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.

matrix with non-negative entries. Either file or prabmatrix should be NA.

logical. If TRUE, rows are interpreted as species and columns are interpreted as regions. In this case, rows and columns are interchanged by prabinit.

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.

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).

matrix of non-negative reals. Geographical distances between regions. Only used if distance="geco".

tuning constant for geco-distance if distance="geco", see geco.

"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.

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.

numerical between 0 and 1, see toprab.

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.

object of class prab.

necessary for print method.

distance matrix between species.

abundance or presence/absence matrix (if presence/absence, the entries are logical). Rows are regions, columns are species.

neighborhood list, see above.

vector of the number of regions occupied by a species.

vector of the number of species present in a region.

number of species (in the prab-object, see nonzero).

number of regions.

string denoting the chosen distance measure.

non-negative matrix. see above.

numeric. see above.

TRUE, if there is a specified neighborhood structure.

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.

see above.