pop.sim: p-value simulation for presence-absence matrices clustering...

In prabclus: Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data

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 = NULL, geodist=NULL, gtf=0.1,
n.species = ncol(regmat),
specperreg = NULL, regperspec = NULL, species.fixed=FALSE, pdfnb=FALSE,
ignore.richness=FALSE)

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", "jaccard" or "geco", see kulczynski, geco 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.
geodist	matrix of non-negative reals. Geographical distances between regions. Only used if dist="geco".
gtf	tuning constant for geco-distance if dist="geco", see "geco".
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.
ignore.richness	logical. If TRUE, there is no assumption of species richnesses to differ between regions in the null model. Regionwise probabilities don't differ in the generation of null data.

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 [e-mail] https://www.unibo.it/sitoweb/christian.hennig/en

References

Hennig, C. and Hausdorf, B. (2004) Distance-based parametric bootstrap tests for clustering of species ranges. Computational Statistics and Data Analysis 45, 875-896. http://stat.ethz.ch/Research-Reports/110.html.

Hausdorf, B. and Hennig, C. (2003) Biotic Element Analysis in Biogeography. Systematic Biology 52, 717-723.

Hausdorf, B. and Hennig, C. (2003) Nestedness of north-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

options(digits=4)
data(kykladspecreg)
data(nb)
set.seed(1234)
pop.sim(t(kykladspecreg), nb, times=5, h0c=0.35, teststat="nn", testc=3)

prabclus documentation built on Oct. 24, 2023, 1:06 a.m.