prabinit {prabclus}

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

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)