pop.sim {prabclus}R Documentation

p-value simulation for presence-absence matrices clustering test

Description

Parametric bootstrap simulation of the p-value of a test of a homogeneity hypothesis against clustering (or significant nestedness). Designed for use within prabtest. The null model is defined by randpop.nb.

Usage

pop.sim(regmat, neighbors, h0c = 1, times = 200, dist = "kulczynski",
teststat = "isovertice", testc = NA, n.species = ncol(regmat),
specperreg = NA, regperspec = NA, species.fixed=FALSE, pdfnb=pdfnb)

Arguments

regmat 0-1-matrix. Columns are species, rows are regions.
neighbors A list with a component for every region. The components are vectors of integers indicating neighboring regions. A region without neighbors (e.g., an island) should be assigned a list numeric(0).
h0c numerical. Parameter p.nb for use in randpop.nb.
times integer. Number of simulation runs.
dist "kulczynski" or "jaccard", see kulczynski and jaccard.
teststat "isovertice", "lcomponent", "distratio", "nn" or "inclusions". See the corresponding functions, homogen.test for "isovertice", incmatrix for "inclusions").
testc numerical. Tuning constant for the test statistics.
n.species integer. Number of species.
specperreg vector of integers. Numbers of species per region (is calculated from the data by default).
regperspec vector of integers. Number of regions per species (is calculated from the data by default).
species.fixed logical. If TRUE, the sizes of the species are taken directly from regmat. Otherwise, they are drawn by random from the empirical distribution of the values from regmat.
pdfnb logical. Probability correction in randpop.nb.

Value

List with components

results vector of teststatistic values for the simulated matrices.
p.above p-value if large test statistic leads to rejection.
p.below p-value if small test statistic leads to rejection.
datac test statistic value for the original data.
testc see above.

Author(s)

Christian Hennig hennig@math.uni-hamburg.de http://www.math.uni-hamburg.de/home/hennig/

References

Hennig, C. and Hausdorf, B. (2002) Distance-based parametric bootstrap tests for clustering of species ranges, submitted, http://stat.ethz.ch/Research-Reports/110.html.

Hausdorf, B. and Hennig, C. (2003) Biotic Element Analysis in Biogeography. To appear in Systematic Biology.

Hausdorf, B. and Hennig, C. (2003) Nestedness of nerth-west European land snail ranges as a consequence of differential immigration from Pleistocene glacial refuges. Oecologia 135, 102-109.

See Also

prabtest, randpop.nb, jaccard, kulczynski, homogen.test, lcomponent, distratio, nn, incmatrix.

Examples

data(kykladspecreg)
# Note: If you do not use the installed package, replace this by
# kykladspecreg <- read.table("(path/)kykladspecreg.dat")
data(nb)
# Note: If you do not use the installed package, replace this by
# nb <- list()
# for (i in 1:34)
#   nb <- c(nb,list(scan(file="(path/)nb.dat",
#                   skip=i-1,nlines=1)))
set.seed(1234)
pop.sim(t(kykladspecreg), nb, times=20, h0c=0.35, teststat="nn", testc=3)

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