[Vegan-commits] r1839 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-09-12 16:02:52 +0200 (Mon, 12 Sep 2011)
New Revision: 1839

Modified:
   pkg/vegan/R/commsimulator.R
   pkg/vegan/inst/ChangeLog
Log:
smaller overhead in commsimulator, but the effects on timing may be small

Modified: pkg/vegan/R/commsimulator.R
===================================================================
--- pkg/vegan/R/commsimulator.R	2011-09-12 14:02:13 UTC (rev 1838)
+++ pkg/vegan/R/commsimulator.R	2011-09-12 14:02:52 UTC (rev 1839)
@@ -4,6 +4,7 @@
     method <- match.arg(method, 
                         c("r0","r1","r2","r00","c0","swap", "tswap",
                           "backtrack", "quasiswap"))
+    x <- as.matrix(x)
     if (any(x > 1))
         x <- ifelse(x > 0, 1, 0)
     nr <- nrow(x)
@@ -23,7 +24,6 @@
     else if (method == "r00") {
         out <- numeric(nr*nc)
         out[sample(length(out), sum(x))] <- 1
-        dim(out) <- dim(x)
     }
     else if (method == "c0") {
         cs <- colSums(x)
@@ -31,22 +31,17 @@
         for (j in 1:nc)
             out[sample(nr, cs[j]), j] <- 1
     } else if (method == "swap") {
-        x <- as.matrix(x)
         out <- .C("swap", m = as.integer(x), as.integer(nrow(x)),
                   as.integer(ncol(x)), as.integer(thin),
                   PACKAGE = "vegan")$m
-        dim(out) <- dim(x)
     } else if (method == "tswap") {
-        x <- as.matrix(x)
         out <- .C("trialswap", m = as.integer(x), as.integer(nrow(x)),
                   as.integer(ncol(x)), as.integer(thin),
                   PACKAGE = "vegan")$m
-        dim(out) <- dim(x)
     } else if (method == "quasiswap") {
         out <- r2dtable(1, rowSums(x), colSums(x))[[1]]
         out <- .C("quasiswap", m = as.integer(out), as.integer(nrow(x)),
                   as.integer(ncol(x)), PACKAGE = "vegan")$m
-        dim(out) <- dim(x)
     }
     else if (method == "backtrack") {
         fill <- sum(x)
@@ -94,7 +89,6 @@
                 out <- oldout
         }
     }
-    colnames(out) <- colnames(x)
-    rownames(out) <- rownames(x)
+    attributes(out) <- attributes(x)
     out
 }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-09-12 14:02:13 UTC (rev 1838)
+++ pkg/vegan/inst/ChangeLog	2011-09-12 14:02:52 UTC (rev 1839)
@@ -7,6 +7,11 @@
 	* New major version opened with the release of vegan_2.0-0 on
 	September 8, 2011.
 
+	* commsimulator: a bit less overhead -- all attributes set
+	simultaneously instead of setting separately dim, rownames and
+	colnames. The results should be identical(), running should be
+	marginally faster or neutral.
+
 	* permatswap: there was a bug in internal C routine, and therefore
 	not all permissible swaps were performed. Based on limited
 	analysis, the effects of this bug seem to be negligible.  It is,