prob.table: Function to extract the probability table from an analysis of...

In cooccur: Probabilistic Species Co-Occurrence Analysis in R

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

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)

Example output

cooccur documentation built on May 2, 2019, 6:44 a.m.