProc)
return(processKeywords_recurse(rearrangedCode, nfProc, RCfunProc))
} else {
## same as processKeywords_recurse
## first line here creates something like nfMethod(model, method)(args)
## which is handled as a chainedCall in later processing
code[[1]] <- processKeywords_recurse(code[[1]], nfProc, RCfunProc)
cl <- length(code)
if(cl >= 2) {
for(i in 2:cl) {
code[[i]] <- processKeywords_recurse(code[[i]], nfProc, RCfunProc)
}
}
return(code)
}
}
processKeywords_recurse <- function(code, nfProc = NULL, RCfunProc) {
cl = length(code)
if(cl == 1) {
if(is.call(code)) {
if(length(code[[1]]) > 1)
if(deparse(code[[1]][[1]] == '$'))
code <- processKeywordCodeMemberFun(code, nfProc, RCfunProc)
else
code[[1]] <- processKeywords_recurse(code[[1]], nfProc, RCfunProc)
}
return(code)
}
if(length(code[[1]]) == 1) {
code <- processKeyword(code, nfProc, RCfunProc)
}
cl = length(code)
if(is.call(code)) {
if(length(code[[1]]) > 1) {
if(deparse(code[[1]][[1]] == '$')) {
code <- processKeywordCodeMemberFun(code, nfProc, RCfunProc) ## case like model$calculate(nodes)
return(code) ## don't recurse on arguments of anything in this category
}
code[[1]] <- processKeywords_recurse(code[[1]], nfProc, RCfunProc)
}
if(cl >= 2) {
for(i in 2:cl) {
code[[i]] <- processKeywords_recurse(code[[i]], nfProc, RCfunProc)
}
}
}
return(code)
}
##### SETUPCODE TEMPLATES
wrtVector_setupCodeTemplate <- setupCodeTemplateClass(
makeName = function(argList){Rname2CppName(paste0('wrtVec_',
deparse(argList$fxn),
paste(deparse(argList$wrt), sep='_'),
'_'))},
codeTemplate = quote(
{
WRTVEC <- nimble:::convertWrtArgToIndices(WRT, #code$wrt
DERIVMETHODARGS,
FXNNAME)
if(length(WRTVEC) == 1)
WRTVEC <- c(WRTVEC, -1)
}
),
makeCodeSubList = function(resultName, argList){
list(WRTVEC = as.name(resultName),
WRT = argList$wrt
,DERIVMETHODARGS = argList$derivMethodArgs
,FXNNAME = deparse(argList$fxnCall)
)##argList$vector)
}
)
length_char_SetupTemplate <- setupCodeTemplateClass(
makeName = function(argList) {Rname2CppName(paste0(paste("length", deparse(argList$string), sep='_'), '_KNOWN_'))},
codeTemplate = quote(LENGTHNAME <- CODE),
makeCodeSubList = function(resultName, argList) {
list(LENGTHNAME = as.name(resultName),
CODE = argList$code)
})
modelVariableAccessorVector_setupCodeTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model, nodes and logProb
makeName = function(argList) {Rname2CppName(paste(deparse(argList$model), deparse(argList$nodes), 'access_logProb', deparse(argList$logProb),'LPO', deparse(argList$logProbOnly), sep = '_'))},
codeTemplate = quote( ACCESSNAME <- nimble:::modelVariableAccessorVector(MODEL, NODES, logProb = LOGPROB, logProbOnly = LOGPROBONLY) ),
makeCodeSubList = function(resultName, argList) {
list(ACCESSNAME = as.name(resultName),
MODEL = argList$model,
NODES = argList$nodes,
LOGPROB = argList$logProb,
LOGPROBONLY = argList$logProbOnly)
})
copierVector_setupCodeTemplate <- setupCodeTemplateClass(
makeName = function(argList) {Rname2CppName(paste0(argList$accessFrom_name, '_', argList$accessTo_name))},
codeTemplate = quote( COPIERNAME <- nimble:::copierVector(ACCESS_FROM, ACCESS_TO, ISMVFROM, ISMVTO) ),
makeCodeSubList = function(resultName, argList) {
list(COPIERNAME = as.name(resultName),
ACCESS_FROM = as.name(argList$accessFrom_name),
ACCESS_TO = as.name(argList$accessTo_name),
ISMVFROM = as.integer(argList$isMVfrom),
ISMVTO = as.integer(argList$isMVto))
})
modelValuesAccessorVector_setupCodeTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are modelValues, nodes and logProb
makeName = function(argList) {Rname2CppName(paste(deparse(argList[['modelValues']]), deparse(argList$nodes), 'access_logProb', deparse(argList$logProb), 'LPO', deparse(argList$logProbOnly), deparse(argList$row), sep = '_'))},
codeTemplate = quote( ACCESSNAME <- nimble:::modelValuesAccessorVector(MODEL, NODES, logProb = LOGPROB, logProbOnly = LOGPROBONLY) ),
makeCodeSubList = function(resultName, argList) {
list(ACCESSNAME = as.name(resultName),
MODEL = argList[['modelValues']],
NODES = argList$nodes,
LOGPROB = argList$logProb,
LOGPROBONLY = argList$logProbOnly)
})
nodeFunctionVector_WithDerivsOutput_SetupTemplate <- setupCodeTemplateClass(
makeName = function(argList){
Rname2CppName(paste(deparse(argList$model),
deparse(argList$nodes),
'nodeFxnVector_WithDerivsOutput', ## The "_derivs_" tag is used later to determine the right class - klugey
deparse(argList$includeData),
if(argList$sortUnique) "SU" else "notSU",
'_derivs_',
sep = '_')
)
},
codeTemplate = quote(
NODEFXNVECNAME <- nimble:::nodeFunctionVector_WithDerivsOutputNodes(
model = MODEL,
calcNodes = CALCNODES,
excludeData = EXCLUDEDATA,
sortUnique = SORTUNIQUE)
),
makeCodeSubList = function(resultName, argList){
list(NODEFXNVECNAME = as.name(resultName),
MODEL = argList$model,
CALCNODES = argList$nodes,
EXCLUDEDATA = !argList$includeData,
SORTUNIQUE = argList$sortUnique
)
})
nodeFunctionVector_DerivsModelUpdateNodes_SetupTemplate <- setupCodeTemplateClass(
makeName = function(argList){
Rname2CppName(paste(deparse(argList$model),
deparse(argList[['updateNodes']]),
deparse(argList[['constantNodes']]),
'nodeFxnVector_DerivsModelUpdateNodes_derivs_', ## The "_derivs_" tag is used later to determine the right class - klugey
sep = '_')
)
},
codeTemplate = quote(
NODEFXNVECNAME <- nimble:::nodeFunctionVector_DerivsModelUpdateNodes(
model = MODEL,
updateNodes = UPDATENODES,
constantNodes = CONSTANTNODES)
),
makeCodeSubList = function(resultName, argList){
list(NODEFXNVECNAME = as.name(resultName),
MODEL = argList$model,
UPDATENODES = argList[["updateNodes"]],
CONSTANTNODES = argList[["constantNodes"]]
)
})
nodeFunctionVector_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model, nodes and includeData
makeName = function(argList){
Rname2CppName(paste(deparse(argList$model),
deparse(argList$nodes),
'nodeFxnVector_includeData',
deparse(argList$includeData),
if(argList$sortUnique) "SU" else "notSU",
if(is.null(argList$wrtNodes)) '' else '_derivs_', sep = '_')
)
},
codeTemplate = quote(
NODEFXNVECNAME <- nimble:::nodeFunctionVector(model = MODEL,
nodeNames = NODES,
wrtNodes = WRTNODES,
excludeData = EXCLUDEDATA,
sortUnique = SORTUNIQUE,
errorContext = ERRORCONTEXT)
),
makeCodeSubList = function(resultName, argList){
list(NODEFXNVECNAME = as.name(resultName),
MODEL = argList$model,
NODES = argList$nodes,
WRTNODES = argList$wrtNodes,
EXCLUDEDATA = !argList$includeData,
SORTUNIQUE = argList$sortUnique,
ERRORCONTEXT = argList$errorContext
)
})
paramInfo_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model, node and param
makeName = function(argList){Rname2CppName(paste(deparse(argList$model), deparse(argList$node), deparse(argList$param), 'paramInfo', sep='_'))},
makeOtherNames = function(name,argList) {Rname2CppName(paste0(name,'_ID'))},
codeTemplate = quote({
PARAMINFONAME <- nimble:::makeParamInfo(model = MODEL, nodes = NODE, param = PARAM, vector = HASINDEX )
PARAMIDNAME <- PARAMINFONAME$paramID
PARAMINFONAME$paramID <- NULL
}),
makeCodeSubList = function(resultName, argList){
list(PARAMINFONAME = as.name(resultName),
PARAMIDNAME = as.name(paste0(resultName,'_ID')),
MODEL = argList$model,
NODE = argList$node,
PARAM = argList$param,
HASINDEX = argList$hasIndex)
})
boundInfo_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model, node and param
makeName = function(argList){Rname2CppName(paste(deparse(argList$model), deparse(argList$node), deparse(argList$bound), 'boundInfo', sep='_'))},
makeOtherNames = function(name,argList) {Rname2CppName(paste0(name,'_ID'))},
codeTemplate = quote({
BOUNDINFONAME <- nimble:::makeBoundInfo(MODEL, NODE, BOUND)
BOUNDIDNAME <- BOUNDINFONAME$boundID
BOUNDINFONAME$boundID <- NULL
}),
makeCodeSubList = function(resultName, argList){
list(BOUNDINFONAME = as.name(resultName),
BOUNDIDNAME = as.name(paste0(resultName,'_ID')),
MODEL = argList$model,
NODE = argList$node,
BOUND = argList$bound)
})
allLHSNodes_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model
makeName = function(argList){
Rname2CppName(paste('allLHSnodes', deparse(argList$model), sep = '_'))
},
codeTemplate = quote(NODENAMES <- MODEL$getMaps('nodeNamesLHSall')),
makeCodeSubList = function(resultName, argList){
list(NODENAMES = as.name(resultName),
MODEL = argList$model)
})
allModelNodes_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are model
makeName = function(argList){
Rname2CppName(paste('allModelNodes', deparse(argList$model), sep = '_'))
},
codeTemplate = quote(NODENAMES <- MODEL$getVarNames()),
makeCodeSubList = function(resultName, argList){
list(NODENAMES = as.name(resultName),
MODEL = argList$model)
})
allModelValuesVars_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are modelValues
makeName = function(argList){
Rname2CppName(paste('allMVVars', deparse(argList$modelValues), sep = '_'))
},
codeTemplate = quote(NODENAMES <- MODELVALUES$getVarNames(includeLogProb = FALSE)),
makeCodeSubList = function(resultName, argList){
list(NODENAMES = as.name(resultName),
MODELVALUES = argList$modelValues)
})
code2Name_fromArgList <- function(argList)
Rname2CppName(deparse(argList$code))
singleVarAccess_SetupTemplate <- setupCodeTemplateClass(
#Note to progammer: required fields of argList are 'code' (raw code to be processed), model and var
makeName = code2Name_fromArgList,
codeTemplate = quote(SINGLEACCESSOR <- nimble:::singleVarAccess(MODEL, VAR)),
makeCodeSubList = function(resultName, argList){
list(SINGLEACCESSOR = as.name(resultName),
MODEL = argList$model,
VAR = argList$var)
})
singleModelIndexAccess_SetupTemplate <- setupCodeTemplateClass(
#Note to progammer: required fields of argList are code, varAndIndices, node (character) and model(expression)
makeOtherNames = function(name, argList){ paste0(name, '_flatIndex')},
makeName = code2Name_fromArgList,
codeTemplate = quote({
VARANDINDICES <- nimble:::nimbleInternalFunctions$getVarAndIndices(NODEVARNAME)
NEWVARNAME <- as.character(VARANDINDICES$varName)
MFLATINDEX <- nimble:::varAndIndices2flatIndex(VARANDINDICES, MODELVAREXPR$getVarInfo(NEWVARNAME))
VARACCESSOR <- nimble:::singleVarAccess(MODELVAREXPR, NEWVARNAME, useSingleIndex = TRUE)
}),
makeCodeSubList = function(resultName, argList){
list(VARACCESSOR = as.name(resultName),
VARANDINDICES = as.name(paste0(resultName, '_varAndIndices') ),
NEWVARNAME = as.name(paste0(resultName, '_newVarName')),
NODEVARNAME = argList$nodeExpr,
MFLATINDEX = as.name(paste0(resultName, '_flatIndex')),
MODELVAREXPR = argList$model)
})
map_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are code, model
makeName = code2Name_fromArgList,
makeOtherNames = function(name, argList){
output <- character()
output[1] = paste0(name, '_strides')
output[2] = paste0(name, '_offset')
output[3] = paste0(name, '_sizes')
return(output)
},
codeTemplate = quote({
VARANDINDICES <- nimble:::nimbleInternalFunctions$getVarAndIndices(NODEVARNAME)
NEWVARNAME <- as.character(VARANDINDICES$varName)
map_SetupTemplate_vi <- MODEL$getVarInfo(NEWVARNAME)
map_SetupTemplate_mapParts <- nimble:::varAndIndices2mapParts(VARANDINDICES, map_SetupTemplate_vi$maxs, map_SetupTemplate_vi$nDim)
MSTRIDES <- map_SetupTemplate_mapParts$strides
MOFFSET <- map_SetupTemplate_mapParts$offset
MSIZES <- map_SetupTemplate_mapParts$sizes
VARACCESSOR <- nimble:::singleVarAccess(model, NEWVARNAME)
}),
makeCodeSubList = function(resultName, argList){
list(VARACCESSOR = as.name(resultName),
NODEVARNAME = argList$nodeExpr,
NEWVARNAME = as.name(paste0(resultName, '_newVarName')),
VARANDINDICES = as.name(paste0(resultName, '_varAndIndices')),
MODEL = argList$model,
MSTRIDES = as.name(paste0(resultName, '_strides')),
MOFFSET = as.name(paste0(resultName, '_offset')),
MSIZES = as.name(paste0(resultName, '_sizes')))
})
singleModelValuesAccessor_SetupTemplate <- setupCodeTemplateClass(
#Note to programmer: required fields of argList are modelValues, var, row, code
makeName = code2Name_fromArgList,
codeTemplate = quote({
MVACCESS <- nimble:::singleModelValuesAccess(MODELVALUES, VAR)
}),
makeCodeSubList = function(resultName, argList){
list(MVACCESS = as.name(resultName),
MODELVALUES = argList$modelValues,
VAR = argList$var)
}
)
#### KEYWORD PROCESSING UTILITIES
isCodeArgBlank <- function(code, arg){
#return(nchar(code[[arg]]) == 0)
return(is.null(code[[arg]]))
}
# Utility functions to make things a little neater
isSetupCodeGenerated <- function(name, nfProc)
name %in% nfProc$newSetupOutputNames
addSetupCodeNames <- function(name, otherNames, nfProc)
nfProc$newSetupOutputNames <- c(name, otherNames, nfProc$newSetupOutputNames)
addBlockFromCppName <- function(name, nfProc)
nfProc$blockFromCppNames <- c(name, nfProc$blockFromCppNames)
addNewCode <- function(name, subList, template, nfProc)
nfProc$newSetupCode[[name]] <- eval(substitute(substitute(TEMPLATE, subList), list(TEMPLATE = template$codeTemplate) ) )
addNecessarySetupCode <- function(name, argList, template, nfProc, allowToCpp = TRUE){
if(is.null(nfProc)) stop("Trying to add setup code for a nimbleFunction with no setup code.")
if(!isSetupCodeGenerated(name, nfProc)){
addSetupCodeNames(name, template$makeOtherNames(name, argList), nfProc)
subList <- template$makeCodeSubList(name, argList)
addNewCode(name, subList, template, nfProc)
if(!allowToCpp) addBlockFromCppName(name, nfProc) ## ignores makeOtherNames for now
}
}
getSymObj_recurse <- function(code, symTab, recurse = FALSE) { #code will be like a$b$c with expectation all are NF or NL
if(length(code) > 1) {
if(deparse(code[[1]]) != '$') return(NULL) ## This is valid if we have makeNewNimbleListObject(...)$member or foo()$member
firstArg <- code[[2]]
memberName <- deparse(code[[3]])
symTab <- getSymObj_recurse(firstArg, symTab, recurse = TRUE) ## when recursing, return the symTab
} else {
memberName <- deparse(code)
}
symObject <- if(is.null(symTab)) NULL else symTab$getSymbolObject(memberName)
if(recurse) {
if(inherits(symObject, 'symbolNimbleFunction')) return(symObject$nfProc$setupSymTab)
if(inherits(symObject, 'symbolNimbleList')) return(symObject$nlProc$symTab) ## can only be known if it was created in setup code
if(is.null(symObject)) return(NULL) ## will assume to be nimbleList, only kind of nested data structure that could be of unknown type right now
} else {
return(symObject)
}
stop(paste0('Problem (ii) working through ', deparse(code)), .call = FALSE)
}
symTypeFromSymTab <- function(codeName, symTab, options = character(0) ){
if(is.language(codeName))
codeName <- as.character(codeName)
if(length(codeName) > 1)
return('NULL')
class <- class(symTab$symbols[[codeName]])[1]
if(length(options) == 0)
return(class)
if(!(class %in% options))
return(NULL) ## nimbleList that was not constructed in setup code
return(class)
}
isSymbolType <- function(symTab, varName, symType)
inherits(symTab$symbols[[varName]], symType)
matchAndFill.call <- function(def, call){
## Note re: matchAndFill.call(function(a = 1, ..., b = 2){}, quote(foo(b = 1, 2, 3))): behavior on this is due to match.call
theseFormals <- formals(def)
formalNames <- names(theseFormals) # formalArgs are the arguments that are defined, i.e. does NOT include anything that is from the args "..."
theseFormals <- theseFormals[nchar(theseFormals) > 0]
matchedCall <- match.call(def, call) # problem with match.call for our needs is it omits formals that were not provided
missingArgs <- which(!(names(theseFormals) %in% names(matchedCall)))
for(ind in missingArgs){ ## this puts back in anything omitted, but order may become wrong
name <- names(theseFormals)[ind]
matchedCall[[name]] <- (if(is.null(theseFormals[[name]])) list(NULL) else theseFormals[[name]])
}
newCall <- matchedCall[1]
if(is.null(names(matchedCall))) names(matchedCall) <- c("CALL_", rep("", length(matchedCall) - 1)) ## strangely assigning all "" values results in NULL
indexAdditionalArgs <- which(!(names(matchedCall)[-1] %in% formalNames))
for(thisArgName in formalNames){ # This is to get the order of the arguments correctly and to insert unmatched arguemnts to ... location if appropriate
if(thisArgName == '...') {
for(thisIndex in indexAdditionalArgs) {
thisName <- names(matchedCall)[thisIndex+1]
if(thisName=="")
newCall[[length(newCall) + 1]] <- matchedCall[[thisIndex + 1]]
else {
newCall[[thisName]] <- matchedCall[[thisName]]
}
}
} else {
thisArg <- matchedCall[[thisArgName]]
if(!is.null(thisArg))
newCall[[thisArgName]] <- thisArg
}
}
return(newCall)
}
determineNdimsFromNfproc <- function(modelExpr, varOrNodeExpr, nfProc) {
allNDims <- lapply(nfProc$instances, function(x) {
model <- eval(modelExpr, envir = x)
if(length(varOrNodeExpr) > 1)
stop("One must request a node from a model using syntax like `model[[node]]` and not syntax such as `model[[nodes[i]]]`. For the latter case use `values()` instead.")
if(!exists(as.character(varOrNodeExpr), x, inherits = FALSE) ) {
stop(paste0('Problem accessing node or variable ', deparse(varOrNodeExpr), '.'), call. = FALSE)
}
lab <- eval(varOrNodeExpr, envir = x)
if(length(lab) != 1)
stop(paste0("Length of ",
deparse(varOrNodeExpr),
" requested from ",
deparse(modelExpr),
" using '[[' is ",
length(lab),
". It must be 1." )
, call. = FALSE)
varAndIndices <- nimbleInternalFunctions$getVarAndIndices(lab)
determineNdimFromOneCase(model, varAndIndices)
} )
return(allNDims)
}
## from a$b(), goal is to get symbolObject for a
## from a$b$c(), goal is to get symbolObject for b
matchKeywordCodeMemberFun <- function(code, nfProc) { ## handles cases like a$b(c) as one unit so the member function template for b can be looked up
dollarSignPart <- code[[1]] ## we already checked that code[[1]][[1]] is '$' before calling this function
leftSide <- dollarSignPart[[2]] ## could have further recursing needed. at the moment, nimbleFunction list can only appear at the end of nesting (member data are not part of inheritance)
rightSide <- dollarSignPart[[3]]
memFunName <- deparse(rightSide)
nestedLeftSide <- FALSE
## Step 1: Find the symbol object for whatever is on left-hand side of $
## This may involve recursion
## Only case where the symbol object can be missing (NULL) is nimbleListDef$new() if nimbleListDef if from global env
if(!is.null(nfProc)) { ## If nfProc is null, we are in an RCfunction and the only valid case is nimbleListDef$new()
if(length(leftSide) != 1) {
if(deparse(leftSide[[1]])=='$') {
symObj <- getSymObj_recurse(leftSide, nfProc$setupSymTab)
nestedLeftSide <- TRUE
} else {
nfNestedCall <- leftSide[[1]]
if(length(nfNestedCall) != 1) stop(paste0("Cannot handle this expression: ", deparse(code)))
if(deparse(nfNestedCall) != '[[') stop(paste0("Cannot handle this expression: ", deparse(code)))
leftLeftSide <- leftSide[[2]]
if(length(leftLeftSide) != 1) {
if(deparse(leftLeftSide[[1]]) == '$') { ##a$b[[i]]$foo()
symObj <- getSymObj_recurse(leftLeftSide, nfProc$setupSymTab)
nestedLeftSide <- TRUE
} else stop('Problem processing something like a$b[[i]]$foo()')
} else {
nfListName <- deparse(leftSide[[2]])
if(nfProc$setupSymTab$symbolExists(nfListName)) { ## look in symbol table
symObj <- nfProc$setupSymTab$getSymbolObject(nfListName)
}
}
}
} else {
symTab <- nfProc$setupSymTab
symObj <- symTab$getSymbolObject(deparse(leftSide))
}
} else {
symTab <- symObj <- NULL
}
if(memFunName=='new') { ## this is unique because in non-nested mode, this can be looking for a nlDef in global environment (or possibly elsewhere, but not dealt with)
## symObj can be null here
if(is.null(symObj)) {
if(nestedLeftSide) stop('Cannot find nested nimbleList definition')
nlGenName <- deparse(leftSide)
if(exists(nlGenName, where = globalenv())) {
possibleNLgen <- get(nlGenName, envir = globalenv())
if(is.nlGenerator(possibleNLgen)) {
thisFunctionMatch <- makeNimbleListTemplateWithBlankFirstArg(nl.getListDef(possibleNLgen))
} else {
stop(paste0('problem with ', deparse(code)))
}
} else {
stop(paste0('problem with ', deparse(code)))
}
} else {
thisFunctionMatch <- makeNimbleListTemplateWithBlankFirstArg(nl.getListDef(symObj$nlProc$nlGenerator))
}
for(i in seq_along(code[-1])) code[[i+1]] <- matchKeywords_recurse(code[[i+1]], nfProc)
code[[ length(code) + 1]] <- leftSide ## add '.LEFTSIDE = leftSide' arg to code
names(code)[length(code)] <- '.LEFTSIDE'
code[[1]] <- as.name('makeNewNimbleListObject') ## modify first arg of code to be desired name of call
return(matchAndFill.call(thisFunctionMatch, code ) ) ## should create makeNewNimbleListObject( nimbleListCallMaybeNested, var1, var2, etc.)
}
if(is.null(symObj)) stop('Problem looking up object')
if(symObj$type == 'nimbleFunction') {
thisRCfunProc <- symObj$nfProc$RCfunProcs[[memFunName]]
if(is.null(thisRCfunProc)) stop(paste0("Cannot handle this expression (member function may not exist): ", deparse(code)), call. = FALSE)
thisFunctionMatch <- thisRCfunProc$RCfun$template
return(matchAndFill.call(thisFunctionMatch, code ) )
}
if(inherits(symObj, 'symbolModel')) {
if(nestedLeftSide) stop('Access to a model cannot be nested.')
thisFunctionMatch <- matchModelMemberFunctions[[ memFunName ]]
if(is.null(thisFunctionMatch)) stop(paste0("Cannot handle this expression (looks like a model with an invalid member function call?): ", deparse(code)))
return(matchAndFill.call(thisFunctionMatch, code) )
}
if(inherits(symObj, 'symbolNimbleFunctionList')) {
thisBaseClass <- symObj$baseClass
thisFunctionMatch <- environment(symObj$baseClass)$methodList[[memFunName]]$template
return(matchAndFill.call(thisFunctionMatch, code ) )
}
stop(paste0("Cannot handle this expression: ", deparse(code)))
}
matchKeywordCode <- function(code, nfProc){
callName <- as.character(code[[1]])
thisFunctionMatch <- matchFunctions[[ callName ]]
## see if this is a member function of an nf object
if(!is.null(nfProc)) {
modCallName <- callName
if(nfProc$setupSymTab$symbolExists(modCallName)) {
symObj <- nfProc$setupSymTab$getSymbolObject(modCallName)
if(inherits(symObj, "symbolMemberFunction")) {
thisRCfunProc <- nfProc$RCfunProcs[[modCallName]]
if(is.null(thisRCfunProc)) stop(paste0("Cannot handle this expression (looks like a member function but something is wrong): ", deparse(code)), call. = FALSE)
thisFunctionMatch <- thisRCfunProc$RCfun$template
return(matchAndFill.call(thisFunctionMatch, code ) )
}
}
}
## see if this is a call to an RCfunction
if(is.null(thisFunctionMatch)) {
if(exists(callName)) {
callObj <- get(callName)
if(is.rcf(callObj)) {
thisFunctionMatch <- callObj
}
}
}
if(!is.null(thisFunctionMatch))
return(matchAndFill.call(thisFunctionMatch, code ) )
return(code)
}
matchKeywords_recurse <- function(code, nfProc = NULL) {
cl = length(code)
if(cl == 1){ ## There are no arguments
if(is.call(code)){
if(length(code[[1]]) > 1) {
if(deparse(code[[1]][[1]]) == '$') code <- matchKeywordCodeMemberFun(code, nfProc)
else
code[[1]] <- matchKeywords_recurse(code[[1]], nfProc) ## recurse on the "a$b" part of a$b() (or the "a(b)" part of a(b)()), etc
} else
code <- matchKeywordCode(code, nfProc)
}
return(code)
}
if(length(code[[1]]) == 1) ## a simple call like a(b,c), not a$b(c)
code <- matchKeywordCode(code, nfProc)
if(is.call(code)) {
if(length(code[[1]]) > 1) {
if(deparse(code[[1]][[1]]) == '$') code <- matchKeywordCodeMemberFun(code, nfProc) ## handle a$b(c) as one unit
else code[[1]] <- matchKeywords_recurse(code[[1]], nfProc) ## handle "a(b)" part of a(b)(c), which is probably *never* triggered
}
if(cl >= 2) { ## recurse through arguments
for(i in 2:cl) {
code[[i]] <- matchKeywords_recurse(code[[i]], nfProc)
}
}
}
return(code)
}
makeSingleIndexAccessExpr <- function(newName, newNameExpr) {
codeNames <- makeSingleIndexAccessCodeNames(newName)
subList <- lapply(codeNames, as.name)
ans <- substitute( name[MflatIndex], c(list(name = newNameExpr), subList))
ans
}
## want map(name, nDim, offset, sizelist, stridelist)
## this is a unique case, where sizelist and stridelist are just lists
## stuck in there
makeMapAccessExpr <- function(newName, newNameExpr, nDim) { ## newNameExpr not used any more!
codeNames <- makeMapSetupCodeNames(newName)
subList <- lapply(codeNames, as.name)
if(nDim == 0) { ## not sure this can happen
sizeExprList <- strideExprList <- list()
}
if(nDim == 1) {
sizeExprList <- list(substitute(Msizes, subList))
strideExprList <- list(substitute(Mstrides, subList))
}
if(nDim >= 2) {
sizeExprList <- rep(list( substitute(Msizes[1], subList)), nDim)
for(i in 1:nDim) sizeExprList[[i]][[3]] <- i
strideExprList <- rep(list( substitute(Mstrides[1], subList)), nDim)
for(i in 1:nDim) strideExprList[[i]][[3]] <- i
}
ans <- substitute(map( name, nDim, Moffset, sizes, strides),
c(subList, list(nDim = nDim, name = newName, sizes = sizeExprList, strides = strideExprList)))
ans
}
determineNdimFromOneCase <- function(model, varAndIndices) {
varInfo <- try(model$getVarInfo(as.character(varAndIndices$varName)))
if(inherits(varInfo, 'try-error')) stop(paste0('In determineNdimFromOneCase: error in extracting varInfo for ', varAndIndices$varName), call. = FALSE)
varNdim <- varInfo$nDim
if(length(varAndIndices$indices) == 0) return(varNdim)
if(length(varAndIndices$indices) != varNdim) {
stop(paste0('Error, wrong number of dimensions in a node label for ', varAndIndices$varName, '. Expected ',varNdim,' indices but got ', length(varAndIndices$indices),'.'))
}
dropNdim <- sum(unlist(lapply(varAndIndices$indices, is.numeric)))
return(varNdim - dropNdim)
}
## steps here are similar to makeMapExprFromBrackets, but that uses exprClasses
varAndIndices2mapParts <- function(varAndIndices, sizes, nDim) {
indices <- varAndIndices$indices
## put together offsetExpr, sizeExprs, strideExprs
## need sizes to get strides
if(length(sizes) == 0) sizes <- 1
if(nDim > 0 & length(indices)==0) {
blockBool <- rep(TRUE, nDim)
firstIndexRexprs <- rep(list(1), nDim)
targetSizes <- sizes
} else {
nDim <- length(indices) ## may be redundant/moot
firstIndexRexprs <- vector('list', nDim)
targetSizes <- integer(nDim)
blockBool <- rep(FALSE, nDim)
for(i in seq_along(indices)) {
if(is.blank(indices[[i]])) {
blockBool[i] <- TRUE
firstIndexRexprs[[i]] <- 1
targetSizes[i] <- sizes[i]
}
else if(is.numeric(indices[[i]])) {
firstIndexRexprs[[i]] <- indices[[i]]
} else {
## better be :
if(indices[[i]][[1]] != ":") stop("error, expecting : here")
blockBool[i] <- TRUE
firstIndexRexprs[[i]] <- indices[[i]][[2]]
targetSizes[i] <- indices[[i]][[3]] - indices[[i]][[2]] + 1
}
}
}
strides <- c(1, cumprod(sizes[-length(sizes)]))
sourceStrideRexprs <- as.list(strides)
targetOffsetRexpr <- makeOffsetRexpr(firstIndexRexprs, sourceStrideRexprs)
targetStrides <- strides[blockBool]
targetSizes <- targetSizes[blockBool]
list(offset = eval(targetOffsetRexpr),
sizes = targetSizes,
strides = targetStrides)
}
getVarAndIndices <- function(code) {
if(is.character(code)) code <- parse(text = code, keep.source = FALSE)[[1]]
if(length(code) > 1) {
if(code[[1]] == '[') {
varName <- code[[2]]
indices <- as.list(code[-c(1,2)])
} else {
stop(paste('Error:', deparse(code), 'is a malformed node label.'))
}
} else {
varName <- code
indices <- list()
}
list(varName = varName, indices = indices)
}
## This takes the indices field returned by getVarAndIndices and turns it into a matrix
## e.g. from getVarAndIndices('x[1:3, 2:4]'), we have varName = 'x' and indices = list(quote(1:3), quote(2:4))
## indexExprs2matrix takes the indices and makes [1 3; 2 4]
varAndIndices2flatIndex <- function(varAndIndices, varInfo) {
if(length(varInfo$maxs) == 0) return(1) ## A -1 is done automatically, later, so here we should stay in R's 1-based indexing
sizes <- varInfo$maxs
strides <- c(1, cumprod(sizes[-length(sizes)]))
flatIndex <- 1 + sum((unlist(varAndIndices$indices)-1) * strides)
flatIndex
}
makeMapSetupCodeNames <- function(baseName) {
list(Mstrides = paste0(baseName, '_strides'),
Msizes = paste0(baseName, '_sizes'),
Moffset = paste0(baseName, '_offset'))
}
makeSingleIndexAccessCodeNames <- function(baseName) {
list(MflatIndex = paste0(baseName, '_flatIndex'))
}
handleScaleAndRateForGamma <- function(code){
## also handles core R dexp, as well as ddexp, and dinvgamma
scaleArg <- code$scale
rateArg <- code$rate
if(is.null(scaleArg) && is.null(rateArg)) stop('neither scale nor rate defined in dgamma, invgamma, dexp, or ddexp')
codeName <- deparse(code[[1]])
dist <- substring(codeName, 2, nchar(codeName))
if(dist == 'invgamma' || dist == 'sqrtinvgamma') { ## For [drpq]invgamma
if(is.null(rateArg)) {
rateArg <- substitute(1.0/(A), list(A = code$scale))
code$scale <- rateArg
names(code)[which(names(code) == 'scale')] <- 'rate' # to preserve correct order
}
code$scale <- NULL
} else if(dist == 'dexp') { ## This is for [drpq]dexp
## The logic here is trickier. scale has a default value and is canonical (what is needed for C).
## If rate was provided, then by the time we are here, matchFunctions has been used (matchAndFill.call),
## so there will also be a scale, since it has a default
setScaleArg <- FALSE
if(is.null(scaleArg)) setScaleArg <- TRUE ## scale is not expected to be null ever (see previous comment), but this is defensive.
if(!is.null(scaleArg) & !is.null(rateArg)) setScaleArg <- TRUE ## Both are there, so set scale from the provided rate
if(setScaleArg) {
code$scale <- NULL
scaleArg <- substitute(1.0/(A), list(A = code$rate))
code$rate <- scaleArg
names(code)[which(names(code) == 'rate')] <- 'scale' # to preserve correct order
}
code$rate <- NULL
} else { # dgamma
if(is.null(scaleArg)) {
scaleArg <- substitute(1.0/(A), list(A = code$rate))
code$rate <- scaleArg
names(code)[which(names(code) == 'rate')] <- 'scale' # to preserve correct order
}
code$rate <- NULL
}
return(code)
}
handleScaleAndRateForExpNimble <- function(code){
scaleArg <- code$scale
rateArg <- code$rate
if(is.null(scaleArg) && is.null(rateArg)) stop('neither scale nor rate defined in dexp_nimble')
if(is.null(rateArg)) {
rateArg <- substitute(1.0/(A), list(A = code$scale))
code$scale <- rateArg
names(code)[which(names(code) == 'scale')] <- 'rate' # to preserve correct order
}
code$scale <- NULL
return(code)
}
## wrtNodes are nodes with respect to which derivatives will be taken
## (i.e. denominator of dy/dx). wrtNodes may or may not be part of
## calcNodes
## extraInputNodes are nodes needed in calculation of derivatives but
## are not wrtNodes. They include two categories: (i) parents of
## any calcNodes that are not themselves calcNodes or wrtNodes;
## (ii) any stochastic calcNodes, because the node values are needed.
## However, stochastic calcNodes that are in constantNodes are not
## included in extraInputNodes.
## constantNodes are nodes that are assumed to be constant for all
## derivative calls throughout the life of the nimbleFunction.
## They will be baked in to the CppAD tape and cannot then be changed.
## They will typically be model data.
## modelOutputNodes are nodes whose values are calculated as part of the
## tape "forward-zero" stage (value calculation) and need to be stored
## in the model. It appears more efficient to copy them in to the model
## than to use the regular model$calculate() itself.
## modelOutputNodes will include all deterministic nodes in calcNodes
## as well as the logProb_ node for any stochastic nodes in calcNodes.
## calcNodes is the same as calcNodes for model$calculate(calcNodes). It is
## the ordered sequence of nodes to be calculated
nimDerivsInfoClass_init_impl <- function(.self
, wrtNodes
, calcNodes
, model) {
.self$model <- model
## wrt nodes
wrtNodes <- model$expandNodeNames(wrtNodes, returnScalarComponents = TRUE)
wrtNodesAccessor <- modelVariableAccessorVector(model,
wrtNodes,
logProb = FALSE)
.self$wrtMapInfo <- makeMapInfoFromAccessorVectorFaster(wrtNodesAccessor)
# See comment in makeModelDerivsInfo for explanation of why both of the next
# two lines are necessary.
calcNodes <- model$expandNodeNames(calcNodes)
calcNodes <- model$expandNodeNames(calcNodes, returnScalarComponents = TRUE)
derivsInfo <- makeModelDerivsInfo_impl(model,
wrtNodes,
calcNodes,
dataAsConstantNodes = TRUE)
constantNodes <- derivsInfo$constantNodes
updateNodes <- derivsInfo$updateNodes
extraInputNodesAccessor <- modelVariableAccessorVector(model,
updateNodes,
logProb = FALSE)
.self$extraInputMapInfo <-
makeMapInfoFromAccessorVectorFaster(extraInputNodesAccessor)
constantNodesAccessor <- modelVariableAccessorVector(model,
constantNodes,
logProb = FALSE)
.self$constantMapInfo <- makeMapInfoFromAccessorVectorFaster(constantNodesAccessor)
## output nodes: deterministic nodes in calcNodes plus logProb nodes
## but not the actual data nodes.
modelOutputNodes <- makeOutputNodes(model, calcNodes)
modelOutputNodesAccessor <- modelVariableAccessorVector(model,
modelOutputNodes,
logProb = FALSE)
.self$modelOutputMapInfo <-
makeMapInfoFromAccessorVectorFaster(modelOutputNodesAccessor)
NULL
}
makeOutputNodes <- function(model,
calcNodes) {
## Need to do `isDeterm` on nodes, not node components (issue 1431).
## Presuming (and based on a simple test) that by now,
## input `calcNodes` would include all encompassing nodes
## and that this next step would not introduce any additional components.
calcNodes <- model$expandNodeNames(calcNodes)
logProbCalcNodeNames <- model$modelDef$nodeName2LogProbName(calcNodes)
isDetermCalcNodes <- model$isDeterm(calcNodes, nodesAlreadyExpanded = TRUE)
modelOutputNodes <- c(model$expandNodeNames(calcNodes[isDetermCalcNodes], returnScalarComponents = TRUE),
logProbCalcNodeNames)
modelOutputNodes
}
nimDerivsInfoClass_output_init_impl <- function(.self,
calcNodes,
model) {
.self$model <- model
wrtNodesAccessor <- modelVariableAccessorVector(model,
character(),
logProb = FALSE)
.self$wrtMapInfo <- makeMapInfoFromAccessorVectorFaster(wrtNodesAccessor)
constantNodesAccessor <- modelVariableAccessorVector(model,
character(),
logProb = FALSE)
.self$constantMapInfo <- makeMapInfoFromAccessorVectorFaster(constantNodesAccessor)
extraInputNodesAccessor <- modelVariableAccessorVector(model,
character(),
logProb = FALSE)
.self$extraInputMapInfo <-
makeMapInfoFromAccessorVectorFaster(extraInputNodesAccessor)
modelOutputNodes <- makeOutputNodes(model, calcNodes)
modelOutputNodesAccessor <- modelVariableAccessorVector(model,
modelOutputNodes,
logProb = FALSE)
.self$modelOutputMapInfo <-
makeMapInfoFromAccessorVectorFaster(modelOutputNodesAccessor)
NULL
}
#' Information on model structure used for derivatives
#'
#' Inspect structure of a nimble model to determine nodes needed as "update"
#' and/or "constant" entries in usage of nimDerivs. This will typically be used
#' in the setup code of a nimbleFunction.
#'
#' @param model a nimble model object, such as returned from \code{nimbleModel}.
#' @param wrtNodes a character vector of node names in the model with respect to
#' which derivatives will be taken through a call to \code{nimDerivs} (same as
#' \code{derivs}).
#' @param calcNodes a character vector of node names in the model that will be
#' used in \code{model$calculate(calcNodes)} while derivatives are being
#' recorded.
#' @param dataAsConstantNodes logical indicating whether data nodes in the model
#' should automatically be treated as "constant" entries (TRUE) or "update"
#' entries (FALSE). Defaults to TRUE.
#'
#' @details In the compilable parts of a \code{nimbleFunction} (i.e. \code{run}
#' or other method code, not \code{setup} code), a call like
#' \code{nimDerivs(foo(x), ...)} records derivatives of \code{foo(x)}. If
#' \code{foo} contains any calls to \code{model$calculate(calcNodes)}, it may
#' be necessary to provide auxiliary information about the model in further
#' arguments to \code{nimDerivs}, specifically the \code{model},
#' \code{updateNodes} and \code{constantNodes} arguments.
#' `makeModelDerivsInfo` is a utility to set up that information for typical
#' use cases. It returns a list with elements \code{updateNodes} and
#' \code{constantNodes} to be passed as arguments of the same name to
#' \code{nimDerivs} (along with passing the \code{model} as the \code{model}
#' argument).
#'
#' The reason auxiliary information is needed is that recording of derivatives
#' uses a different model than for regular calculations. Together,
#' \code{updateNodes} and \code{constantNodes} should contain all nodes whose
#' values are needed for the model calculations being recorded and that are not
#' part of \code{wrtNodes}. These may include parents of nodes that are in
#' \code{calcNodes} but are not themselves in \code{calcNodes}, as well as the
#' values of stochastic nodes in \code{calcNodes}, which are needed to calculate
#' the corresponding log probabilities. \code{updateNodes} will have their
#' values updated from the regular model every time that recorded derivative
#' calculations are used. \code{constantNodes} will not be updated every time,
#' which means their values will be permanently fixed either the first time the
#' call to `nimDerivs` is invoked or on any subsequent call that has
#' \code{reset=TRUE}. Use of \code{constantNodes} can be slightly more
#' efficient, but one must be careful to be aware that values will not be
#' updated unless \code{reset=TRUE}. See the automatic differentiation section
#' of the User Manual for more information.
#'
#' In the above explanation, care must be taken to understand what should be
#' included in \code{wrtNodes}. In a typical use case, some arguments to
#' \code{foo} are put into the model using \code{values(model, nodes) <-
#' some_foo_arguments}. Next there is typically a call to
#' \code{model$calculate(calcNodes)}. Here the \code{nodes} are considered
#' "with-respect-to" nodes because derivative tracking will follow the arguments
#' of \code{foo}, including when they are put into a model and hence used in
#' \code{model$calculate}. Therefore these \code{nodes} should be the
#' \code{wrtNodes} for \code{makeModelDerivsInfo}.
#'
#' @return A list with elements \code{updateNodes} and \code{constantNodes}.
#' These shouls be provided as the same-named arguments to \code{nimDerivs}
#' (same as \code{derivs}).
#'
#' When using double-taping of derivatives (i.e. \code{foo} contains another
#' call to \code{nimDerivs}), both calls to \code{nimDerivs} should include the
#' \code{model}, \code{updateNodes}, and \code{constantNodes} arguments.
#'
#' @export
makeModelDerivsInfo <- function(model,
wrtNodes,
calcNodes,
dataAsConstantNodes = TRUE) {
wrtNodes <- model$expandNodeNames(wrtNodes, returnScalarComponents = TRUE)
# This ensures that elements of a non-scalar node become the entire non-scalar node.
calcNodes <- model$expandNodeNames(calcNodes)
# And then this splits into scalar components.
# E.g. if calcNodes is 'mu[1]' but 'mu[1:3]' is a vector node,
# the above call gets `mu[1:3]` and then the below call splits it.
calcNodes <- model$expandNodeNames(calcNodes, returnScalarComponents = TRUE)
makeModelDerivsInfo_impl(model,
wrtNodes,
calcNodes,
dataAsConstantNodes)
}
getImmediateParentNodes <- function(nodes, model) {
## adapted from BUGS_modelDef creation of edgesFrom2To
maps <- model$modelDef$maps
maxNodeID <- length(maps$vertexID_2_nodeID) ## should be same as length(maps$nodeNames)
edgesLevels <- if(maxNodeID > 0) 1:maxNodeID else numeric(0)
fedgesTo <- factor(maps$edgesTo, levels = edgesLevels) ## setting levels ensures blanks inserted into the splits correctly
edgesTo2From <- split(maps$edgesFrom, fedgesTo)
nodeIDs <- model$expandNodeNames(nodes, returnType = "ids")
fromIDs <- sort(unique(unlist(edgesTo2From[nodeIDs])))
fromNodes <- maps$graphID_2_nodeName[fromIDs]
fromNodes
}
makeModelDerivsInfo_impl <- function(model,
wrtNodes,
calcNodes,
dataAsConstantNodes = TRUE) {
## Gymnastics to convert to actual nodes for computational efficiency are needed because `setdiff` needs to
## operate on node components because `wrt` is in terms of components not nodes.
nonWrtCalcNodes <- setdiff(calcNodes, wrtNodes) # Node components here, since `calcNodes`, `wrtNodes` are as components upon input.
nonWrtCalcActualNodes <- model$expandNodeNames(nonWrtCalcNodes) # Nodes here. Can be costly for large multivar nodes (say 3 sec. for a 1m-element node).
nonWrtStochCalcNodes <- nonWrtCalcActualNodes[ model$isStoch(nonWrtCalcActualNodes,
nodesAlreadyExpanded = TRUE) ] # Run `isStoch` on nodes not components (issue #1431).
parentNodes <- getImmediateParentNodes(calcNodes, model)
parentNodes <- model$expandNodeNames(parentNodes, returnScalarComponents = TRUE)
neededParentNodes <- setdiff(parentNodes, c(wrtNodes, nonWrtCalcNodes))
extraInputNodes <- model$expandNodeNames(c(neededParentNodes,
nonWrtStochCalcNodes)) # Need as nodes so `isData` below run on nodes for efficiency.
constantNodes <- character()
if(dataAsConstantNodes) {
boolData <- model$isData(extraInputNodes)
constantNodes <- model$expandNodeNames(extraInputNodes[boolData], returnScalarComponents = TRUE, sort = TRUE)
extraInputNodes <- model$expandNodeNames(extraInputNodes[!boolData], returnScalarComponents = TRUE, sort = TRUE)
## `wrtNodes` components could have crept in when initializing `extraInputNodes` based on nodes.
extraInputNodes <- setdiff(extraInputNodes, wrtNodes)
constantNodes <- setdiff(constantNodes, wrtNodes)
} else {
extraInputNodes <- model$expandNodeNames(extraInputNodes, returnScalarComponents = TRUE, sort = TRUE)
## `wrtNodes` components could have crept in when initializing `extraInputNodes` based on nodes.
extraInputNodes <- setdiff(extraInputNodes, wrtNodes)
}
list(updateNodes = extraInputNodes,
constantNodes = constantNodes)
}
nimDerivsInfoClass_update_init_impl <- function(.self,
updateNodes = NULL,
constantNodes = NULL,
model) {
if(is.null(updateNodes)) updateNodes <- character()
if(is.null(constantNodes)) constantNodes <- character()
.self$model <- model
wrtNodesAccessor <- modelVariableAccessorVector(model,
character(),
logProb = FALSE)
.self$wrtMapInfo <- makeMapInfoFromAccessorVectorFaster(wrtNodesAccessor)
constantNodesAccessor <- modelVariableAccessorVector(model,
constantNodes,
logProb = FALSE)
.self$constantMapInfo <- makeMapInfoFromAccessorVectorFaster(constantNodesAccessor)
extraInputNodesAccessor <- modelVariableAccessorVector(model,
updateNodes,
logProb = FALSE)
.self$extraInputMapInfo <-
makeMapInfoFromAccessorVectorFaster(extraInputNodesAccessor)
modelOutputNodesAccessor <- modelVariableAccessorVector(model,
character(),
logProb = FALSE)
.self$modelOutputMapInfo <-
makeMapInfoFromAccessorVectorFaster(modelOutputNodesAccessor)
NULL
}
nimDerivsInfoClass <- setRefClass(
'nimDerivsInfoClass',
fields = list(
wrtMapInfo = 'ANY'
, extraInputMapInfo = 'ANY'
, modelOutputMapInfo = 'ANY'
, constantMapInfo = 'ANY'
, model = 'ANY'
),
methods = list(
initialize = function(wrtNodes = NULL,
calcNodes = NULL,
updateNodes = NULL,
constantNodes = NULL,
thisModel = NULL,
case = "nimDerivsCalculate",
...) {
if(!isTRUE(thisModel$modelDef$buildDerivs)) {
stop(paste0("To use automatic differentiation involving model calculations,\n",
"include 'buildDerivs = TRUE' in the call to 'nimbleModel' or set\n",
"'nimbleOptions(buildModelDerivs = TRUE)' before calling 'nimbleModel'."), call. = FALSE)
}
switch(case,
nimDerivsCalculate = nimDerivsInfoClass_init_impl(.self = .self,
wrtNodes = wrtNodes,
calcNodes = calcNodes,
model = thisModel),
updateOnly = nimDerivsInfoClass_update_init_impl(.self = .self,
updateNodes = updateNodes,
constantNodes = constantNodes,
model = thisModel),
outputOnly = nimDerivsInfoClass_output_init_impl(.self = .self,
calcNodes = calcNodes,
model = thisModel)
)
}
)
)
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