merged in master branch

README.md

@@ -2,21 +2,36 @@
 
 [![tests](https://github.com/nimble-dev/nimbleHMC/workflows/tests/badge.svg)](https://github.com/nimble-dev/nimbleHMC/actions)
 
-Provides derivative-based MCMC sampling algorithms for use in conjunction with the `nimble` package.  These include:
+Provides derivative-based MCMC sampling algorithms and convenence functions, for use in conjunction with the MCMC engine avaialble in the `nimble` package.  Sampling algorithms include:
 
-- Hamiltonian Monte Carlo (HMC-NUTS) sampler
+- No-U-Turn Hamiltonian Monte Carlo (`NUTS`) sampler
+- Historical implementation of the original No-U-Turn HMC (`NUTS_classic`) sampler
 - Langevin sampler (*under development*)
 
-See the [nimble website](https://r-nimble.org/) for more information and examples.
+See the HMC section of the [nimble user manual](https://r-nimble.org/html_manual/cha-mcmc.html#subsec:HMC) for more information and examples.
+
+[General package information](https://cran.r-project.org/web/packages/nimbleHMC/) about `nimbleHMC`, and the [complete API for package functions](https://cran.r-project.org/web/packages/nimbleHMC/nimbleHMC.pdf) are available on CRAN.
+
+Additional information about the `nimble`package itself is available at the [nimble website](https://r-nimble.org/).
 
-<!--
-The nimbleHMC package must be used with nimble version XXXX or 
-higher. To check the current version number of nimble use `packageVersion("nimble")`. 
--->
 
-### Package Requirements
 
-`nimbleHMC` must be used with version `1.0.0` or higher of the `nimble` package.
+### Installation and Package Requirements
+
+Use of `nimbleHMC` requires installation of the core `nimble` package.  Detailed instructions for installing `nimble` are available in the [`nimble` package README](https://github.com/nimble-dev/nimble/blob/devel/README.md).
+
+`nimbleHMC` must be used with version `1.0.0` or higher of `nimble`, or the latest version available on CRAN.  To check the version number of the currently installed version of `nimble`, use:
+
+```r
+packageVersion("nimble")
+```
+
+The `nimbleHMC` package itself can be installed directly from CRAN, using:
+
+```r
+install.packages("nimbleHMC")
+```
+
 
 <!--
 library(remotes)
@@ -61,6 +76,11 @@ dmy_distribution <- nimbleFunction(
 ```
 
 
+### Contributing and Support
+
+Contributions to the `nimbleHMC` package should be submitted via pull request on GitHub.  For additional guideliens on making contributions, please see the [contributing guidelines for the `nimble` package](https://github.com/nimble-dev/nimble/blob/devel/CONTRIBUTING.md).
 
+Issues, feature requests, or bugs should be reported using GitHub issues, submitted to the `nimbleHMC` repository.
 
+For additional support using `nimble` or `nimbleHMC`, please see the [nimble user manual](https://r-nimble.org/html_manual/cha-welcome-nimble.html).  Any additional questions can be submitted to the [nimble-users Google group](https://groups.google.com/g/nimble-users).
 

make_package.R

@@ -11,9 +11,9 @@ library(devtools)
 
 setwd('~/github/nimble/nimbleHMC')
 
-document('nimbleHMC')
+devtools::document('nimbleHMC')
 
-system('R CMD BUILD nimbleHMC')
+devtools::build('nimbleHMC')
 
 check('nimbleHMC')
 
@@ -23,6 +23,8 @@ suppressMessages(try(remove.packages('nimbleHMC'), silent = TRUE))
 message('installing package version ', gsub('\\.tar\\.gz$', '', lastTarFile))
 system(paste0('R CMD install ', lastTarFile))
 
+##devtools::install('nimbleHMC')
+
 q('no')
 
 1

nimbleHMC/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: nimbleHMC
 Title: Hamiltonian Monte Carlo and Other Gradient-Based MCMC Sampling Algorithms for 'nimble'
-Version: 0.2.0
-Date: 2023-09-11
+Version: 0.2.2
+Date: 2024-02-08
 Authors@R: c(person("Daniel", "Turek", role = c("aut", "cre"), email = "[email protected]"),
 	     person("Perry", "de Valpine", role = "aut"),
 	     person("Christopher", "Paciorek", role = "aut"))
@@ -14,4 +14,4 @@ License: BSD_3_clause + file LICENSE | GPL (>= 2)
 Copyright: See COPYRIGHTS file.
 Encoding: UTF-8
 LazyData: false
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1

nimbleHMC/R/HMC_configuration.R

@@ -5,7 +5,7 @@
 #' Add a No-U-Turn (NUTS) Hamiltonian Monte Carlo (HMC) sampler to an existing nimble MCMC configuration object
 #'
 #' @param conf A nimble MCMC configuration object, as returned by `configureMCMC`.
-#' @param target A character vector of continuous-valued stochastic node names to sample.  If this argument contains any discrete-valued nodes, an error is produced and no sampler is added.
+#' @param target A character vector of continuous-valued stochastic node names to sample.  If this argument contains any discrete-valued nodes, an error is produced and no HMC sampler is added.  If this argument is omitted, then no HMC sampler is added.
 #' @param type A character string specifying the type of HMC sampler to add, either "NUTS" or "NUTS_classic".  See `help(NUTS)` or `help(NUTS_classic)` for details of each sampler.  The default sampler type is "NUTS".
 #' @param control Optional named list of control parameters to be passed as the `control` argument to the HMC sampler.  See `help(NUTS)` or `help(NUTS_classic)` for details of the control list elements accepted by each sampler.
 #' @param replace Logical argument.  If `TRUE`, any existing samplers operating on the specified nodes will be removed, prior to adding the HMC sampler.  Default value is `FALSE`.
@@ -46,11 +46,14 @@
 #'
 #' Rmodel <- nimbleModel(code, constants, data, inits, buildDerivs = TRUE)
 #'
-#' ## create MCMC configuration object
-#' conf <- configureMCMC(Rmodel, nodes = NULL)
+#' ## create default MCMC configuration object
+#' conf <- configureMCMC(Rmodel)
 #'
-#' ## add HMC sampler operating on all stochastic model nodes
-#' addHMC(conf)
+#' ## remove default samplers operating on b0 and b1
+#' conf$removeSamplers(c("b0", "b1"))
+#'
+#' ## add an HMC sampler operating on b0 and b1
+#' addHMC(conf, target = c("b0", "b1"))
 #'
 #' Rmcmc <- buildMCMC(conf)
 #'