[Vegan-commits] r702 - in pkg/vegan: R man

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

Author: psolymos
Date: 2009-02-24 19:16:06 +0100 (Tue, 24 Feb 2009)
New Revision: 702

Modified:
   pkg/vegan/R/oecosimu.R
   pkg/vegan/man/oecosimu.Rd
   pkg/vegan/man/permatfull.Rd
Log:
new arguments added to oecosimu through permat.control


Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R	2009-02-24 14:13:31 UTC (rev 701)
+++ pkg/vegan/R/oecosimu.R	2009-02-24 18:16:06 UTC (rev 702)
@@ -85,6 +85,8 @@
             if (control$method %in% c("swap", "tswap")) {
             if (burnin > 0) {
                 m <- permatswap(comm, method=control$method,
+                    fixedmar=control$fixedmar,
+                    shuffle=control$shuffle,
                     strata=control$strata,
                     mtype=control$mtype, times=1, 
                     burnin=burnin, thin=0)$perm[[1]]
@@ -92,6 +94,8 @@
             }
             for (i in 1:nsimul) {
                 x <- permatswap(comm, method=control$method,
+                    fixedmar=control$fixedmar,
+                    shuffle=control$shuffle,
                     strata=control$strata,
                     mtype=control$mtype, times=1, 
                     burnin=0, thin=thin)

Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd	2009-02-24 14:13:31 UTC (rev 701)
+++ pkg/vegan/man/oecosimu.Rd	2009-02-24 18:16:06 UTC (rev 702)
@@ -47,7 +47,7 @@
   Function \code{oecosimu} is a wrapper that evaluates a nestedness
   statistic using function given by \code{nestfun}, and then simulates a
   series of null models using \code{commsimulator} or 
-  \code{permatfull}/\code{permatswap} (depending on method), and evaluates the
+  \code{permatfull} / \code{permatswap} (depending on method), and evaluates the
   statistic on these null models. The \pkg{vegan} packages contains some
   nestedness functions that are described separately
   (\code{\link{nestedchecker}}, \code{\link{nesteddisc}},

Modified: pkg/vegan/man/permatfull.Rd
===================================================================
--- pkg/vegan/man/permatfull.Rd	2009-02-24 14:13:31 UTC (rev 701)
+++ pkg/vegan/man/permatfull.Rd	2009-02-24 18:16:06 UTC (rev 702)
@@ -75,6 +75,7 @@
 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).
 
 The algorithm \code{"abuswap"} produces two kinds of null models (based on \code{fixedmar="columns"} or \code{fixedmar="rows"}) as described in Hardy (2008; randomization sheme 2x and 3x, respectively).
+These preserve column and row occurrences, and column or row sums at the same time.
 
 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