updated nimbleHMC to include userEnv argument

Author: danielturek

nimbleHMC/DESCRIPTION

@@ -1,13 +1,13 @@
 Package: nimbleHMC
 Title: Hamiltonian Monte Carlo and Other Gradient-Based MCMC Sampling Algorithms for 'nimble'
-Version: 0.2.3
+Version: 0.2.4
 Date: 2024-12-18
 Authors@R: c(person("Daniel", "Turek", role = c("aut", "cre"), email = "danielturek@gmail.com"),
 	     person("Perry", "de Valpine", role = "aut"),
 	     person("Christopher", "Paciorek", role = "aut"))
 Maintainer: Daniel Turek <danielturek@gmail.com>
 Description: Provides gradient-based MCMC sampling algorithms for use with the MCMC engine provided by the 'nimble' package.  This includes two versions of Hamiltonian Monte Carlo (HMC) No-U-Turn (NUTS) sampling, and (under development) Langevin samplers.  The `NUTS_classic` sampler implements the original HMC-NUTS algorithm as described in Hoffman and Gelman (2014) <doi:10.48550/arXiv.1111.4246>.  The `NUTS` sampler is a modern version of HMC-NUTS sampling matching the HMC sampler available in version 2.32.2 of Stan (Stan Development Team, 2023). In addition, convenience functions are provided for generating and modifying MCMC configuration objects which employ HMC sampling. Functionality of the 'nimbleHMC' package is described further in Turek, et al (2024) <doi: 10.21105/joss.06745>.
-Depends: R (>= 3.5.0), nimble (>= 1.0.0)
+Depends: R (>= 3.5.0), nimble (>= 1.4.0)
 Imports: methods
 Suggests: testthat
 License: BSD_3_clause + file LICENSE | GPL (>= 2)

nimbleHMC/R/HMC_configuration.R

@@ -320,11 +320,12 @@ nimbleHMC <- function(code,
                       samples = TRUE,
                       samplesAsCodaMCMC = FALSE,
                       summary = FALSE,
-                      WAIC = FALSE) {
+                      WAIC = FALSE,
+                      userEnv = parent.frame()) {
     if(missing(code) && missing(model)) stop('must provide either code or model argument')
     if(!samples && !summary && !WAIC) stop('no output specified, use samples = TRUE, summary = TRUE, or WAIC = TRUE')
     if(!missing(code) && inherits(code, 'modelBaseClass')) model <- code   ## let's handle it, if model object is provided as un-named first argument
-    Rmodel <- mcmc_createModelObject(model, inits, nchains, setSeed, code, constants, data, dimensions, check, buildDerivs = TRUE)
+    Rmodel <- mcmc_createModelObject(model, inits, nchains, setSeed, code, constants, data, dimensions, check, buildDerivs = TRUE, userEnv = userEnv)
     Rmcmc <- buildHMC(Rmodel, type = type, monitors = monitors, thin = thin, enableWAIC = WAIC, print = FALSE)
     compiledList <- compileNimble(Rmodel, Rmcmc)    ## only one compileNimble() call
     Cmcmc <- compiledList$Rmcmc