[Vegan-commits] r1878 - in pkg/vegan: R inst man

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

Author: psolymos
Date: 2011-09-23 07:15:36 +0200 (Fri, 23 Sep 2011)
New Revision: 1878

Modified:
   pkg/vegan/R/make.commsim.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/commsim.Rd
Log:
storage mode changes

Modified: pkg/vegan/R/make.commsim.R
===================================================================
--- pkg/vegan/R/make.commsim.R	2011-09-23 05:15:07 UTC (rev 1877)
+++ pkg/vegan/R/make.commsim.R	2011-09-23 05:15:36 UTC (rev 1878)
@@ -293,18 +293,18 @@
             out
         }),
         "r00_samp" = commsim(method="r00_samp", binary=FALSE, isSeq=FALSE,
-        mode="integer",
+        mode="double",
         fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
-            out <- matrix(0L, nr * nc, n)
+            out <- matrix(0, nr * nc, n)
             for (k in seq_len(n))
                 out[, k] <- sample(x)
             dim(out) <- c(nr, nc, n)
             out
         }),
         "c0_samp" = commsim(method="c0_samp", binary=FALSE, isSeq=FALSE,
-        mode="integer",
+        mode="double",
         fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
-            out <- array(0L, c(nr, nc, n))
+            out <- array(0, c(nr, nc, n))
             J <- seq_len(nc)
             for (k in seq_len(n))
                 for (j in J)
@@ -312,9 +312,9 @@
             out
         }),
         "r0_samp" = commsim(method="r0_samp", binary=FALSE, isSeq=FALSE,
-        mode="integer",
+        mode="double",
         fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
-            out <- array(0L, c(nr, nc, n))
+            out <- array(0, c(nr, nc, n))
             I <- seq_len(nr)
             for (k in seq_len(n))
                 for (i in I)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-09-23 05:15:07 UTC (rev 1877)
+++ pkg/vegan/inst/ChangeLog	2011-09-23 05:15:36 UTC (rev 1878)
@@ -4,6 +4,16 @@
 
 Version 2.1-1 (opened September 20, 2011)
 
+	* permatfull/swap is using the new simulate(nullmodel(...)...)
+	infrastructure. permatfull1 and permatswap1 removed from vegan 
+	devel.
+
+	* Value of 'mode' is set to "double" for the following
+	null model algorithms in make.commsim: abuswap_r, abuswap_c,
+	r00_samp, r0_samp, c0_samp. These can take any nonnegative real 
+	valued matrix as input. nullmodel function now handles storage
+	mode reliably.
+
 	* meandist bug fix: tapply() function used to find mean group x
 	group dissimilarities could reorder the class levels and return a
 	confused matrix. This could happen in particular when the

Modified: pkg/vegan/man/commsim.Rd
===================================================================
--- pkg/vegan/man/commsim.Rd	2011-09-23 05:15:07 UTC (rev 1877)
+++ pkg/vegan/man/commsim.Rd	2011-09-23 05:15:36 UTC (rev 1878)
@@ -199,7 +199,8 @@
     modified by shuffling original nonzero samples among the new
     nonzero cells of the binary matrix, individuals of the
     nonzero cells are also shuffled, separately for each columns.}
-  \item{\code{"abuswap_r"}: }{sequential algorithm for count matrices 
+  \item{\code{"abuswap_r"}: }{sequential algorithm for count 
+    or nonnegative real valued (\code{mode = "double"}) matrices 
     described in the page of \code{\link{permatswap}} (\code{"abuswap"} 
     algorithm with fixed row freqencies).
     The algorithm produces matrices by swapping
@@ -207,7 +208,8 @@
     column sums, but honours matrix fill, row sums,
     and row/column frequencies, 
     as described in Hardy (2008; randomization scheme 2x).}
-  \item{\code{"abuswap_c"}: }{sequential algorithm for count matrices 
+  \item{\code{"abuswap_c"}: }{sequential algorithm for count 
+    or nonnegative real valued (\code{mode = "double"}) matrices 
     described in the page of \code{\link{permatswap}} (\code{"abuswap"} 
     algorithm with fixed column freqencies).
     The algorithm produces matrices by swapping
@@ -231,15 +233,18 @@
     described in the page of \code{\link{permatfull}}.
     This algorithm keeps column sums constant,
     individuals are shullfed among cells of each column of the matrix.}
-  \item{\code{"r00_samp"}: }{non-sequential algorithm for count matrices 
+  \item{\code{"r00_samp"}: }{non-sequential algorithm for count 
+    or nonnegative real valued (\code{mode = "double"}) matrices 
     described in the page of \code{\link{permatfull}}.
     This algorithm keeps total sum constant,
     cells of the matrix are shuffled.}
-  \item{\code{"r0_samp"}: }{non-sequential algorithm for count matrices 
+  \item{\code{"r0_samp"}: }{non-sequential algorithm for count 
+    or nonnegative real valued (\code{mode = "double"}) matrices 
     described in the page of \code{\link{permatfull}}.
     This algorithm keeps row sums constant,
     cells within each row are shuffled.}
-  \item{\code{"c0_samp"}: }{non-sequential algorithm for count matrices 
+  \item{\code{"c0_samp"}: }{non-sequential algorithm for count 
+    or nonnegative real valued (\code{mode = "double"}) matrices 
     described in the page of \code{\link{permatfull}}.
     This algorithm keeps column sums constant,
     cells within each columns are shuffled.}