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-requ...@r-project.org wrote:
Message: 3
Date: Tue, 24 Sep 2013 20:07:58 +0200 (CEST)
From:v_coudr...@voila.fr
To:r-sig-ecology@r-project.org
Subject: [R-sig-eco] null model for testing nestedness
Message-ID: <1121167144.286531380046078873.JavaMail.www@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: l...@ut.ee
website: larsgoetzenberger.wordpress.com
I am currently funded by the plantfellows fellowship program.
www.plantfellows.ch
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