/packages/archive/2010/04.2010/04.20.2010/spacodi/man/resamp.1a.Rd

 1\name{resamp.1a}
 2
 3\alias{resamp.1a}
 4
 5\title{randomizing a species-by-plots matrix: '1a' of Hardy (2008)}
 6
 7\usage{resamp.1a(obj, abund.class.ratio = 4)}
 8
 9\arguments{
10  \item{obj}{a species-by-plots matrix}
11  \item{abund.class.ratio}{a ratio defining abundance classes}
12}
13
14\details{A resampling procedure for a species-by-plots matrix, where species are shuffled within abundance classes. 
15Species are grouped into distinct abundance classes characterized by a fixed ratio: 
16\code{abund.class.ratio} = maximal abundance / minimal abundance.  For instance, if \code{abund.class.ratio = 4},
17the limits between abundance classes could be 1, 4, 16, ... .  Species are randomly permuted within each 
18class, which maintains most of the abundance phylogenetic structure originally present in a dataset.  
19}
20
21\value{a shuffled dataset}
22
23\references{
24  HARDY OJ. 2008. Testing the spatial phylogenetic 
25  structure of local communities: statistical performances of 
26  different null models and test statistics on a locally neutral 
27  community. Journal of Ecology 96:914-926.
28}
29
30\author{Timothy Paine and Jonathan Eastman}
31
32\seealso{\code{\link{Bst.permutation}} for permutation tests of community diversity and additional randomization methods; 
33see \code{\link{spacodi.calc}} for the main underlying function}
34
35\examples{
36sp_plot <- r.plot(species=10,plots=4,missing.prop=0.15,sim.tree=FALSE)
37sp_plot
38
39# shuffle dataset
40resamp.1a(obj=sp_plot, abund.class.ratio=3) 
41}