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Merged
paciorek merged 5 commits into from
Jul 13, 2026
Merged

add topologicallySortNodes #43

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c7c7680
Add topologicallySortNodes as a wrapper around getNodes (via expandNo…
paciorek Jul 13, 2026
4a31137
Add another test of topoSortNodes.
paciorek Jul 13, 2026
9de23db
Remove duplicated definition.
paciorek Jul 13, 2026
1a9dac3
Revert attempt to more efficiently handle idempotency in getNodes.
paciorek Jul 13, 2026
330bfe8
Fix syntax error.
paciorek Jul 13, 2026
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7 changes: 4 additions & 3 deletions nimbleModel/R/model.R
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Original file line number Diff line number Diff line change
Expand Up @@ -382,8 +382,8 @@ getNodes <- function(model, nodes = NULL,

if (!topOnly && !latentOnly && !endOnly) {
result <- lapply(nodes, function(node) applyRules(model$modelDef$declRules, node))
}

}
if (topOnly) result <- lapply(nodes, function(node) applyRules(model$modelDef$topRules, node))
if (latentOnly) result <- lapply(nodes, function(node) applyRules(model$modelDef$latentRules, node))
if (endOnly) result <- lapply(nodes, function(node) applyRules(model$modelDef$endRules, node))
Expand All @@ -402,7 +402,7 @@ getNodes <- function(model, nodes = NULL,
if (includeRHSonly && !stochOnly && !determOnly) { # RHSonly are considered neither determ not stoch.
rhsResult <- lapply(nodes, function(node) applyRules(model$modelDef$rhsOnlyRules, node))
if (!.sort)
result <- c(result, flatten(rhsResult)) # TODO: flatten() seems to be deprecated; can we use unlist?
result <- c(result, flatten(rhsResult))
}

if (.sort) {
Expand Down Expand Up @@ -469,3 +469,4 @@ expandNodeNames <- function(model, nodes, returnScalarComponents = FALSE,
if (unique) result <- unique(result)
return(result)
}

3 changes: 3 additions & 0 deletions nimbleModel/R/modelBaseClass.R
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Expand Up @@ -406,6 +406,9 @@ modelBase_nClass <- nClass(
returnType = "names", sort = FALSE, unique = TRUE) {
nimbleModel::expandNodeNames(self, nodes, returnScalarComponents, "names", sort, unique)
},
topologicallySortNodes = function(nodes) {
nimbleModel::expandNodeNames(self, nodes, sort = TRUE, unique = TRUE)
},
calc_op = function(instr, fn, fn_cpp) {
if (missing(instr)) {
instr <- getVarNames()
Expand Down
10 changes: 6 additions & 4 deletions nimbleModel/tests/testthat/test-nodeChars.R
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Expand Up @@ -55,9 +55,8 @@ test_that("old model API calls", {
y[i,j] ~ dnorm(mu + x,1)
mu ~dnorm(0,1)
})


m <- nimbleModel(code, data = list(y=matrix(rnorm(6),2)))

chars <- m$getNodes(nodesAsChars = TRUE)
expect_identical(chars, c("lifted_mu_plus_x", "y[1, 1]","y[1, 2]","y[1, 3]", "y[2, 1]", "y[2, 2]", "y[2, 3]", "mu"))
chars <- m$getNodes(includeRHSonly = TRUE, nodesAsChars = TRUE)
Expand All @@ -76,7 +75,9 @@ test_that("old model API calls", {
expect_identical(chars, c("mu", "y[1, 1]","y[1, 2]","y[1, 3]", "y[2, 1]", "y[2, 2]", "y[2, 3]", "x"))
chars <- m$expandNodeNames(c('mu','y','x'), sort = TRUE)
expect_identical(chars, c("x", "mu", "y[1, 1]","y[1, 2]","y[1, 3]", "y[2, 1]", "y[2, 2]", "y[2, 3]"))

chars <- m$topologicallySortNodes(c('mu','y','x'))
expect_identical(chars, c("x", "mu", "y[1, 1]","y[1, 2]","y[1, 3]", "y[2, 1]", "y[2, 2]", "y[2, 3]"))

chars <- m$expandNodeNames(c('y','y[2,1]'))
expect_identical(chars, c("y[1, 1]","y[1, 2]","y[1, 3]", "y[2, 1]", "y[2, 2]", "y[2, 3]"))
chars <- m$expandNodeNames(c('y','y[2,1]'), unique = FALSE)
Expand Down Expand Up @@ -220,7 +221,8 @@ test_that("Use of .sort in cases with multiple and/or overlapping sortID values"
expect_identical(m$getNodes(.sort=TRUE,nodesAsChars=TRUE), truth)
expect_identical(m$getParents('y', .sort=TRUE, nodesAsChars = TRUE, self = TRUE), truth)
expect_identical(m$getParents('y[4]', .sort=TRUE, nodesAsChars = TRUE, self = TRUE), c('tau','lifted_d1_over_sqrt_oPtau_cP','y[3]','lifted_rho_times_y_oBi_minus_1_cB_L2[4]', 'y[4]'))

nrs <- m$getNodes()
expect_identical(m$topologicallySortNodes(nrs), truth)

code <- nimbleCode({
for(i in 1:5)
Expand Down
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