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) from which a 0-1 matrix can be generated. print.prab is a print method for such objects.

Usage

prabinit(file = NULL, prabmatrix = NULL, rows.are.species = TRUE,
neighborhood = "none", 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. nen-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 is tested by nbtest.
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), 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 both smaller than 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 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

An object of class prab, which is a list with components

distmat distance matrix between species.
prab presence-absence or abundance matrix. 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.
nonzero 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.

Author(s)

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

See Also

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

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 2.1-2 Index]