/packages/archive/2010/05.2010/05.01.2010/spacodi/man/resamp.3x.Rd
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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 81:2606รข€“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}