prob.table {cooccur} R Documentation

## 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

### Author(s)

Daniel M Griffith

pair, pair.attributes

### Examples

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


[Package cooccur version 1.3 Index]