R: p-value simulation for presence-absence matrices clustering...

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 = 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 chrish@stats.ucl.ac.uk http://www.homepages.ucl.ac.uk/~ucakche

### 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)

[Package prabclus version 2.2-6 Index]