prabclus: pop.sim – R documentation

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pop.sim

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 christian.hennig@unibo.it 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.

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

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

v2.3-2

GPL

Authors

Christian Hennig <christian.hennig@unibo.it>, Bernhard Hausdorf <Hausdorf@zoologie.uni-hamburg.de>

Initial release

2020-01-06