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

2013-09-25 Thread v_coudrain
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

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

2013-09-25 Thread Jari Oksanen
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 (prese

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

2013-09-25 Thread v_coudrain
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 an

Re: [R-sig-eco] null model for testing nestedness (v_coudr...@voila.fr)

2013-09-25 Thread 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 detai