/packages/archive/2010/05.2010/05.01.2010/spacodi/man/resamp.3x.Rd

 1\name{resamp.3x}
 2
 3\alias{resamp.3x}
 4
 5\title{null models: randomizing a community phylogenetics matrix: '3x' of Hardy (2008)}
 6
 7\usage{resamp.3x(obj, level=0.1)}
 8
 9\arguments{
10  \item{obj}{a community-phylogenetic dataset in \code{SPACoDi} format (see \code{\link{as.spacodi}})}
11  \item{level}{a proportion specifying the extent of data shuffling}
12}
13
14\details{
15  A resampling procedure for a species-by-plots matrix, based on Gotelli swapping.
16  Shuffles abundances within species and for a pair of plots.  The \code{level} defines
17  the degree of sampling, with larger values dictating a higher level of reshuffling.
18  For instance, if \code{level = 0.1} and the dataset involves 20 species and 20 plots, 
19  a total of 40 (\code{0.1*20*20}) Gotelli swaps are performed.
20}
21
22\value{A shuffled dataset}
23
24\references{
25  HARDY OJ. 2008. Testing the spatial phylogenetic 
26  structure of local communities: statistical performances of 
27  different null models and test statistics on a locally neutral 
28  community. Journal of Ecology 96:914-926.
29  
30  GOTELLI NJ. 2000. Null model analysis of species co-occurrence patterns. Ecology 81:2606–2621.
31}
32
33\author{Jonathan Eastman}
34
35\seealso{\code{\link{Bst.by.nodes}} for permutation tests of community diversity and additional randomization methods; 
36see \code{\link{spacodi.calc}} for the main underlying function; \code{\link[picante]{randomizeMatrix}}}
37
38\examples{
39sp.plot <- sim.spacodi(species=10,plots=4,missing.prop=0.15,sim.tree=FALSE)
40sp.plot
41
42# shuffle dataset
43resamp.3x(obj=sp.plot, level=0.2) 
44}