# nested: Calculates any of several measures of nestedness In bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices

## Description

Wrapper function calling one, several or all currently implemented nestedness measures

## Usage

 `1` ```nested(web, method = "binmatnest2", rescale=FALSE, normalised=TRUE) ```

## Arguments

 `web` A matrix with elements of a set (e.g., plants) as rows, elements of a second set (e.g., pollinators) as columns and number of interactions as entries. `method` One or more of the following: discrepancy, discrepancy2, binmatnest, binmatnest2, NODF, NODF2, C score, checker, weighted NODF, wine, ALL. See details for details on each method.
 `rescale` Should all measures be rescaled so that higher values mean higher nestedness? Defaults to FALSE, i.e. the standard interpretation of each measure is maintained. `normalised` Logical, defaulting to TRUE. Should C-scores be normalised to a value between 0 and 1? See `C.score` for details.

## Details

There are five different measures currently available:

1

binmatnest calculates nestedness temperature following the function `nestedness` (0 = cold = highly nested; 100 = hot = not nested at all). It uses the original program of Miguel Rodriguez-Girones, only called from R; binmatnest2, in contrast, is the implementation in `nestedtemp` of the same algorithm by Jari Oksanen. Because binmatnest sometimes (and to us unexplicably) invert the matrix, we prefer the binmatnest2 option.

2

Discrepancy calculates the number of non-nested 0s and 1s. While `discrepancy` calls the function with the same name, discrepancy2 calls `nesteddisc`, which handles ties differently. Most of the time, these two should deliver very, very similar results. Higher values indicate lower nestedness.

3

NODF is the nestedness measure proposed by Almeida-Neto et al., correcting for matrix fill and matrix dimensions. Values of 0 indicate non-nestedness, those of 100 perfect nesting. NODF2 sorts the matrix before calculating the measure. NODF is, I understand, closer to the version presented in the paper, while NODF2 seems to make more sense for comparisons across different networks (because it is independent of the initial presentation of the matrix). Both call `nestednodf` in vegan. (Yes, I initially programmed NODF myself, only to find that it was there already. Luckily, there was a perfect agreement between my (depricated) version and nestednodf.) A weighted version is also now available (see point 6 below), following the paper of Almeida-Neto and Ulrich (2010).

4

`C.score` calculates the number of checkerboard pattern in the matrix. As default, it normalises this value between min and max, so that values of 0 indicate no checkerboards (i.e. nesting), while a value of 1 indicates a perfect checkerboard. checker is the non-normalised version, based on `nestedchecker`.

5

wine is one of two nestedness measure using the information on the weight of a link. See `wine` for details.

6

weighted NODF is a version of 3, but now incorporating information on the weights of the link; it is the second quantitative nestedness measure, (chronologically) after wine. It uses the sorted matrix to compute NODF. If you want NODF of the unsorted, you have to directly use `nestednodf` in vegan.

## Value

A vector with values for each of the selected nestedness measures.

## Note

The idea behind this function is to encourage the comparison of different nestedness measures. That does not mean, we necessarily see much ecological sense in them (see, e.g., the paper by Blüthgen et al. 2008).

`nested` uses one non-default setting for the `nestedness` measures called: null.models=FALSE. This is simply to speed up the computation. Null models should be built for all nestedness measures, of course, not only for `nestedness`!

## Author(s)

Carsten F. Dormann [email protected]

## References

Almeida-Neto, M., Guimaraes, P., Guimaraes, P.R., Loyola, R.D. and Ulrich, W. 2008. A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos 117, 1227–1239.

Almeida-Neto, M. and Ulrich, W. (2011) A straightforward computational approach for measuring nestedness using quantitative matrices. Environmental Modelling & Software, 26, 173–178

Blüthgen, N., J. Fründ, D. P. Vazquez, and F. Menzel. 2008. What do interaction network metrics tell us about specialisation and biological traits? Ecology 89, 3387–3399.

Brualdi, R.A. and Sanderson, J.G. 1999. Nested species subsets, gaps, and discrepancy. Oecologia 119, 256–264.

Galeano, J., Pastor, J.M., Iriondo and J.M. 2008. Weighted-Interaction Nestedness Estimator (WINE): A new estimator to calculate over frequency matrices. arXiv 0808.3397v2 [physics.bio-ph]

Rodríguez-Gironés, M.A. and Santamaría, L. 2006. A new algorithm to calculate the nestedness temperature of presence-absence matrices. J. Biogeogr. 33, 924–935.

Stone, L. and Roberts, A. 1990. The checkerboard score and species distributions. Oecologia 85, 74–79.

Almeida-Neto, M. and Ulrich, W. 2010. A straightforward computational approach for measuring nestedness using quantitative matrices. Environmental Modelling & Software, in press.

`C.score`, `wine`, `nestedness`, `discrepancy`; and, within vegan: `nestedtemp`, `nestedchecker`, `nesteddisc`, `nestednodf`

## Examples

 ```1 2 3 4 5 6 7 8``` ```## Not run: data(Safariland) nested(Safariland, "ALL") nested(Safariland, "ALL", rescale=TRUE) # illustration that non-normalised C.score and checker are the same: nested(Safariland, c("C.score", "checker"), normalise=FALSE) ## End(Not run) ```

### Example output

```Loading required package: vegan
This is vegan 2.4-4

Attaching package: 'statnet.common'

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

order

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 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

binmatnest2.temperature               binmatnest discrepancy2.discrepancy
19.8540553                5.7626076               15.0000000
discrepancy                  C.score                  checker
21.0000000                0.5616097                1.0227920
NODF2                     NODF            weighted NODF
24.5478036               18.0878553               11.6063738
wine
0.3712611
binmatnest2.temperature               binmatnest discrepancy2.discrepancy
78.9967443               94.2373924               15.0000000
discrepancy                  C.score                  checker
21.0000000                0.5616097                1.0227920
NODF2                     NODF            weighted NODF
24.5478036               18.0878553               11.6063738
wine
0.3292093
C.score   checker
0.5616097 1.0227920
```

bipartite documentation built on July 13, 2018, 1:04 a.m.