togetherness: Calculates the number of identical co-presences and...

In bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Description

Togetherness, or T-score, describes the level of similarity in the distributional pattern of two species. Originally proposed by Stone & Roberts (1992) for biogeographical situations can it also be applied e.g. to pollinators on different host plants.

Usage

togetherness(web, normalise=TRUE, FUN = mean, ...)

Arguments

web	A matrix with binary or counted interactions/links, where the higher trophic level is represented by columns.
normalise	Logical; shall index be normalised to a range of 0-1?
FUN	The function to summarise species-pair T-scores with; defaults to mean.
...	Arguments passed on to FUN, especially na.rm=T or colours for hist.

Value

Returns the average (default) togetherness of all species combinations.

Author(s)

Carsten F. Dormann

References

Stone, L. and Roberts, A. (1992) Competitive exclusion, or species aggregation? An aid in deciding. Oecologia 91, 419–424

See Also

C.score for another of Stone & Roberts' indices.

Examples

(m <- matrix(c(0,1,0,0,1,1,0,1,1,0), ncol=2, byrow=TRUE))
togetherness(m)
# or, with two togethernesses:
(n <- matrix(c(0,1,1,0,1,1,0,0,1,1,0,1,0,1), ncol=2, byrow=TRUE))
togetherness(n, normalise=FALSE)

data(Safariland)
togetherness(m)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: sna
Loading required package: statnet.common

Attaching package: 'statnet.common'

The following object is masked from 'package:base':

    order

Loading required package: network
network: Classes for Relational Data
Version 1.13.0 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.

sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

 This is bipartite 2.08
 For latest changes see versionlog in  ?"bipartite-package".
 For citation see: citation("bipartite").
 Have a nice time plotting and analysing two-mode networks.


Attaching package: 'bipartite'

The following object is masked from 'package:vegan':

    nullmodel

     [,1] [,2]
[1,]    0    1
[2,]    0    0
[3,]    1    1
[4,]    0    1
[5,]    1    0
[1] 0.1666667
     [,1] [,2]
[1,]    0    1
[2,]    1    0
[3,]    1    1
[4,]    0    0
[5,]    1    1
[6,]    0    1
[7,]    0    1
[1] 2
[1] 0.1666667

bipartite documentation built on May 30, 2017, 1:25 a.m.