[Vegan-commits] r628 - pkg/vegan/man

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

Author: psolymos
Date: 2008-12-09 07:20:47 +0100 (Tue, 09 Dec 2008)
New Revision: 628

Modified:
   pkg/vegan/man/dispindmorisita.Rd
   pkg/vegan/man/oecosimu.Rd
Log:
quasiswap included in example, + typo corrected


Modified: pkg/vegan/man/dispindmorisita.Rd
===================================================================
--- pkg/vegan/man/dispindmorisita.Rd	2008-12-09 02:42:55 UTC (rev 627)
+++ pkg/vegan/man/dispindmorisita.Rd	2008-12-09 06:20:47 UTC (rev 628)
@@ -11,7 +11,7 @@
 \arguments{
   \item{x}{community data matrix, with sites (samples) as rows and species as columns.}
   \item{unique.rm}{logical, if \code{TRUE}, unique species (occurring in only one sample) are removed from the result.}
-  \item{crit}{two-sided p-value to use calculating critical Chi-squared values.}
+  \item{crit}{two-sided p-value used to calculate critical Chi-squared values.}
 }
 \details{
 The Morisita index of dispersion is defined as (Morisita 1959, 1962):
@@ -55,10 +55,9 @@
 }
 \author{\enc{P\'eter S\'olymos}{Peter Solymos}, \email{solymos at ualberta.ca}}
 \note{
-A common error found in several papers is that when standardizing as in the case (b), the denominator is given as \code{Muni - 1}. This reult in a hiatus in the [0, 0.5] interval of the standardized index. The roort of this typo is the book of Krebs (1999), see the Errata for the book (Page 217, \url{http://www.zoology.ubc.ca/~krebs/downloads/errors_2nd_printing.pdf}).
+A common error found in several papers is that when standardizing as in the case (b), the denominator is given as \code{Muni - 1}. This reult in a hiatus in the [0, 0.5] interval of the standardized index. The root of this typo is the book of Krebs (1999), see the Errata for the book (Page 217, \url{http://www.zoology.ubc.ca/~krebs/downloads/errors_2nd_printing.pdf}).
 }
 \examples{
-library(vegan)
 data(dune)
 x <- dispindmorisita(dune)
 x

Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd	2008-12-09 02:42:55 UTC (rev 627)
+++ pkg/vegan/man/oecosimu.Rd	2008-12-09 06:20:47 UTC (rev 628)
@@ -214,10 +214,10 @@
 meandist <- function(x) mean(vegdist(x, "bray"))
 out.mbc <- oecosimu(dune, meandist, "permat")
 out.mbc
-## Use the quantitative swap algorithm
+## Use the quantitative quasiswap 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)
+contr <- permat.control(ptype="swap", method="quasiswap")
+out.div <- oecosimu(dune, diversity, "permat", control=contr)
 out.div
 }
 \keyword{ multivariate }