Angelique, Many thanks for explanations and for the link, I will try the software for sure. I have on year more untill my PhD end, maybe I will disturb you for more helps... I am also planning to come to Germany for the final foreign period of my PhD! How small is the world? :) Cheers,
Gian 2010/6/9 Angelique Gobet <[email protected]> > Hi Gian, > > I'm happy if I could help you a bit :) Multivariate analyses are not easy > (it's been almost 4 years I work with it and I am still learning...), so you > are completely right to ask for help and the R-sig-ecology mailing list is a > great source of help. About having a workshop on community ecology > statistics, I think it is a really good idea but unfortunately I do not have > that much time right now to be involved in such a thing...I am currently > finishing my PhD and I think I will be quite busy until this Autumn. > However, I would be glad to try to help if you have any other questions on > community ecology statistics :) > By the way, in case you don't know it, there is a cool website where you > can download an easy software (with the according documentation) to do > quickly some multivariate analyses (this is what I use to propose to people > just starting with statistics and I still use it when I need a quick > overview on my analyses): http://folk.uio.no/ohammer/past/ > > > Cheers > Angélique > > Gian Maria Niccolò Benucci wrote: > >> Hi Angélique, >> >> Many many thanks about your help, I will read the paper carefully. It's >> always a pleasure to find matherial where to study above all for me that I >> am at least the only one in my faculty that study fungal community ecology. >> I am doing the best I can with my own skills and with a big passione for >> that job. >> >> The overlapping is sure indeed, the two communities are form the same >> site, but they come from 2 different host species. It's interesting for me >> to elucidate the effect of host in structuring the community, and that's >> seems to be true in reason of that some species I found, live only >> associated with one host tree only. As you argued some other species are >> shared, and indeed the communities have some species in common. >> I would try to do again the ANOSIM test, maybe with differend >> standardizaion of the dataset and also with the rough data matrix. >> >> Thanks :) >> >> PS. For Rookies like me, would be interesting to have a workshop on >> community ecology statistics, or a work group for talking and exchanging >> experiences, opinions and skills. don't you think? >> >> >> G. >> >> >> >> >> >> 2010/6/9 Angelique Gobet <[email protected] <mailto: >> [email protected]>> >> >> >> Hi Gian, >> >> I just read the thread about the ANOSIM test and I would like to >> give you a bit more insights about the interpretation of the R >> value. You probably have read it already but the ANOSIM tests for >> the significance of difference between two or more groups of >> samples, based on a dissimilarity matrix. The ANOSIM compares >> distances among groups with distances between groups. An /R/ value >> > 0.75 indicates clearly different groups, an /R/ value > 0.5 >> indicates separated groups but with some overlapping between the >> groups while an /R/ value < 0.25 indicates almost no differences >> between the groups. The significance of the ANOSIM can then be >> computed with permutation tests (as you did). In your case, I >> would say that the two fungal mycorrhizal communities are >> different but with some overlapping. >> >> Also, I would also use the same approach as you did: first and >> NMDS followed by an ANOSIM. As you said, in an NMDS, you can only >> compare the groups (here, the two fungal mycorrhizal communities) >> on a 2 dimension plot and an ANOSIM test would give you more >> information about the relationships between the two fungal >> mycorrhizal communities. >> >> I attached some papers that might also help. The Ramette paper is >> a clear review of multivariate analyses. For more details, you can >> still have a look at the Legendre and Legendre (1998) book. >> >> Hope this helps :) >> Cheers >> Angélique >> >> >> >> >> >> Gian Maria Niccolò Benucci wrote: >> >> Hi Dulce, >> >> Unfortunately isn't possible to post graphs here, anyway I >> have a nMDS >> graphs where you can see the spread of community data. For one >> community >> samples are more close one to each other, while for the second >> communty >> samples look more scattered but no one fills in the area of >> the first one. >> The stress is ok for 2 dimensions, it is 24 if I do not >> remember bad. I just >> talked about it in another post, and I was suggested to look >> to graph more >> than to the stress value. >> Anyway, I looked for ANOSIM test just to include it as a >> support for my >> data. I think that could work for that aim, don't you think? >> Thanks a lot! >> >> G. >> >> >> >> >> 2010/6/9 Maria Dulce Subida <[email protected] >> <mailto:[email protected]>> >> >> >> >> Hi Gian, >> >> In an ANOSIM the value of the R statistic is at least as >> important as its >> statistical significance. So you must always look at both. >> Besides, if you >> have a lot of replicates you increase the chance of a >> small value of R being >> significantly different from zero. >> I would say that 0.15 is a rather small value for R but >> one must always >> look at the data. In your particular case, with an R = >> 0.27, I would take a >> look to the nMDS of the data (using the same similarity >> measure as for >> ANOSIM, of course!). If it has a low stress, it gives a >> reliable picture of >> the positioning of your samples and if your samples are >> definitely grouped, >> you should also be able to see it in the nMDS. More >> important than any >> significance level is what you think your data is telling you! >> >> Kind regards, >> >> Dulce >> >> Maria Dulce Subida >> >> >> >> ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* >> >> >> >> Instituto de Ciencias Marinas de Andalucía (ICMAN) >> >> Consejo Superior de Investigaciones Científicas (CSIC) >> >> Campus Universitário Río San Pedro >> >> 11510 Puerto Real - Cádiz. España. >> >> >> >> www.icman.csic.es <http://www.icman.csic.es> >> 0034 956832612 ext. 316 >> >> >> >> >> ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* >> >> >> >> >> Gian Maria Niccolò Benucci escribió: >> >> Barbara, >> >> Thank you very much, indeed I red the two values on a >> paper, that were of >> R=0.15 and P=0.006, and they states that the difference >> between the two >> groups is significant with them. So, my values, that are >> aloso higher, are >> better for sure to support the difference between my two >> community. Don't >> you agree? >> Thank you really much for all, >> >> G. >> >> >> >> >> 2010/6/8 <[email protected] >> <mailto:[email protected]>> >> <[email protected] <mailto:[email protected]>> >> >> >> >> Hi Gian, >> I'm not sure if anyone else has answered your question yet. >> But basically: the R statistic is a measure of the >> strength of the >> difference between your 2 groups. It considers the >> variance both within, >> and between, your groups. It can be from 0-1, with 1 the >> strongest >> difference. >> The significance value tests the significance of the >> difference, like >> any other p-value. The statistics you derived from your >> ANOSIM analysis >> are somewhat analogous to an F-statistic, and a p-value, for a >> univariate ANOVA test. >> When including the results in a paper or dissertation, it >> would be >> normal to quote both values (R and significance). >> I hope that's helpful, >> >> Barbara >> >> >> >> ----- Original Message ----- >> From: Gian Maria Niccolò Benucci <[email protected] >> <mailto:[email protected]>> <[email protected] >> <mailto:[email protected]>> >> Date: Tuesday, June 8, 2010 4:57 am >> Subject: [R-sig-eco] ANOSIM test >> >> >> >> Hi everybody, >> >> I am tring to get some statistical evidence of differences >> between >> my two >> fungal mycorrhizal communities (samples from two different >> Host >> species)with ANOSIM test, that's my code: >> >> >> >> dist.ABCD <- vegdist(sqrt.ABCD.1) >> attach(env.table1) >> ABCD.ano <- anosim(dist.ABCD, Host) >> summary(ABCD.ano) >> >> >> Call: >> anosim(dat = dist.ABCD, grouping = Host) >> Dissimilarity: bray >> >> ANOSIM statistic R: 0.272 >> Significance: 0.001 >> >> Based on 999 permutations >> >> Empirical upper confidence limits of R: >> 90% 95% 97.5% 99% >> 0.0407 0.0554 0.0724 0.0952 >> >> As I read in a paper, also an R value of 0.27 could be >> considered >> significant. So similar samples are inside the communities >> and not >> outsidethem, is it roght? >> Thank you for you time and patience, >> >> >> Gian >> >> >> >> -- >> Gian Maria Niccolò Benucci >> Ph.D. Candidate >> Department of Applied Biology - University of Perugia >> Borgo XX Giugno, 74 >> I-06121 - Perugia, ITALY >> Tel: +39.0755856433 >> Fax: +39.0755856069 >> Email: [email protected] <mailto:[email protected]> >> >> >> >> ----- Do not print this e-mail If you do not need it. 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