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