[Vegan-commits] r2061 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2012-02-04 10:25:22 +0100 (Sat, 04 Feb 2012)
New Revision: 2061

Modified:
   pkg/vegan/R/adonis.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/adonis.Rd
Log:
parallel processing in adonis

Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R	2012-02-01 08:53:17 UTC (rev 2060)
+++ pkg/vegan/R/adonis.R	2012-02-04 09:25:22 UTC (rev 2061)
@@ -1,7 +1,7 @@
 `adonis` <-
     function(formula, data=NULL, permutations=999, method="bray", strata=NULL,
              contr.unordered="contr.sum", contr.ordered="contr.poly",
-             ...)
+             parallel = getOption("mc.cores"), ...)
 {
     ## formula is model formula such as Y ~ A + B*C where Y is a data
     ## frame or a matrix, and A, B, and C may be factors or continuous
@@ -108,11 +108,42 @@
     tIH.snterm <- t(I-H.snterm)
     ## Apply permutations for each term
     ## This is the new f.test (2011-06-15) that uses fewer arguments
-    f.perms <- sapply(1:nterms, function(i) {
-        sapply(1:permutations, function(j) {
-            f.test(tH.s[[i]], G[p[,j], p[,j]], df.Exp[i], df.Res, tIH.snterm)
-        } )
-    })
+    ## Set first parallel processing for all terms
+    if (is.null(parallel) && getRversion() >= "2.15.0")
+        parallel <- get("default", envir = parallel:::.reg)
+    if (is.null(parallel) || getRversion() < "2.14.0")
+        parallel <- 1
+    hasClus <- inherits(parallel, "cluster")
+    isParal <- (hasClus || parallel > 1) && require(parallel)
+    isMulticore <- .Platform$OS.type == "unix" && !hasClus
+    if (isParal && !isMulticore && !hasClus) {
+        parallel <- makeCluster(parallel)
+        clusterEvalQ(parallel, library(vegan))
+    }
+    if (isParal) {
+        if (isMulticore) {
+            f.perms <-
+                sapply(1:nterms, function(i)
+                       unlist(mclapply(1:permutations, function(j)
+                                       f.test(tH.s[[i]], G[p[,j], p[,j]],
+                                              df.Exp[i], df.Res, tIH.snterm))))
+        } else {
+            f.perms <-
+                sapply(1:nterms, function(i)
+                       parSapply(parallel, 1:permutations, function(j)
+                                 f.test(tH.s[[i]], G[p[,j], p[,j]],
+                                        df.Exp[i], df.Res, tIH.snterm)))
+        }
+    } else {
+        f.perms <-
+            sapply(1:nterms, function(i) 
+                   sapply(1:permutations, function(j) 
+                          f.test(tH.s[[i]], G[p[,j], p[,j]],
+                                 df.Exp[i], df.Res, tIH.snterm)))
+    }
+    ## Close socket cluster if created here
+    if (isParal && !isMulticore && !hasClus)
+        stopCluster(parallel)
     ## Round to avoid arbitrary P-values with tied data
     f.perms <- round(f.perms, 12)
     F.Mod <- round(F.Mod, 12)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-02-01 08:53:17 UTC (rev 2060)
+++ pkg/vegan/inst/ChangeLog	2012-02-04 09:25:22 UTC (rev 2061)
@@ -8,8 +8,8 @@
 	seems to confuse users. Make this change in adonis() instead of
 	print.adonis to be prepared to add other policies.
 
-	* anomsim, mantel, mantel.partial, mrpp: implemented parallel
-	processing.
+	* adonis, anosim, mantel, mantel.partial, mrpp: implemented
+	parallel processing.
 
 	* RsquareAdj: implemented adjusted R2 for partial RDA results.
 	The adjusted R2 of model rda(Y ~ X1 + Condition(X2)) is defined so

Modified: pkg/vegan/man/adonis.Rd
===================================================================
--- pkg/vegan/man/adonis.Rd	2012-02-01 08:53:17 UTC (rev 2060)
+++ pkg/vegan/man/adonis.Rd	2012-02-04 09:25:22 UTC (rev 2061)
@@ -12,7 +12,7 @@
 \usage{
 adonis(formula, data, permutations = 999, method = "bray",
        strata = NULL, contr.unordered = "contr.sum",
-       contr.ordered = "contr.poly", ...)
+       contr.ordered = "contr.poly", parallel = getOption("mc.cores"), ...)
 }
 
 \arguments{  
@@ -34,6 +34,10 @@
   \item{contr.unordered, contr.ordered}{contrasts used for the design
     matrix (default in R is dummy or treatment contrasts for unordered
     factors). }
+  \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.}
   \item{\dots}{Other arguments passed to \code{vegdist}.}
 }