cooccur (version 1.3)

prob.table: Function to extract the probability table from an analysis of species co-occurrence.

Description

Returns a results table for all analyzed species pairs in a cooccur object.

Usage

prob.table(mod)

Arguments

mod

Object of class cooccur.

Value

Returns a data.frame with the following columns.

sp1

Numeric label giving the identity of species 1, assigned based on the order in the input matrix

sp2

Numeric label for species 2

sp1_inc

Number of sites (or samples) that have species 1

sp2_inc

Number of sites that have species 2

obs

cooccur Observed number of sites having both species

prob

cooccur Probability that both species occur at a site

exp

cooccur Expected number of sites having both species

p_lt

Probability that the two species would co-occur at a frequency less than the observed number of co-occurrence sites if the two species were distributed randomly (independently) of one another

p_gt

Probability of co-occurrence at a frequency greater than the observed frequency

sp1_name

If species names were specified in the community data matrix this field will contain the supplied name of sp1

sp2_name

The supplied name of sp2

See Also

pair, pair.attributes

Examples

#data(finches)
#cooccur.finches <- cooccur(mat=finches,
#			   type="spp_site",
#			   thresh=TRUE,
#			   spp_names=TRUE)
#prob.table(cooccur.finches)