[Vegan-commits] r1821 - in pkg/vegan: . inst man

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

Author: psolymos
Date: 2011-09-09 23:04:11 +0200 (Fri, 09 Sep 2011)
New Revision: 1821

Modified:
   pkg/vegan/NAMESPACE
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/permatfull.Rd
Log:
documenting permat*1 additions (note also that some checks are done for nestedness.c)

Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE	2011-09-09 21:03:09 UTC (rev 1820)
+++ pkg/vegan/NAMESPACE	2011-09-09 21:04:11 UTC (rev 1821)
@@ -19,7 +19,8 @@
 ordiplot, ordipointlabel, ordiresids, ordirgl, ordisegments,
 ordispider, ordisplom, ordistep, ordisurf, orditkplot, orditorp,
 ordixyplot, orglpoints, orglsegments, orglspider, orgltext, 
-pcnm, permatfull, permatswap, permutest, poolaccum, postMDS, prc,
+pcnm, permatfull, permatswap, permatfull1, permatswap1, 
+permutest, poolaccum, postMDS, prc,
 prestondistr, prestonfit, procrustes, protest, radfit, radlattice,
 rankindex, rarefy, rda, renyiaccum, renyi, rrarefy, scores,
 showvarparts, spandepth, spantree, specaccum, specnumber,

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-09-09 21:03:09 UTC (rev 1820)
+++ pkg/vegan/inst/ChangeLog	2011-09-09 21:04:11 UTC (rev 1821)
@@ -8,10 +8,15 @@
 	September 8, 2011.
 
 	* permatswap: there was a bug in internal C routine, and therefore
-	not all permissible swaps were performed. We have not yet analysed
-	the effects of this bug, and do not know its severity. It is
-	recommended to re-run all analyses.
+	not all permissible swaps were performed. Based on limited
+	analysis, the effects of this bug seem to be negligible. 
+	It is, however, recommended to re-run all analyses.
 
+	* New functions: permatfull1 and permatswap1. Both functions
+	return a single permuted matrix. These functions are now 
+	called repeatedly by the corresponding permatfull and permatswap
+	functions.
+
 Version 2.0-0 (released September 8, 2011)
 
 	* opened the release candidate ov vegan_2.0-0 on September 3,

Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd	2011-09-09 21:03:09 UTC (rev 1820)
+++ pkg/vegan/man/permatfull.Rd	2011-09-09 21:04:11 UTC (rev 1821)
@@ -1,7 +1,9 @@
 \encoding{UTF-8}
 \name{permat}
 \alias{permatfull}
+\alias{permatfull1}
 \alias{permatswap}
+\alias{permatswap1}
 \alias{summary.permat}
 \alias{print.summary.permat}
 \alias{print.permat}
@@ -20,6 +22,10 @@
 Details section.}
 
 \usage{
+permatfull1(m, fixedmar = "both", shuffle = "both", strata = NULL, 
+    mtype = "count")
+permatswap1(m, method = "quasiswap", fixedmar="both", shuffle = "both",
+    strata = NULL, mtype = "count", thin = 1)
 permatfull(m, fixedmar = "both", shuffle = "both", strata = NULL, 
     mtype = "count", times = 99)
 permatswap(m, method = "quasiswap", fixedmar="both", shuffle = "both",
@@ -177,7 +183,12 @@
   is useful for accessing diagnostic tools available in the \pkg{coda}
   package.  }
 
-\value{ Functions \code{permatfull} and \code{permatswap} return an
+\value{ Functions \code{permatfull1} and \code{permatswap1} return a
+  single permuted matrix. These functions are called repeatedly
+  by the corresponding \code{permatfull} and \code{permatswap}
+  functions.
+
+  Functions \code{permatfull} and \code{permatswap} return an
   object of class \code{"permat"} containing the the function call
   (\code{call}), the original data matrix used for permutations
   (\code{orig}) and a list of permuted matrices with length \code{times}