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 > > ___________________________________________________________ > > Quiz TV : Vous êtes fan de la série "Friends" ? 5 questions ici > > http://tv.voila.fr/quiz/quiz-special-friends_14538959.html > > > > _______________________________________________ > > R-sig-ecology mailing list > > R-sig-ecology@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > ___________________________________________________________ Quiz TV : Vous êtes fan de la série "Friends" ? 5 questions ici http://tv.voila.fr/quiz/quiz-special-friends_14538959.html _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
