[R-sig-eco] null model for testing nestedness (v_coudrain at voila.fr)

[Lars Götzenberger]

Hi,

there should be an easy solution to your problem by using the oecosimu 
function of the vegan package. It allows you to specify your null model 
and then use the nestednodf function as an argument within the oecusimu 
function. Simply look up the help for the oecosimu function for more 
details.

Hope that helps,

Lars Götzenberger



On 25.9.2013 12:00 PM, r-sig-ecology-request at r-project.org wrote:
> Message: 3
> Date: Tue, 24 Sep 2013 20:07:58 +0200 (CEST)
> From:v_coudrain at voila.fr
> To:r-sig-ecology at r-project.org
> Subject: [R-sig-eco] null model for testing nestedness
> Message-ID: <1121167144.286531380046078873.JavaMail.www at wwinf7125>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all,
> I would like to implement a null model to test if nestedness of a matrix departs from chance. There is an example in package "bipartite" with the function "nullmodel":
>
> obs <- unlist(networklevel(web, index="weighted NODF"))
> nulls <- nullmodel(web, N=100, method=1)
> null <- unlist(sapply(nulls , networklevel, index="weighted NODF"))
>
> This works well, however, I have the impress that prior to apply the function "networklevel", the initial matrix is being reordered to achieve maximal packing.
> However, I don't want my matrix to be reordered, but I did not manage to find how to specify it. In the package vegan, there is the function nestednodf with the
> option "order=FALSE", but I could not implement a null model based on this function (because the output contain multiple attributes).
>
> Any help welcomed
>
>
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-- 
Dr Lars Götzenberger
Institute of Botany
Czech Academy of Science
Dukelská 135
CZ-379 82 Třeboň
Czech Republic

email: lars at ut.ee
website: larsgoetzenberger.wordpress.com

I am currently funded by the plantfellows fellowship program. www.plantfellows.ch