[Vegan-commits] r693 - in pkg/vegan: . inst man

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

Author: psolymos
Date: 2009-02-24 08:48:11 +0100 (Tue, 24 Feb 2009)
New Revision: 693

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/permatfull.Rd
Log:
changes in docs due to the addition of "abuswap"


Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2009-02-24 07:47:18 UTC (rev 692)
+++ pkg/vegan/DESCRIPTION	2009-02-24 07:48:11 UTC (rev 693)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-13
-Date: February 15, 2009
+Version: 1.16-14
+Date: February 24, 2009
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-02-24 07:47:18 UTC (rev 692)
+++ pkg/vegan/inst/ChangeLog	2009-02-24 07:48:11 UTC (rev 693)
@@ -2,8 +2,17 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-13 (opened Feb 15, 2009)
+Version 1.16-13 (opened Feb 24, 2009)
 
+    * permatswap: two new method ("abuswap") added based on the paper of
+    Hardy 2008 (J Ecol 96, 914-926). This preserves 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).
+
+Version 1.16-13 (closed Feb 24, 2009)
+
 	* anova.cca: documented the 'cutoff' argument for by = "axis".
 
 	* text.procrustes: added text() function for procrustes() result plots.

Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd	2009-02-24 07:47:18 UTC (rev 692)
+++ pkg/vegan/man/permatfull.Rd	2009-02-24 07:48:11 UTC (rev 693)
@@ -20,8 +20,8 @@
 \usage{
 permatfull(m, fixedmar = "both", shuffle = "ind", strata = NULL, 
 mtype = "count", times = 99)
-permatswap(m, method = "quasiswap", shuffle = "both", strata = NULL,
-mtype = "count", times = 99, burnin = 10000, thin = 1000)
+permatswap(m, method = "quasiswap", fixedmar="both", shuffle = "both",
+strata = NULL, mtype = "count", times = 99, burnin = 10000, thin = 1000)
 permat.control(ptype = "full", mtype = "count", method = "quasiswap",
 fixedmar = "both", shuffle = "ind", strata = NULL, 
 burnin = 10000, thin = 1000)
@@ -74,6 +74,8 @@
 
 The algorithm \code{"swsh"} in the function \code{permatswap} is a hybrid algorithm. First, it makes binary quasiswaps to keep row and column incidences constant, then non-zero values are modified according to the \code{shuffle} argument (only \code{"samp"} and \code{"both"} are available in this case, because it is applied only on non-zero values).
 
+FIXME! The algorithm \code{"abuswap"} need documentation here once done.
+
 Constraints on row/colum sums, matrix fill, total sum and sums within
 strata can be checked by the \code{summary} method. \code{plot} method is for
 visually testing the randomness of the permuted matrices, especially for the