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update dmnorm handling #65

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update dmnorm handling #65

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dc77cc4
Some fixes to allow dmnorm.
paciorek Oct 24, 2026
90a2ce2
Update tests related to dmnorm
paciorek Oct 24, 2026
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2 changes: 1 addition & 1 deletion nimbleModel/R/getSymbolicParentNodes.R
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ nimbleOrRfunctionNames <- c(
"sd", "var",
"max", "min",
"asRow", "asCol",
"chol",
"nChol",
"inverse",
"forwardsolve", "backsolve", "solve",
"nimEigen", "nimSvd",
Expand Down
1 change: 1 addition & 0 deletions nimbleModel/R/modelDef.R
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Expand Up @@ -542,6 +542,7 @@ modelDefClass <- R6Class(
newValueExpr <- as.call(c(as.list(newValueExpr), boundExprs, nonReqdArgExprs))
newCode <- decl$code
newCode[[3]] <- newValueExpr
newCode <- modelCode <<- nCompiler:::nf_changeKeywords(newCode, nmKeywords)

# Note at this point `boundExprs` set back to NULL as all info in `lower` , `upper` in `valueExpr`.
declInfo[[i]] <<- modelDeclClass$new(
Expand Down
42 changes: 26 additions & 16 deletions nimbleModel/tests/testthat/test-nimbleModel.R
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Expand Up @@ -800,24 +800,23 @@ test_that("non-sequential indexing cases", {
)
m <- mclass$new()

# No opDef for chol so comment out compiled operations.
# cmclass <- nCompile(mclass)
# cm <- cmclass$new()
## C++ compilation error
cmclass <- nCompile(mclass)
cm <- cmclass$new()
truth <- nCompiler:::dmnorm_chol(m$y[c(2, 3, 5)], rep(0, 3), diag(3), log = TRUE)
expect_equal(m$calculate(), truth)
m$simulate("y", includeData = TRUE)
expect_identical(y[c(1, 4)], m$y[c(1, 4)])
expect_false(any(y[c(2, 3, 5)] == m$y[c(2, 3, 5)]))
# expect_equal(cm$calculate('y'), truth)
# cm$simulate(y, includeData = TRUE)
# expect_false(any(y[c(2,3,5)] == cm$y[c(2,3,5)]))
expect_equal(cm$calculate('y'), truth)
cm$simulate(y, includeData = TRUE)
expect_false(any(y[c(2,3,5)] == cm$y[c(2,3,5)]))

nr <- m$getNodes()[[2]]
expect_true(inherits(nr$indexRanges[[1]], "indexRangeMatrixClass"))
expect_identical(nr$numExternalIndexRanges, 0L)
expect_identical(nr$toChar(), "`y[c(2, 3, 5)]`")

# Cannot compile. No operator def for nimC: This was part of the call: y[i = nimC(2, 3, 5)]
code <- nimbleCode({
y[c(2, 3, 5)] <- x[1:3] + 1
})
Expand All @@ -828,12 +827,12 @@ test_that("non-sequential indexing cases", {
m <- mclass$new()
m$calculate()
expect_identical(m$y, c(NA, 2, 3, NA, 4))
expect_error({
cmclass <- nCompile(mclass)
cm <- cmclass$new()
cm$calculate()
expect_identical(cm$y, c(NA, 2, 3, NA, 4))
})
cmclass <- nCompile(mclass)
cm <- cmclass$new()
cm$y <- rep(NA, 5) # Otherwise, y[1],y[4] end up being 5e-310.
cm$calculate()
# TODO: NAs not being represented correctly.
expect_failure(expect_identical(cm$y, c(NA, 2, 3, NA, 4)))
})

test_that("calculate with index offset and switched indices", {
Expand Down Expand Up @@ -2011,11 +2010,11 @@ test_that("duplication cases", {
})
set.seed(99)
mclass <- nimbleModel(code, data = list(y = rnorm(3)), inits = list(z = rep(0, 3), pr = diag(3)), returnClass = TRUE)
# cmclass <- nCompile(mclass)
cmclass <- nCompile(mclass)
m <- mclass$new()
# cm <- cmclass$new()
# C++ compilation error
cm <- cmclass$new()

## TODO: add compiled simulate when {d,r}mnorm_chol is resolved.
m$calculate()
nodes <- c("y[1]", "y[2]")
result <- sum(dnorm(m$y, log = TRUE))
Expand All @@ -2027,6 +2026,17 @@ test_that("duplication cases", {
m$simulate(nodes, includeData = TRUE)
expect_identical(vals, m$y)

cm$calculate()
nodes <- c('y[1]','y[2]')
result <- sum(dnorm(cm$y,log=TRUE))
expect_equal(cm$calculate(nodes), result)

set.seed(1)
vals <- rnorm(3)
set.seed(1)
cm$simulate(nodes, includeData = TRUE)
expect_identical(vals, cm$y)

# With SSM situation.
code <- nimbleCode({
for (i in 3:8) {
Expand Down
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