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extending dimension extent based on inits, with warning #1571

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Merged
paciorek merged 2 commits into from
Jul 26, 2025
Merged

extending dimension extent based on inits, with warning #1571

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60e1817
Address NCT 564 by extending dim extent based on inits
paciorek Jul 10, 2025
77d4339
Merge branch 'devel' into inconsistent_inits
paciorek Jul 26, 2025
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7 changes: 6 additions & 1 deletion packages/nimble/R/BUGS_modelDef.R
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Original file line number Diff line number Diff line change
Expand Up @@ -351,7 +351,9 @@ modelDefClass$methods(assignDimensions = function(dimensions, initsList, dataLis
if(!(length(initDim) == 1 && initDim == 1)) { # i.e., non-scalar inits; 1-length vectors treated as scalars and not passed along as dimension info to avoid conflicts between scalars and one-length vectors/matrices/arrays in various places
if(initName %in% names(dL)) {
if(!identical(as.numeric(dL[[initName]]), as.numeric(initDim))) {
messageIfVerbose(' [Warning] Inconsistent dimensions between inits and dimensions arguments: ', initName, '; ignoring dimensions in inits.')
messageIfVerbose(" [Warning] Inconsistent dimensions between `inits` and `dimensions`\n",
" Ignoring dimensions in `dimensions`.")
dL[[initName]] <- initDim ## Changed 2025-07-09 to avoid inconsistent compiled/uncompiled behavior.
}
} else {
dL[[initName]] <- initDim
Expand Down Expand Up @@ -2732,6 +2734,9 @@ modelDefClass$methods(genVarInfo3 = function() {
if(!(dimVarName %in% names(varInfo))) next
if(length(dimensionsList[[dimVarName]]) != varInfo[[dimVarName]]$nDim) stop('inconsistent dimensions for variable ', dimVarName)
if(any(dimensionsList[[dimVarName]] < varInfo[[dimVarName]]$maxs)) stop(paste0('dimensions specified are smaller than model specification for variable \'', dimVarName, '\''))
if(any(dimensionsList[[dimVarName]] > varInfo[[dimVarName]]$maxs))
messageIfVerbose(" [Warning] dimensions specified are larger than model specification\n",
" for variable `", dimVarName, "`.")
varInfo[[dimVarName]]$maxs <<- dimensionsList[[dimVarName]]
}

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31 changes: 27 additions & 4 deletions packages/nimble/tests/testthat/test-models.R
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Expand Up @@ -383,7 +383,29 @@ test_that("test of using dimensions of inits when dimension information not avai
expect_error(m <- nimbleModel(code, data = list(y = rep(1, 3))), info = "expected error because dimension of mu is unknown")
m <- nimbleModel(code, data = list(y = rep(1, 3)), inits = list(k = rep(1, 3), mu = 1:5))
expect_equal(m$modelDef$dimensionsList$mu, 5, info = "dimension for mu not equal to that given in inits")
expect_message(m <- nimbleModel(code, data = list(y = rep(1, 3)), inits = list(k = rep(1, 3), mu = 1:8), dimensions = list(mu = 5)), "Inconsistent dimensions between inits and dimensions")
expect_message(m <- nimbleModel(code, data = list(y = rep(1, 3)), inits = list(k = rep(1, 3), mu = 1:8), dimensions = list(mu = 5)), "Inconsistent dimensions between `inits` and `dimensions`")
})

test_that("test of using dimensions of inits different than LHS dimensions:", {
code <- nimbleCode({
for(i in 1:4){
y[i] ~ dnorm(S[site[i]], 1)
S[i] ~ dnorm(0,1)
}
})
expect_error(m <- nimbleModel(code, data = list(y = rnorm(4)), inits=list(site=rep(1,4), S=rnorm(2))),
"dimensions specified are smaller")

code <- nimbleCode({
for(i in 1:4){
y[i] ~ dnorm(S[site[i]], 1)
S[i] ~ dnorm(0,1)
}
})
expect_message(m <- nimbleModel(code, data = list(y = rnorm(4)), inits=list(site=rep(1,4), S=rnorm(10))),
"dimensions specified are larger than model specification")
cm <- compileNimble(m)
expect_identical(m$S, cm$S)
})

test_that("test of using dimensions of data when dimension information not available:", {
Expand Down Expand Up @@ -945,7 +967,8 @@ test_that("bad size or dimension of initial values", {

## For better or worse, length of 5 gets baked in based on inits.
## TODO: do we want to reconsider whether this should error out?
m <- nimbleModel(code, inits = list(z = rnorm(5)))
expect_message(m <- nimbleModel(code, inits = list(z = rnorm(5))),
"dimensions specified are larger than model specification")
cm <- compileNimble(m)
expect_identical(m$z, cm$z)

Expand All @@ -958,8 +981,8 @@ test_that("bad size or dimension of initial values", {
### matrix

## For better or worse, 4x2 gets baked in based on inits.
## TODO: do we want to reconsider whether this should error out?
m <- nimbleModel(code, inits = list(b = matrix(rnorm(8),4,2)))
expect_message(m <- nimbleModel(code, inits = list(b = matrix(rnorm(8),4,2))),
"dimensions specified are larger than model specification")
cm <- compileNimble(m)
expect_identical(m$b, cm$b)

Expand Down
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