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Extract laplace/aghq from nimble #1597

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Merged
paciorek merged 18 commits into from
Nov 28, 2025
Merged

Extract laplace/aghq from nimble #1597

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e740cac
Add marginalization tooling from nimbleQuad codebase.
paciorek Nov 9, 2025
e4dc998
Add node marginalization functionality separate from Laplace.R.
paciorek Nov 9, 2025
0ad72f0
Add node marginalization functionality separate from Laplace.R (2).
paciorek Nov 9, 2025
a157adf
Make placeholders for Laplace/AGHQ functions now in nimbleQuad.
paciorek Nov 9, 2025
4b771b8
Remove Laplace.R.
paciorek Nov 9, 2025
916878a
Remove laplace/aghq test files now in nimbleQuad.
paciorek Nov 9, 2025
3418e14
Fix up file stuff for removing Laplace.
paciorek Nov 9, 2025
a5e3b35
Update Rd files.
paciorek Nov 10, 2025
9018cb2
Fix namespace exports.
paciorek Nov 10, 2025
e6eb2c0
Remove duplicated normTooling stuff from MCMC_samplers.
paciorek Nov 11, 2025
9ee7328
Fix MCEM test relying on laplace.
paciorek Nov 11, 2025
f33cacf
Fix install of nimbleQuad from GH temporarily.
paciorek Nov 11, 2025
ca7e810
Fix syntax in install_requirements.R.
paciorek Nov 11, 2025
89cb307
Use remotes not devtools in CI.
paciorek Nov 11, 2025
ca0ca31
Monkey with MCEM test and nimbleQuad.
paciorek Nov 11, 2025
8d3057f
Monkey with mcem testing while reconciling nimble and nimbleQuad.
paciorek Nov 12, 2025
14915ec
Temporarily comment out use of nimbleQuad in test-mcem.
paciorek Nov 28, 2025
d1a17ee
Merge branch 'devel' into no-laplace
paciorek Nov 28, 2025
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2 changes: 1 addition & 1 deletion UserManual/src/chapter_Laplace.Rmd
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Expand Up @@ -3,7 +3,7 @@

```{r, echo=FALSE}
require(nimble)
require(nimbleSMC, quietly = TRUE, warn.conflicts = FALSE)
require(nimbleQuad, quietly = TRUE, warn.conflicts = FALSE)
```

# Laplace, AGHQ, and nested approximations {#cha-laplace}
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2 changes: 2 additions & 0 deletions install_requirements.R
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Expand Up @@ -12,6 +12,7 @@ requirements <- c(
'pracma', ## for AD
'numDeriv', ## for AD
'mcmcse' ## for MCEM
# 'nimbleQuad' ## for laplace for MCEM test
# 'lme4' ## for test-ADlaplace.R
)

Expand All @@ -26,3 +27,4 @@ for (package in requirements) {

install.packages("lme4", type = "source")


8 changes: 4 additions & 4 deletions packages/nimble/DESCRIPTION
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Expand Up @@ -28,7 +28,7 @@ Authors@R: c(
person("Claudia", "Wehrhahn Cortes", role = "aut", comment = "Bayesian nonparametrics system"),
person("Abel", "Rodr\u00edguez", role = "aut", comment = "Bayesian nonparametrics system"),
person("Duncan", "Temple Lang", role = "aut", comment = "packaging configuration"),
person("Wei", "Zhang", role = "aut", comment = "Laplace approximation"),
person("Wei", "Zhang", role = "aut", comment = "node marginalization"),
person("Sally", "Paganin", role = "aut", comment = "reversible jump MCMC"),
person("Joshua", "Hug", role = "aut", comment = "WAIC"),
person("Paul", "van Dam-Bates", role = "aut", comment = "P\u00f3lya-Gamma sampler, nimIntegrate, matrix exponential"),
Expand Down Expand Up @@ -129,7 +129,6 @@ Collate:
initializeModel.R
parameterTransform.R
CAR.R
Laplace.R
MCMC_utils.R
MCMC_configuration.R
MCMC_build.R
Expand All @@ -144,13 +143,14 @@ Collate:
crossValidation.R
BNP_distributions.R
BNP_samplers.R
setupMargNodes.R
NF_utils.R
miscFunctions.R
normTooling.R
miscAlgorithms.R
makevars.R
setNimbleInternalFunctions.R
registration.R
nimble-package.r
QuadratureGrids.R
miscAlgorithms.R
zzz.R
RoxygenNote: 7.3.2
2 changes: 2 additions & 0 deletions packages/nimble/NAMESPACE
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Expand Up @@ -18,8 +18,10 @@ S3method(as.list, modelValuesBaseClass)
S3method(length, nimPointerList)
export(calc_dmnormConjugacyContributions)
export(calc_dmnormAltParams)
export(calc_dmnorm_inv_ld_AltParams)
export(calc_dwishAltParams)
export(calc_dcatConjugacyContributions)
export(PDinverse_logdet)
export(calc_dcar_normalConjugacyContributionShape)
export(calc_dcar_normalConjugacyContributionRate)
export(CAR_calcM)
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