prob.table: Function to extract the probability table from an analysis of...
In griffithdan/cooccur: Probabilistic Species Co-Occurrence Analysis in R

Description Usage Arguments Value Author(s) See Also Examples

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

1	prob.table(mod)

mod

Object of class cooccur.

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

Daniel M Griffith

pair, pair.attributes

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