Maria,
*...Nevertheless you still do not know if your communities are significantly different between each other, within each host. Now it depends on the hypothesis you intend to test.*.. I think no sense for "Community" inside "Host"... Couse A and B are from the same host "Corylus", and C and D are from host "Ostrya". So the effect between two host tree species is real, but difference between two community inside the same host (A vs B i.g.) could not be. That is also confirmed by my diversity indices data I got (see my lastest post), they show that A and B are alwasy different from C and D, but between A and B (and for sure also between C and D ) there are no statistical differences (ANOVA). I think both "host" and "community" effect and if use them separately I got : > adonis(sqrtABCD ~ Host, method="bray", data=env.table, permutations=99) Call: adonis(formula = sqrtABCD ~ Host, data = env.table, permutations = 99, method = "bray") Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) Host 1.00000 1.64429 1.64429 5.38984 0.1242 0.01 ** Residuals 38.00000 11.59276 0.30507 0.8758 Total 39.00000 13.23705 1.0000 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 > adonis(sqrtABCD ~ Community, method="bray", data=env.table, permutations=99) Call: adonis(formula = sqrtABCD ~ Community, data = env.table, permutations = 99, method = "bray") Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) Community 3.00000 2.43264 0.81088 2.70182 0.1838 0.01 ** Residuals 36.00000 10.80441 0.30012 0.8162 Total 39.00000 13.23705 1.0000 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 > Thank you so much to all want to write any comments on that... Cheers, Gian -- Dr. Gian Maria Niccolò Benucci Department of Applied Biology - University of Perugia Borgo XX Giugno, 74 I-06121 - Perugia, ITALY Email: gian.benu...@gmail.com Tel: +39.075.5856433 2009/12/10 Maria Dulce Subida <mdsub...@icman.csic.es> Dear Gian, > > I'm still not quite sure about the functioning of adonis(). I made some > proofs and I don't understand how does it calculate the degrees of freedom > of a nested factor. But this is most probably due to my lack of experience > with this function (as I told you I usually work with the PERMANOVA add-in > for PRIMER developed by Marti Jane Anderson and others). > Anyway, in your table of results *I think* you miss the effect of the term > Community(Host) [which means: the factor community nested in the factor > host]. In the table you send me you can only see that there is a significant > effect of the term Host (which I think it means that the communities are > significantly different between hosts). Nevertheless you still do not know > if your communities are significantly different between each other, within > each host. Now it depends on the hypothesis you intend to test. It probably > does not make any sense to ask if communities differ within each host, but > *I think* you still have to include the term Community(Host) in your > table. Though, I would wait for the opinion of a more experienced user of > adonis() and ANOVA testing in general. > > HTH > > > Cheers, > > 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 0034 956832612 ext. 316 > > > > ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* > > > > > Gian Maria Niccolò Benucci escribió: > > Hi Maria, > > Yes, I think it's right, maybe now I did the correct function, It seems that > the "area" effect is also visible... > > > > adonis(ABCDsqrt ~ Host, method="bray", data=env.table, permutations=99, > > > strata=env.table$Community) > > Call: adonis(formula = ABCDsqrt ~ Host, data = env.table, permutations = 99, > method="bray", strata = env.table$Community) > > Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) > Host 1.00000 1.64429 1.64429 5.38984 0.1242 0.01 ** > Residuals 38.00000 11.59276 0.30507 0.8758 > Total 39.00000 13.23705 1.0000 > --- > Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 > > > don't you think? > > > Gian > > > > > 2009/12/9 Maria Dulce Subida <mdsub...@icman.csic.es> <mdsub...@icman.csic.es> > > Hi Gian, > > > I've never used adonis() [I'm a R beginner] but I've been doing > multivariate analysis for some time: I usually use PRIMER with the PERMANOVA > add-in. nMDS followed by PERMANOVA works quite well for me in experimental > designs similar to yours. But it seems to me that you have nestedness in > your design and this should be considered when you do adonis(). After a > quick look to the ?adonis? documentation, *I think* you should state > strata = env.table$Community in your adonis() function, since your > "community" factor is nested within the "host" factor. Otherwise you're > getting wrong pseudo-F values as well as wrong p-values. > Good luck! > > Cheers, > > Dulce > > > Maria Dulce Subida > > > > ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* > > > > Instituto de Ciencias Marinas de Andalucía (ICMAN) > > Consejo Superior de Investigaciones Científicas (CSIC) > > Campus Universitário Río San Pedro > > 11510 Puerto Real - Cádiz. España. > > > www.icman.csic.es 0034 956832612 ext. 316 > > > > ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* > > > > > Gian Maria Niccolò Benucci escribió: > > Jari, Gavin, Chris, Gabriel and Carsten... > > Many thank you all for your support and kindness... and for your competence > and experience that could not be ever comparized to mine at least in that > stuffs... > > Gabriel said: .*..I found this mailing list very helpful many times for my > own questions, but also very informative when just following the threads on > other questions... > * > I complitely agree about that, so here I am to go deeper inside my > statistical problems... > > As Gavin argued the plot: > > > > NMS.2$stress > > > [1] 24.53723 > > > NMS.3$stress > > > [1] 16.29226 > > > NMS.4$stress > > > [1] 11.79951 > > > plot(2:4, c(24.53723, 16.29226, 11.79951), type = "b") > > > didn't show significally differences... > > ...so as him suggested I did the stressplot() and got shepard graphs... > (just to specify, sqrtABCD is the square roots transforming of the species > matrix) > > > > stressplot(NMS.2) > > > Using step-across dissimilarities: > Too long or NA distances: 230 out of 780 (29.5%) > Stepping across 780 dissimilarities... > > > Non-metric fit, R2=0.94 > Linear fit, R2=0.719 > > > > stressplot(NMS.3) > > > Using step-across dissimilarities: > Too long or NA distances: 230 out of 780 (29.5%) > Stepping across 780 dissimilarities... > > > Non-metric fit, R2=0.973 > Linear fit, R2=0.815 > > > > stressplot(NMS.4) > > > Using step-across dissimilarities: > Too long or NA distances: 230 out of 780 (29.5%) > Stepping across 780 dissimilarities... > > Non-metric fit, R2=0.986 > Linear fit, R2=0.875 > > >From this data is clear that the fit is better for the NMS.4 (k=4) also the > blue points into the graph are more near to red line, less spare around the > graph space... > > But maybe the R2 values of the NMS.2 aren't so bad in correlation terms, are > they? > > In reason of what Gabriel said: *...I personally like a combination of NMDS > with the permutational MANOVA approach (by Marti Anderson) implemented in > the function adonis() in vegan. You can use the same dissimilarity measure > (Bray-Curtis) used for the NMDS and can test the "Area" vs. the "Host" > effect on parasite (was it?) composition. I think that could be a very > useful complement to an NMDS-derived ordination plot and then you may also > regard high-stress "representations" (and that´s what all the > low-dimensional ordination plots really ARE!) in a different light.*.. > > > > > adonis(sqrtABCD ~ Host*Community, method="bray", data=env.table, > > > permutations=99) > > Call: > adonis(formula = sqrtABCD ~ Host * Community, data = env.table, > permutations = 99, method = "bray") > > Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) > Host 1.00000 1.64429 1.64429 5.47874 0.1242 0.01 ** > Community 2.00000 0.78834 0.39417 1.31337 0.0596 0.23 > Residuals 36.00000 10.80441 0.30012 0.8162 > Total 39.00000 13.23705 1.0000 > --- > Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 > > > ...So, I would explain a little about my datasets: > > - the species matrix is done by roots samples in which were counted the > ectomycorrhizal fungal species present (cells entities are different tips > individuals); > - sample where taken into four "Area" (A,B,C,D). The ares are about 30 > meters far away one to each other; > - areas A and B are both form Corylus roots while areas C and D are both > from Ostrya roots. > > To be more clear that is the enviromental matix used: > > > > env.table > > > Community Host > A1 A Corylus > A2 A Corylus > A3 A Corylus > A4 A Corylus > A5 A Corylus > A6 A Corylus > A7 A Corylus > A8 A Corylus > A9 A Corylus > A10 A Corylus > B1 B Corylus > B2 B Corylus > B3 B Corylus > B4 B Corylus > B5 B Corylus > B6 B Corylus > B7 B Corylus > B8 B Corylus > B9 B Corylus > B10 B Corylus > C1 C Ostrya > C2 C Ostrya > C3 C Ostrya > C4 C Ostrya > C5 C Ostrya > C6 C Ostrya > C7 C Ostrya > C8 C Ostrya > C9 C Ostrya > C10 C Ostrya > D1 D Ostrya > D2 D Ostrya > D3 D Ostrya > D4 D Ostrya > D5 D Ostrya > D6 D Ostrya > D7 D Ostrya > D8 D Ostrya > D9 D Ostrya > D10 D Ostrya > > > ...maybe could be helpfull to say that I calculated diversity indices > (richness, shannon, simpson and evenness) for my 4 areas and I use ANOVA to > see if them are diffent one from each other. > The results show me that area A and B are always different form areas C and > D but no differences are between them, so clearly Corylus fungal community > is alwasy different from Ostrya one. > > ...So, I think that "Host" effect is clear while the effect of "Community" > couldn't be the same in reason to that areas are similar 2 by 2, ...is it > right? > > When I plot the MNS.2 and I watch to the Graph I clearly see that sample > points of A,B areas or Corylus are positioned on the left side while areas C > and D of Ostrya are more sparse and are positioned into the low right > side... > > So, what else to say... I'll leave you space for any comments :)))) > > Tank you all, > > Gian > > [[alternative HTML version deleted]] > > > > ------------------------------ > > _______________________________________________ > R-sig-ecology mailing list > r-sig-ecol...@r-project.orghttps://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > ------------------------------ > > _______________________________________________ > R-sig-ecology mailing > listr-sig-ecol...@r-project.orghttps://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > -- Dr. Gian Maria Niccolò Benucci Department of Applied Biology - University of Perugia Borgo XX Giugno, 74 I-06121 - Perugia, ITALY Email: gian.benu...@gmail.com Tel: +39.075.5856433 [[alternative HTML version deleted]]
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