[Vegan-commits] r1986 - in pkg/vegan: R inst man

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2011-11-05 14:40:24 +0100 (Sat, 05 Nov 2011)
New Revision: 1986

Modified:
   pkg/vegan/R/permutest.cca.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/anova.cca.Rd
Log:
parallel processing modelled like in oecosimu()

Modified: pkg/vegan/R/permutest.cca.R
===================================================================
--- pkg/vegan/R/permutest.cca.R	2011-11-03 07:23:37 UTC (rev 1985)
+++ pkg/vegan/R/permutest.cca.R	2011-11-05 13:40:24 UTC (rev 1986)
@@ -7,10 +7,8 @@
 `permutest.cca` <-
     function (x, permutations = 99,
               model = c("reduced", "direct", "full"), first = FALSE,
-              strata = NULL, parallel = 1, ..., kind = c("snow", "multicore")) 
+              strata = NULL, parallel = getOption("mc.cores", 1L) , ...) 
 {
-    kind <- match.arg(kind)
-    parallel <- as.integer(parallel)
     model <- match.arg(model)
     isCCA <- !inherits(x, "rda")
     isPartial <- !is.null(x$pCCA)
@@ -115,18 +113,24 @@
                          function(x) vegan:::permuted.index(N, strata=strata))) 
     }
     nperm <- nrow(permutations)
-    if (parallel > 1 && getRversion() >= "2.14" && require(parallel)) {
-        if (kind == "snow") {
-            cl <- makeCluster(parallel)
-            clusterEvalQ(cl, library(vegan))
-            tmp <- parRapply(cl, permutations, function(i) getF(i))
-            tmp <- matrix(tmp, ncol=3, byrow=TRUE)
-            stopCluster(cl)
-        } else {
+    ## Parallel processing (similar as in oecosimu)
+    hasClus <- inherits(parallel, "cluster") || is.null(parallel)
+    if ((hasClus || parallel > 1)  && require(parallel)) {
+        if(.Platform$OS.type == "unix" && !hasClus) {
             tmp <- do.call(rbind,
                            mclapply(1:nperm,
                                     function(i) getF(permutations[i,]),
                                     mc.cores = parallel))
+        } else {
+            ## if hasClus, do not set up and stop a temporary cluster
+            if (!hasClus) {
+                parallel <- makeCluster(parallel)
+                clusterEvalQ(parallel, library(vegan))
+            }
+            tmp <- parRapply(parallel, permutations, function(i) getF(i))
+            tmp <- matrix(tmp, ncol=3, byrow=TRUE)
+            if (!hasClus)
+                stopCluster(parallel)
         }
     } else {
         tmp <- getF(permutations)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-11-03 07:23:37 UTC (rev 1985)
+++ pkg/vegan/inst/ChangeLog	2011-11-05 13:40:24 UTC (rev 1986)
@@ -42,6 +42,8 @@
 	(incl. MacOS X and Linux) to use the socket processing instead of
 	forking.
 
+	* permutest.cca: parallel processing modelled after oecosimu().
+
 Version 2.1-5 (closed October 30, 2011)
 
 	* opened a new version with the release of vegan 2.0-1 on Oct 20,

Modified: pkg/vegan/man/anova.cca.Rd
===================================================================
--- pkg/vegan/man/anova.cca.Rd	2011-11-03 07:23:37 UTC (rev 1985)
+++ pkg/vegan/man/anova.cca.Rd	2011-11-05 13:40:24 UTC (rev 1986)
@@ -25,8 +25,8 @@
 
 \method{permutest}{cca}(x, permutations = 99,
           model = c("reduced", "direct", "full"),
-          first = FALSE, strata = NULL, parallel = 1, ..., 
-          kind = c("snow", "multicore"))
+          first = FALSE, strata = NULL, 
+	  parallel = getOption("mc.cores", 1L) , ...)
 }
 
 \arguments{
@@ -55,15 +55,10 @@
     permutation. If supplied, observations are permuted only within the
     specified strata.}
 
-  \item{parallel, kind}{Number of parallel processes. The parallel
-    processing is only possible in \R version 2.14.x and later. The
-    argument is silently ignored if the system is not capable of
-    parallel processing. There are two \code{kind} of parallelization:
-    \code{kind = "snow"} selects a socket cluster which is available
-    in all operationg systems, and \code{kind = "multicore"} selects a
-    fork cluster that is available only in unix-like systems (Linux,
-    MacOS X), but is usually faster. These arguments are experimental
-    and may change or disappear in any version. }
+  \item{parallel}{Number of parallel processes or a predefined socket
+    cluster.  With \code{parallel = 1} uses ordinary, non-parallel
+    processing. The parallel processing is done with \pkg{parallel}
+    package which is available only for \R 2.14.0 and later.}
 
 }
 \details{