Adding example using cl cluster

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fmcmc
 Title: A friendly MCMC framework
-Version: 0.5-2
+Version: 0.5-2.9000
 Date: 2023-08-29
 Authors@R: c(person("George", "Vega Yon", email = "[email protected]", role =
          c("aut", "cre"), comment = c(ORCID = "0000-0002-3171-0844")),

NEWS.md

@@ -1,3 +1,9 @@
+# fmcmc 0.5-2.9000
+
+* Added an example using cluster objects.
+
+
+
 # fmcmc 0.5-2
 
 * Adressing [`roxygen2` issue #1491](https://github.com/r-lib/roxygen2/issues/1491)

R/mcmc.R

@@ -246,6 +246,80 @@
 #' summary(ans)
 #' }
 #' 
+#' # Example using a user-defined cl object -------------------------------------
+#' 
+#' # A silly function that gets the first two parameters of the
+#' # vector. Using the default multicore example will cause and error
+#' get_m <- function(pars) {
+#'   pars[1:2]
+#' }
+#' 
+#' fun <- function(pars, D) {
+#'   # Putting the parameters in a sensible way
+#'   m <- get_m(pars)
+#'   s <- cbind( c(pars[3], pars[4]), c(pars[4], pars[5]) )
+#'   
+#'   # Computing the unnormalized log likelihood
+#'   sum(log(mvtnorm::dmvnorm(D, m, s)))
+#' }
+#' 
+#' if (FALSE) {
+#' 
+#'   # Thi will fail with the error
+#'   # Error in checkForRemoteErrors(val) :
+#'   #   4 nodes produced errors; first error: could not find function "get_m"
+#'   ans <- MCMC(
+#'     initial = c(mu0=5, mu1=5, s0=5, s01=0, s2=5), 
+#'     fun,
+#'     kernel  = kernel_normal_reflective(
+#'       lb    = c(-10, -10, .01, -5, .01),
+#'       ub    = 5,
+#'       scale = 0.01
+#'     ),
+#'     nsteps  = 1e3,
+#'     thin    = 10,
+#'     burnin  = 5e2,
+#'     D       = D,
+#'     # Multiple chains using parallel computing
+#'     multicore = TRUE,
+#'     nchains = 4
+#'   )
+#'   
+#'   summary(ans)
+#' 
+#' }
+#' 
+#' # To solve the error, we need to build the cluster object
+#' library(parallel)
+#' cl <- makePSOCKcluster(4)
+#' 
+#' # Export the function `get_m` to the cluster. The function `fun` and data `D`
+#' # are automatically exported by the `MCMC` function.
+#' clusterExport(cl, "get_m")
+#' 
+#' # Run the MCMC
+#' ans <- MCMC(
+#'   initial = c(mu0=5, mu1=5, s0=5, s01=0, s2=5), 
+#'   fun,
+#'   kernel  = kernel_normal_reflective(
+#'     lb    = c(-10, -10, .01, -5, .01),
+#'     ub    = 5,
+#'     scale = 0.01
+#'   ),
+#'   nsteps  = 1e3,
+#'   thin    = 10,
+#'   burnin  = 5e2,
+#'   D       = D,
+#'   # Multiple chains using parallel computing
+#'   multicore = TRUE,
+#'   nchains = 4,
+#'   # Use the cluster object
+#'   cl = cl
+#' )
+#' 
+#' summary(ans)
+#' 
+#' 
 #' @aliases Metropolis-Hastings
 #' @seealso [get_logpost()], [get_logpost()] ([mcmc-output]) for post execution of `MCMC`, and
 #' [ith_step()] for accessing objects within an `MCMC` call.

inst/NEWS

@@ -1,3 +1,7 @@
+fmcmc 0.5-2.9000
+
+-   Added an example using cluster objects.
+
 fmcmc 0.5-2
 
 -   Adressing roxygen2 issue #1491