[Vegan-commits] r1882 - pkg/vegan/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Sep 24 19:32:52 CEST 2011
Author: jarioksa
Date: 2011-09-24 19:32:52 +0200 (Sat, 24 Sep 2011)
New Revision: 1882
Modified:
pkg/vegan/man/oecosimu.Rd
Log:
document oecosimu change in -r1881
Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd 2011-09-24 17:32:09 UTC (rev 1881)
+++ pkg/vegan/man/oecosimu.Rd 2011-09-24 17:32:52 UTC (rev 1882)
@@ -34,9 +34,9 @@
result object for \code{as.ts}, \code{as.mcmc}, \code{density} and
\code{densityplot}.}
\item{nestfun}{Function to analyse nestedness. Some functions are
- provided in \pkg{vegan}, but any function can be used if it accepts the
- community as the first argument, and returns either a plain number or
- the result in list item with the name defined in argument
+ provided in \pkg{vegan}, but any function can be used if it accepts the
+ community as the first argument, and returns either a plain number or
+ the result in list item with the name defined in argument
\code{statistic}. See Examples for defining your own functions.}
\item{method}{Null model method. See details.}
\item{nsimul}{Number of simulated null communities.}
@@ -59,8 +59,7 @@
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 other
- functions (depending on method argument), and evaluates the
+ a series of null models based on \code{nullmodel}, 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}},
@@ -76,6 +75,10 @@
an example. Raup-Crick index (\code{\link{raupcrick}}) gives an
example of using a dissimilarities index.
+ The description of the function \code{commsimulator} below is
+ obsolescent: the function is not used any longer, but
+ \code{oecosimu} uses null models described in \code{\link{commsim}}.
+
Function \code{commsimulator} implements binary (presence/absence)
null models for community composition.
The implemented models are \code{r00} which maintains the
@@ -89,7 +92,7 @@
frequencies, but they are not strictly constrained. All these methods
are reviewed by Wright et al. (1998). Method \code{c0} maintains
species frequencies, but does not honour site (row) frequencies (Jonsson
- 2001).
+ 2001).
The other methods maintain both row and column frequencies.
Methods \code{swap} and \code{tswap} implement sequential methods,
@@ -165,18 +168,6 @@
load the \pkg{lattice} library before calling \code{densityplot}, or
use the longer form \code{densityplot.oecosimu} when you first time
call the function.
-
- As a result of \code{method = "r2dtable"} in \code{oecosimu}, quantitative
- community null models are used to evaluate the statistic. This setting uses
- the \code{\link{r2dtable}} function to generate random matrices with fixed
- row and column totals (hypergeometric distribution). This null model is
- used in diversity partitioning function (see \code{\link{adipart}}).
-
- The \code{method} argument can be a function with first argument taking the
- community matrix, and optionally with \code{burnin} and \code{thin} argument.
- The function must return a matrix-like object with same dimensions.
- But be careful, blindly applying permuted matrices for null model testing
- can be dangerous.
}
\value{
@@ -236,13 +227,16 @@
If you wonder about the name of \code{oecosimu}, look at journal
names in the References (and more in \code{\link{nestedtemp}}). }
-\seealso{ \code{\link{r2dtable}} generates table with given marginals but
- with entries above one. Functions \code{\link{permatfull}} and
- \code{\link{permatswap}} generate Null models for count data.
+\seealso{Function \code{oecosimu} currently defines null models with
+ \code{\link{commsim}} and generates the simulated null model
+ communities with \code{\link{nullmodel}} and
+ \code{\link{simulate.nullmodel}}.
+
Function \code{\link[labdsv]{rndtaxa}}
(\pkg{labdsv} package) randomizes a community table. See also
\code{\link{nestedtemp}} (that also discusses other nestedness
- functions) and \code{\link{treedive}} for another application. }
+ functions) and \code{\link{treedive}} for another application.
+}
\examples{
## Use the first eigenvalue of correspondence analysis as an index
## of structure: a model for making your own functions.
@@ -262,14 +256,7 @@
meandist <- function(x) mean(vegdist(x, "bray"))
mbc1 <- oecosimu(dune, meandist, "r2dtable")
mbc1
-## Define a custom function that shuffles
-## cells in each rows
-f <- function(x) {
- apply(x, 2, function(z) sample(z, length(z)))
}
-mbc2 <- oecosimu(as.matrix(dune), meandist, f)
-mbc2
-}
\keyword{ multivariate }
\keyword{ datagen }
More information about the Vegan-commits
mailing list