improvements; doFuture

.Rbuildignore

@@ -10,7 +10,7 @@ inst/doc/(.+?).md
 inst/doc/(.+?).Rmd
 man/roxygen
 LICENSE\.md$
-README\.md$
+README\.(.?)$
 CRAN\.md$
 TODO\.md$
 ^\.gitignore$

.github/workflows/r-cmd-check.yml

@@ -55,4 +55,4 @@ jobs:
       - uses: actions/[email protected]
         with:
           name: ${{ matrix.config.os }}-${{ matrix.config.r }}-results
-          path: check/circumstance.Rcheck
+          path: check/${{ vars.repo_name }}.Rcheck

DESCRIPTION

@@ -1,15 +1,16 @@
 Package: circumstance
 Type: Package
 Title: pomp parallelized
-Version: 0.0.3.0
-Date: 2023-01-11
+Version: 0.0.4.0
+Date: 2023-01-24
 Maintainer: Aaron A. King <[email protected]>
 Description: Helper functions for parallelizing pomp computations.
 Authors@R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="[email protected]"))
 URL: https://kingaa.github.io/circumstance/
-Depends: R(>= 4.1.0), methods, foreach, pomp(>= 4.5)
-Suggests: doParallel, doRNG, tidyr, ggplot2
+Depends: R(>= 4.1.0), pomp(>= 4.6)
+Imports: methods, foreach
+Suggests: doFuture, doRNG, dplyr, tidyr, ggplot2
 Remotes: kingaa/pomp
 License: GPL-3
 LazyData: true
@@ -19,5 +20,5 @@ Encoding: UTF-8
 Roxygen: list(roclets = c("collate", "namespace", "rd"))
 RoxygenNote: 7.2.3
 Collate: 
-    'circumstance-package.R'
+    'package.R'
     'pfilter.R'

R/circumstance-package.R → R/package.R

@@ -4,6 +4,8 @@
 ##' \pkg{circumstance} provides tools for parallelizing certain \pkg{pomp} calculations.
 ##'
 ##' @name circumstance-package
+##' @aliases circumstance,package
+##' @docType package
 ##' @import methods
 ##' @importFrom utils globalVariables
 ##'

R/pfilter.R

@@ -6,14 +6,14 @@
 ##' @rdname pfilter
 ##' @importFrom pomp pfilter
 ##' @importFrom foreach foreach %dopar%
-##' @include circumstance-package.R
+##' @include package.R
 ##'
-##' @param data passed to \code{pomp::\link[pomp]{pfilter}}
+##' @param data passed to \code{\link[pomp:pfilter]{pomp::pfilter}}
 ##' @param Nrep number of replicate particle filter computations to run.
 ##' By default, \code{Nrep = 1}.
-##' @param ... all additional arguments are passed to \code{pomp::\link[pomp]{pfilter}}
+##' @param ... all additional arguments are passed to \code{\link[pomp:pfilter]{pomp::pfilter}}
 ##'
-##' @seealso \code{pomp::\link[pomp]{pfilter}}.
+##' @seealso \code{\link[pomp:pfilter]{pomp::pfilter}}.
 ##'
 ##' @example examples/pfilter.R
 ##'
@@ -25,8 +25,6 @@ setGeneric(
     standardGeneric("pfilter")
 )
 
-##' @aliases pfilter
-##' @aliases pfilter-ANY,numeric
 ##' @rdname pfilter
 ##' @export
 setMethod(
@@ -41,7 +39,6 @@ setMethod(
   }
 )
 
-##' @aliases pfilter-ANY,missing
 ##' @rdname pfilter
 ##' @export
 setMethod(
@@ -50,7 +47,6 @@ setMethod(
   definition = pomp::pfilter
 )
 
-##' @aliases pfilter-pompList,numeric
 ##' @rdname pfilter
 ##' @export
 setMethod(
@@ -64,31 +60,19 @@ setMethod(
       rep <- (iter_i-1)%/%npo+1
       pomp::pfilter(data[[ipo]],...)
     } -> res
-    if (is.null(names(data))) {
-      names(res) <- sprintf("%d_%d",seq_len(npo),rep(seq_len(Nrep),each=npo))
-    } else {
-      names(res) <- sprintf("%s_%d",names(data),rep(seq_len(Nrep),each=npo))
-    }
+    nm <- names(data)
+    if (is.null(nm)) nm <- seq_len(npo)
+    names(res) <- sprintf("%s_%d",nm,rep(seq_len(Nrep),each=npo))
     res
   }
 )
 
-##' @aliases pfilter-pompList,missing
 ##' @rdname pfilter
 ##' @export
 setMethod(
   "pfilter",
   signature=signature(data = "pompList", Nrep = "missing"),
   definition = function (data, ...) {
-    jobs <- seq_len(length(data))
-    foreach (iter_i=jobs,.combine=c) %dopar% {
-      pomp::pfilter(data[[iter_i]],...)
-    } -> res
-    if (is.null(names(data))) {
-      names(res) <- jobs
-    } else {
-      names(res) <- names(data)
-    }
-    res
+    circumstance::pfilter(data,Nrep=1L,...)
   }
 )

examples/pfilter.R

@@ -1,4 +1,13 @@
 library(circumstance)
+library(doFuture)
+library(doRNG)
+registerDoFuture()
+registerDoRNG()
 
 ou2() -> ou2
-ou2 |> pfilter(Np=1000,Nrep=6) -> pfs
+
+plan(sequential)
+system.time(ou2 |> pfilter(Np=10000,Nrep=6) -> pfs)
+
+plan(multicore)
+system.time(ou2 |> pfilter(Np=10000,Nrep=6) -> pfs)

inst/NEWS

@@ -1,5 +1,17 @@
 _N_e_w_s _f_o_r _p_a_c_k_a_g_e '_c_i_r_c_u_m_s_t_a_n_c_e'
 
+_C_h_a_n_g_e_s _i_n '_c_i_r_c_u_m_s_t_a_n_c_e' _v_e_r_s_i_o_n _0._0._4:
+
+        • Use with ‘doFuture’ is intended.
+
+        • Streamline some of the definitions.
+
+        • Improve coverage.
+
+_C_h_a_n_g_e_s _i_n '_c_i_r_c_u_m_s_t_a_n_c_e' _v_e_r_s_i_o_n _0._0._3:
+
+        • Updates for new version of ‘pomp’.
+
 _C_h_a_n_g_e_s _i_n '_c_i_r_c_u_m_s_t_a_n_c_e' _v_e_r_s_i_o_n _0._0._1:
 
         • Improved the parallel ‘pfilter’ facility.

inst/NEWS.Rd

@@ -1,5 +1,17 @@
 \name{NEWS}
 \title{News for package `circumstance'}
+\section{Changes in \pkg{circumstance} version 0.0.4}{
+  \itemize{
+    \item Use with \pkg{doFuture} is intended.
+    \item Streamline some of the definitions.
+    \item Improve coverage.
+  }
+}
+\section{Changes in \pkg{circumstance} version 0.0.3}{
+  \itemize{
+    \item Updates for new version of \pkg{pomp}.
+  }
+}
 \section{Changes in \pkg{circumstance} version 0.0.1}{
   \itemize{
     \item Improved the parallel \code{pfilter} facility.

rules.mk

@@ -19,7 +19,7 @@ SOURCE = $(sort $(wildcard R/*R src/*.c src/*.h data/* examples/*))
 CSOURCE = $(sort $(wildcard src/*.c))
 TESTS = $(sort $(wildcard tests/*R))
 INSTDOCS = $(sort $(wildcard inst/doc/*))
-SESSION_PKGS = datasets,utils,grDevices,graphics,stats,methods,tidyverse,$(PKG)
+SESSION_PKGS = datasets,utils,grDevices,graphics,stats,methods,tidyverse,doFuture,doRNG,$(PKG)
 
 .PHONY: .check check clean covr debug default fresh \
 htmlhelp manual publish qcheck qqcheck \
@@ -38,7 +38,7 @@ session: RSESSION = emacs -f R
 debug: RSESSION = R -d gdb
 rsession: RSESSION = R
 
-default:
+default: .roxy .NEWS .instdocs .source .includes .headers
 	@echo $(PKGVERS)
 
 roxy: .roxy