[Vegan-commits] r699 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2009-02-24 10:57:38 +0100 (Tue, 24 Feb 2009)
New Revision: 699

Modified:
   pkg/vegan/R/permatswap.R
   pkg/vegan/inst/ChangeLog
Log:
permatswap method = 'abuswap' uses now C code of nestedness.c (needs thorough testing)

Modified: pkg/vegan/R/permatswap.R
===================================================================
--- pkg/vegan/R/permatswap.R	2009-02-24 09:51:06 UTC (rev 698)
+++ pkg/vegan/R/permatswap.R	2009-02-24 09:57:38 UTC (rev 699)
@@ -122,10 +122,10 @@
                             as.integer(nn.row), as.integer(nn.col),
                             as.integer(1), PACKAGE = "vegan")$m
                     if (method == "abuswap")
-#                        temp <- .C("abuswap", m = as.double(temp),
-#                            as.integer(nn.row), as.integer(nn.col),
-#                            as.integer(1), as.integer(direct), PACKAGE = "vegan")$m
-                        temp <- abuswap(temp, fixedmar, thin=1)
+                       temp <- .C("abuswap", m = as.double(temp),
+                            as.integer(nn.row), as.integer(nn.col),
+                            as.integer(1), as.integer(direct), PACKAGE = "vegan")$m
+#                        temp <- abuswap(temp, fixedmar, thin=1)
             } else
                 for (k in 1:burnin)
                     temp <- commsimulator(temp, method=method)
@@ -139,14 +139,14 @@
                                     as.integer(thin),
                                     PACKAGE = "vegan")$m
                     if (method == "abuswap")
-#                        perm[[i]][id,] <- .C("abuswap",
-#                                    m = as.double(temp),
-#                                    as.integer(nn.row),
-#                                    as.integer(nn.col),
-#                                    as.integer(thin),
-#                                    as.integer(direct),
-#                                    PACKAGE = "vegan")$m
-                        perm[[i]][id,] <- abuswap(temp, fixedmar, thin)
+                        perm[[i]][id,] <- .C("abuswap",
+                                    m = as.double(temp),
+                                    as.integer(nn.row),
+                                    as.integer(nn.col),
+                                    as.integer(thin),
+                                    as.integer(direct),
+                                    PACKAGE = "vegan")$m
+#                        perm[[i]][id,] <- abuswap(temp, fixedmar, thin)
 	           } else perm[[i]][id,] <- commsimulator(temp, method=method, thin=thin)
             temp <- perm[[i]][id,]
             } # for i end

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-02-24 09:51:06 UTC (rev 698)
+++ pkg/vegan/inst/ChangeLog	2009-02-24 09:57:38 UTC (rev 699)
@@ -4,12 +4,13 @@
 
 Version 1.16-14 (opened Feb 24, 2009)
 
-    * permatswap: two new methods (under "abuswap") added based on the paper of
-    Hardy 2008 (J Ecol 96, 914-926). These preserve row *and* colunm occurrences,
-    and row *or* column sums at the same time. Thus these complement the methods
-    available in vegan. C code is added, but does not work. So now the
-    much slower R internal function is used. Needs some more work, and
-    documentation (examples and reference in Rd file).
+	* permatswap: two new methods (under "abuswap") added based on the
+	paper of Hardy 2008 (J Ecol 96, 914-926). These preserve row *and*
+	colunm occurrences, and row *or* column sums at the same
+	time. Thus these complement the methods available in vegan. Uses C
+	coce (not thoroughly tested yet). So now the much slower R
+	internal function is used. Needs some more work, and
+	documentation (examples and reference in Rd file).
 
 Version 1.16-13 (closed Feb 24, 2009)