[R-sig-eco] wascores() for metaMDS?

to compute species scores using the function wascores() I have now pondered for 2 days how these scores are calculated and what their precise meaning would be. Would these species scores be appropriate to show as vectors in the MDS? Thanks for any answer... Gabriel Singer

Re: [R-sig-eco] wascores() for metaMDS?

Dear Jari and Gavin, thanks a lot, everything clear... with the connection to CCA I now get the meaning of the species scores, almost trivial after all... gg Gavin Simpson wrote: On Wed, 2009-08-19 at 11:40 +0200, gabriel singer wrote: Hi sig-ecology! Here comes a probably stupid

Re: [R-sig-eco] vegan: envfit (vectorfit)

, 2009-09-15 at 17:02 +0200, gabriel singer wrote: Hi vegan-users and programmers, Can anybody tell me how the function vectorfit (envfit) computes arrow lengths (as fits of a metric variable onto an ordination) exactly? I understand the scaling bit in the end, but have troubles to understand how

Re: [R-sig-eco] how to calculate axis variance in metaMDS, pakage vegan?

hi gian, no, there is no such way. A MDS can´t express explained variance. However, the stress value is the overall measure of quality of fit of your MDS to the data. There are various measures of stress, but loosely speaking you can regard the stress as a percentage of variation NOT

[R-sig-eco] capscale() for PCoA-CDA

Hi everybody, Anybody has used capscale() in package vegan to compute a PCoA-CDA as suggested by Anderson and Willis 2003 (Ecology 84: 511 ff) using one or more factors as predictors? Then I wonder about: *) How to interpret interactions of factors? Why are interactions (specified as

Re: [R-sig-eco] Fwd: how to calculate axis variance in metaMDS, pakage vegan?

-- Dr. Gabriel Singer Department of Freshwater Ecology - University of Vienna and Wassercluster Lunz Biologische Station GmbH +43-(0)664-1266747 gabriel.sin...@univie.ac.at Gian Maria Niccolò Benucci wrote: Hi Gavin and Hi all, I will not go in front of a bus for sure, I not mad, at least I am

Re: [R-sig-eco] Fwd: Fwd: how to calculate axis variance in metaMDS, pakage vegan?

A difference between two communities within a host could still exist and could make perfect sense, too, when you regard community as a random factor. Then community may introduce some extra variation (compared to the within-community variation), experimentally seen interesting and important,

Re: [R-sig-eco] adonis question

Hi Jaime, The interactions are just a matter of defining the formula as such, e.g. adonis(dist~factor1*factor2). I suppose, a multiple comparison (with the reasoning of a post-hoc test) can just be done using adonis() for pairwise comparisons and then use p.adjust(). Cheers, gabriel On

Re: [R-sig-eco] NMS axis variance and legend

dear alida, legend() should help to get the legends, just ask for help(legend), it´s pretty easy. then for the variance explained: with an NMS the only measure of fit you get is the stress value, there isn´t anything like a percentage of explained variance. you may want to regard the stress

Re: [R-sig-eco] is 1 hour long enough to assume independance?

-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Dr. Gabriel Singer Department of Limnology - University

[R-sig-eco] cluster defined by environment followed by mrpp

Hi list, Conducting sort of an opinion poll among list members. Start with two matrices, one environmental, one species, same sites. I wondered what people think of defining groups by a cluster analysis based on the environmental variables (say, hclust or similar). Then testing for a

Re: [R-sig-eco] Change in rotated NMDS scores as a response variable

___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Dr. Gabriel Singer Department of Limnology - University of Vienna and Wassercluster Lunz Biologische Station GmbH +43-(0)664-1266747 gabriel.sin...@univie.ac.at

Re: [R-sig-eco] interpreting adonis results

list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Dr. Gabriel Singer Department of Limnology - University of Vienna and Wassercluster Lunz Biologische Station GmbH +43-(0)664-1266747 gabriel.sin...@univie.ac.at ___ R

Re: [R-sig-eco] post hoc in Kruskal Wallis

list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Dr. Gabriel Singer Department of Limnology - University of Vienna and Wassercluster Lunz Biologische Station GmbH +43-(0)664-1266747 gabriel.sin...@univie.ac.at ___ R

Re: [R-sig-eco] 'grouping' grouping variable

hi jakub, I would suggest starting with standardizing your environmental variables with scale(), then compute Euclidean distances with e.g. vegdist() in {vegan} and run a cluster analysis on the distance matrix with hclust(). Choose a cutoff for minimum dissimilarity and group your sites