an object of class prab (presence-absence data), as generated by prabinit.

string, indicating the test statistics. "isovertice": number of isolated vertices in the graph of tuning smallest distances between species. "lcomponent": size of largest connectivity component in this graph. "distratio": ratio between tuning smallest and largest distances. "nn": average distance of species to tuningth nearest neighbor. "inclusions": number of inclusions between areas of different species (tests for nestedness structure, not for clustering, and treats abundance matrices as presence-absence-data). "mean": mean of the distances between species (this is a rough measure of species co-occurrence). "groups": this requires a specification of a vector defining different groups of species via parameter groupvector. The test statistic is then the mean of the distances between species of the same group. This is computed over all species, but also for every single group of species. It also includes the "mean"-test, so that the number of tests carried out is number of species groups with more than one element plus two.

integer or (if teststat="distratio") numerical between 0 and 1. Tuning constant for test statistics, see teststat.

integer. Number of simulation runs.

numerical between 0 and 1. The probability that a new region is drawn from the non-neighborhood of the previous regions belonging to a species under generation. If NULL (the default), and prabobj$spatial, prabtest estimates this by function autoconst. Otherwise the next five parameters have no effect. If NULL, and !prabobj$spatial, spatial structure is ignored.

numerical range vector, lower value not smaller than 0, larger value not larger than 1. Range where pd is to be found. Used by function autoconst.

integer. Number of simulations per pd-value. Used by function autoconst.

numerical between 0 and 1. Interval length between subsequent choices of pd for the first simulation. Used by function autoconst.

numerical between 0 and 1. Interval length between subsequent choices of pd for the second simulation (see parameter twostep). Used by function autoconst.

logical. If TRUE, a first estimation step for pd is carried out in the whole prange, and then the final estimation is determined between the preliminary estimator -5*step2 and +5*step2. Else, the first simulation determines the final estimator. Used by function autoconst.

logical. Indicates if the range sizes of the species are held fixed in the test simulation (TRUE) or generated from their empirical distribution in x (FALSE) for presence-absence data. See function randpop.nb. Use always TRUE for abundance data (not necessary if teststat="inclusions").

prabinit-object based on presence-absence matrix of same dimensions than the abundance matrix of prabobj. This specifies the presences and absences on which the presence/absence step of abundance-based tests is based (see details). If NULL (which is usually the only reasonable choice), prab01 is computed in order to indicate the nonzeroes of prabobj$prab.

integer vector. For every species, a number indicating the species' group membership. Needed only if teststat="groups".

Estimator of the parameters of a simultaneous autoregression model corresponding to the null model for abundance data from Hausdorf and Hennig (2007) as generated by prab.sarestimate. This requires package spdep. Note that by explicitly specifying sarestimate=NULL simulation of 0-1 matrices can be enforced.

One of "jaccard", "kulczynski", "qkulczynski" or "logkulczynski" specifying the distance measure on which the test is based. By default, this is taken from prabobj.

number of species. By default this is taken from prabobj. This should normally not be changed.

vector of test statistic values for all simulated populations. For teststat="groups" a list with components overall (means of within group-distances), mean (means of all distances), gr (matrix with a row for every group, giving the groupwise within-group distance means).

p-value against an alternative that generates large values of the test statistic (usually reasonable for teststat="inclusions", "groups", "mean").

p-value against an alternative that generates small values of the test statistic (usually reasonable for "lcomponent", "nn", "distratio"; for "isovertice", the two-sided p may make sense which is twice the smaller one of p.above and p.below).

test statistic value for the original data. (specgroups-output for teststat="groups").

see above.

dist above.

see above.

p.nb above.

TRUE if simultaneous autoregression has been used (i.e., a sarestimate has been supplied or computed).

Estimator of the autocorrelation parameter lambda (see errorsarlm) defined so that the average weight of neighbors (see nb2listw) is standardized to 1.

the output object of prab.sarestimate.

list containing information from "groups" tests, with components lg (levels of groupvector), ng (number of groups), nsg (vector of group sizes), testm (value of "means" test statistic for input prabobj), pa (group-wise p.above), pb (group-wise p.below), pma (p.above of "means" test), pmb (p.below of "means" test).