R: Presence-absence/abundance matrix initialization

prabinit {prabclus} | R Documentation

## Presence-absence/abundance matrix initialization

### Description

`prabinit` converts a matrix into an object of class `prab` (presence-absence). The matrix may be read from a file or an R-object. It may be a 0-1 matrix or a matrix with non-negative entries (usually abundances). `print.prab` is a print method for such objects.

Documentation here is in terms of biotic elements analysis (species are to be clustered). For species delimitation with dominant markers, see Hausdorf and Hennig (2010), individuals take the role of species and loci take the role of regions.

### Usage

    prabinit(file = NULL, prabmatrix = NULL, rows.are.species = TRUE,
    neighborhood = "none", nbbetweenregions=TRUE, geodist=NULL, gtf=0.1,
    distance = "kulczynski", toprab = FALSE, toprabp
    = 0.05, outc = 5.2)

    ## S3 method for class 'prab'
    print(x, ...)

### Arguments

`file` | string. non-negative matrix ASCII file (such as example dataset `kykladspecreg.dat`) from which the matrix is read by `read.table`. The usual interpretation is that it is a species-by-regions matrix of species presences/absences (0-1 matrix) or abundances.
`prabmatrix` | matrix with non-negative entries. Either `file` or `prabmatrix` should be `NA`.
`rows.are.species` | logical. If `TRUE`, rows are interpreted as species and columns are interpreted as regions. In this case, rows and columns are interchanged by `prabinit`.
`neighborhood` | A string or 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 vector `numeric(0)`. If `neighborhood` is a filename, it is attempted to read such a list from a file, where every row should correspond to one region (such as example dataset `nb.dat`). If `neighborhood="none"`, all neighborhoods are set to `numeric(0)`. The neighborhood can be tested by `nbtest` for consistency.
`nbbetweenregions` | logical. If `TRUE`, the neighborhood is defined between regions as explained above. Otherwise it is defined between species (or individuals, if this is used for species delimitation).
`geodist` | matrix of non-negative reals. Geographical distances between regions. Only used if `distance="geco"`.
`gtf` | tuning constant for geco-distance if `distance="geco"`, see `geco`.
`distance` | `"kulczynski"`, `"jaccard"`, `"geco"`, `"qkulczynski"`, `"logkulczynski"` (this calls function `qkulczynski` with `log.distance=TRUE`), `"dice"`, or `"none"`. The distance measure between species to compute by `prabinit`.
`toprab` | logical. If `TRUE`, a presence-absence matrix is computed from the non-negative input matrix. "Absence", i.e., the entry 0, is chosen if the original entry is 0, or the original entry is smaller than or equal to `toprabp` times the sum of entries in the corresponding region, and log(original entry) is considered to be a lower outlier compared with the other entries of the corresponding species (see `outc`). "Presence", i.e., the entry 1, thus means that the original entry is non-negligible w.r.t. the species or w.r.t. the region.
`toprabp` | numerical between 0 and 1, see `toprab`.
`outc` | numerical. Tuning constant for the outlier identification associated with `toprab=TRUE`. An entry smaller than or equal to `outc*mad` times the median is considered as a lower outlier.
`x` | object of class `prab`.
`...` | necessary for print method.

### Details

Species that are absent in all regions are omitted.

### Value

`prabinit` produces an object of class `prab`, which is a list with components

`distmat` | distance matrix between species.
`prab` | abundance or presence/absence matrix (if presence/absence, the entries are logical). Rows are regions, columns are species.
`nb` | neighborhood list, see above.
`regperspec` | vector of the number of regions occupied by a species.
`specperreg` | vector of the number of species present in a region.
`n.species` | number of species (in the `prab`-object, see `nonzero`).
`n.regions` | number of regions.
`distance` | string denoting the chosen distance measure.
`geodist` | non-negative matrix. see above.
`gtf` | numeric. see above.
`spatial` | `TRUE`, if there is a specified neighborhood structure.
`nonempty.species` | logical vector. The length is the number of species in the original file/matrix. If `FALSE`, the corresponding species had only zero entries and was therefore absent. Note that these species are not included in any other component of a `prab` object, i.e., `n.species` is the number of `TRUE`-entries in `nonzero`.
`nbbetweenregions` | see above.

### Author(s)

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

### References

Hausdorf, B. and Hennig, C. (2010) Species Delimitation Using Dominant and Codominant Multilocus Markers. Systematic Biology, 59, 491-503.

### See Also

`read.table`, `jaccard`, `kulczynski`, `geco`, `qkulczynski`, `nbtest`, `alleleinit`

### Examples

    # If you want to use your own ASCII data files, use
    # x <- prabinit(file="path/prabmatrixfile",
    # neighborhood="path/neighborhoodfile")
    data(kykladspecreg)
    data(nb)
    prabinit(prabmatrix=kykladspecreg, neighborhood=nb)

[Package prabclus version 2.2-6 Index]