[Vegan-commits] r584 - in pkg/vegan: inst man

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

Author: psolymos
Date: 2008-11-20 18:11:54 +0100 (Thu, 20 Nov 2008)
New Revision: 584

Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/oecosimu.Rd
Log:
oecosimu changes documented


Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2008-11-20 17:10:38 UTC (rev 583)
+++ pkg/vegan/inst/ChangeLog	2008-11-20 17:11:54 UTC (rev 584)
@@ -4,6 +4,10 @@
 
 Version 1.16-4 (opened November 1, 2008)
 
+    * oecosimu: got a new control argument for quantitative null
+    model analyses, and this is available if method = "permat".
+    The print method and help file modified accordingly.
+
 	* vignettes: Figures with narrower margins. Vignetted
 	"diversity-vegan" adds functional diversity ('treedive'), 'beals'
 	and 'radfit' graphics updated to current vegan. Still missing
@@ -11,7 +15,7 @@
 	additive diversity partioninng, Tsallis entropy.
 
 	* radlattice: a new function to display each radfit model in a
-	separate panel together with their AIC or BIC values. I wanter to
+	separate panel together with their AIC or BIC values. I wanted to
 	have this for a manuscript.
 
 	* plot.cca: takes care that plotted items have non-NULL names that
@@ -20,7 +24,7 @@
 	plots. Reported by Daniel Borcard.
 	
 	* permatwsap: quasiswap method is implemented for count data based
-	on the idea of Carsten Dormann in the swap.web::bipartite
+	on the idea of Carsten Dormann in the bipartite::swap.web
 	function. This takes a random matrix first with same row and
 	column sums as the original (via r2dtable), and than restores the
 	original matrix fill through steps of swaping 2x2 submatrices. The

Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd	2008-11-20 17:10:38 UTC (rev 583)
+++ pkg/vegan/man/oecosimu.Rd	2008-11-20 17:11:54 UTC (rev 584)
@@ -16,7 +16,7 @@
 
 \usage{
 oecosimu(comm, nestfun, method, nsimul = 99, burnin = 0, thin = 1,
-   statistic = "statistic",  ...)
+   statistic = "statistic", control, ...)
 commsimulator(x, method, thin=1)
 }
 
@@ -36,6 +36,9 @@
   \code{"swap"} and \code{"tswap"}.}
   \item{statistic}{The name of the statistic returned by
     \code{nestedfun}} 
+  \item{control}{a list of arguments passed to quantitative
+    permutation algorithms. If missing, the function 
+    \code{permat.control} is used.}
   \item{\dots}{Other arguments to functions.}
 }
 
@@ -120,6 +123,14 @@
   backtracking is done so may times that all incidences will be filled
   into matrix. The \code{quasiswap} method is not sequential, but it produces
   a random incidence matrix with given marginal totals. 
+
+  As a result of method \code{permat} in \code{oecosimu}, quantitative
+  community null models are used to evaluate the statistic. Through the \code{control}
+  argument, further options can be set via the function \code{\link{permat.control}}.
+  A full description of these settings can be found on the help pages of the
+  functions \code{\link{permatfull}} and \code{\link{permatswap}}. Note, that
+  \code{burnin} and \code{thin} arguments given in the \code{oecosimu} function call
+  overwrite the respective ones specified by \code{permat.control}.
 }
 
 \value{
@@ -195,6 +206,17 @@
 out
 ## Inspect the swap sequence
 matplot(t(out$oecosimu$simulated), type="l")
+## Use quantitative null models to compare
+## mean Bray-Curtis dissimilarities
+data(dune)
+meandist <- function(x) mean(vegdist(x, "bray"))
+out.mbc <- oecosimu(dune, meandist, "permat")
+out.mbc
+## Use the quantitative swap algorithm
+## to compare Shannon diversities by samples
+contr <- permat.control(ptype="swap", method="swap")
+out.div <- oecosimu(dune, diversity, "permat", burnin=100, thin=10, control=contr)
+out.div
 }
 \keyword{ multivariate }