[R-sig-eco] null model for testing nestedness

[v_coudrain at voila.fr]

Dear Jari,

Thank you very much for this clear answer. I did not get that quasiswap only concerned binary data. After reading your explanations, I think I'll stay to binary 
data and avoid the issue of weighted ones, which are much less straightforward to interpret. Anyway, I will have a look at the development versions.

Best wishes,
Valérie


> Message du 25/09/13 à 15h45
> De : "Jari Oksanen" 
> A : "" 
> Copie à : "" 
> Objet : Re: [R-sig-eco] null model for testing nestedness
> 
> Valerie,
> 
> There are at least two problems here: the way you call oecosimu() and how nestdnodf(..., weighted =TRUE) works with binary data. 
> 
> If you specify a *binary* null model as method, then you will get binary data. Even if you supplied quantitative data, they are transformed into 1/0 
(presence/absence) data. You specified method = "quasiswap", and that is binary model. Another problem is that nestednodf(..., weighted = TRUE) seems to 
evaluate the statistics all as zeros if you request weighted (= quantitative data) analysis of non-quantitative data (binary). It cannot perform weighted analysis if 
there are no weights, but still I think it should return something else than zeros. We'll have a look at that issue. 
> 
> You should specify a non-binary null model if you want to have a non-binary (weighted) analysis. Quantitative null models are problematic, and vegan release 
version does not have much choice here. I think "r2dtable" may be the only one. Development version of vegan in http://www.r-forge.r-project.org/ has a wider 
gamme of non-binary null models, but I think you need to be brave to use quantitative null models. They are something for people who are not afraid of going to 
areas where angels fear to tread.
> 
> FWIW, weighted nestednodf seems to work in oecosimu if you ask for a quantitative nullmodel ("r2dtable" in my tests) both with the release version (2.0-8 or 
2.0-9) and with the development version (2.1-35 or 2.1-36). But you really need to to specify a quantitative null model. Both null models and oecosimu are 
completely re-written and re-designed in development versions.
> 
> Cheers, Jari Oksanen
> 
> On 25/09/2013, at 15:56 PM, 
> wrote:
> 
> > Thank you very much. Yes it is working with oecosimu, exept that it does not seem to work for weighted data. There is the possibility to specify "weighted = 
TRUE": 
> > 
> > oecosimu(matrix,nestednodf, method = "quasiswap", nsimul = 999, order = FALSE, weighted =TRUE)
> > 
> > However, I get only null values and p=1. For weighted = F, I get good values.
> > 
> > Best wishes
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