I would venture a guess that your data may not be of the correct form. Can
you show us the output of str() of your summary data.frame? As a side note,
it may be unwise to name your data objects after functions, especially like
a commonly used one as summary().


Cheers,
Roman



On Wed, Nov 24, 2010 at 11:53 PM, Pekin, Burak K <bpekin@purdue.edu> wrote:

> When I run adonis with the following code:  adonis (MamPA ~ Mam_tot,
> data=summary, method="bray", zerodist="add")
>
> I get the error message: Error in G * t(hat) : non-conformable arrays
>
> What does non-conformble arrays mean?
>
>
> -----Original Message-----
> From: Jari Oksanen [mailto:jari.oksanen@oulu.fi]
> Sent: Wednesday, November 24, 2010 5:43 PM
> To: Pekin, Burak K
> Cc: 'r-sig-ecology@r-project.org'
> Subject: Re: [R-sig-eco] relative compositional dissimilarity among sites
> against a continuous variable
>
> On 25/11/10 00:37 AM, "Pekin, Burak K" <bpekin@purdue.edu> wrote:
>
> > Thanks Jari, so in essence I would be doing something like a PERMANOVA.
>
> Burak,
>
> Very vaguely similar (some people would say "no, not at all"). If you want
> to do something like PERMANOVA and do it in R (instead of using Marti
> Anderson's PERMANOVA standalone software binaries in Windows), you can use
> adonis() of vegan  which does this like it should be done.
>
> Cheers, Jari Oksanen
> >
> > -----Original Message-----
> > From: Jari Oksanen [mailto:jari.oksanen@oulu.fi]
> > Sent: Wednesday, November 24, 2010 5:35 PM
> > To: Pekin, Burak K; 'Andy Rominger'
> > Cc: 'r-sig-ecology@r-project.org'
> > Subject: Re: [R-sig-eco] relative compositional dissimilarity among
> > sites against a continuous variable
> >
> > On 24/11/10 23:48 PM, "Pekin, Burak K" <bpekin@purdue.edu> wrote:
> >
> >> Thanks Andy, that's a simple enough calculation. So the larger the
> >> average dissimilarity, the more the site is dissimilar in its
> >> composition to other sites. I could then do a regression between the
> >> average dissimilarity of sites and other site factors and say
> >> something like 'compositional dissimilarity increases as factor X
> increases'.
> > Burak,
> >
> > If this is really what you need, remember that diagonal elements of
> > the dissimilarity matrix are zeros (dissimilarity between the object and
> itself).
> > This means that the row or column mean of the dissimilarity to
> > *other* sites is underestimated. You should either make the diagonal to
> NA:
> >
> > d <- as.matrix(vegdist(x))
> > diag(d) <- NA
> > rowMeans(d, na.rm = TRUE)
> >
> > or adjust the means for one zero element:
> >
> > d <- as.matrix(vegdist(x))
> > rowMeans(d)*(nrow(d)/(nrow(d)-1))
> >
> > This does not influence the ranks, but it doesn't hurt if your numbers
> > are correct.
> >
> >
> >>
> >> Is there a method that regresses the relative compositional
> >> dissimilarity among sites against a continuous variable?
> >>
> >
> > The mean dissimilarity is found for your observations, so it is of the
> > same length as your data vectors. You can use functions like lm(),
> > glm(), nls(),
> > gam() or some hundred other alternatives in packages to analyse the
> results.
> >
> > Cheers, Jari Oksanen
> >
> >> -Burak
> >>
> >> From: Andy Rominger [mailto:ajrominger@gmail.com]
> >> Sent: Tuesday, November 23, 2010 4:11 PM
> >> To: Steve_Friedman@nps.gov
> >> Cc: Pekin, Burak K; r-sig-ecology-bounces@r-project.org;
> >> r-sig-ecology@r-project.org
> >> Subject: Re: [R-sig-eco] Dissimilarity ranking
> >>
> >> or perhaps could you use something as simple as the mean
> >> dissimilarity?  i'm thinking something like this:
> >>
> >> library(vegan)
> >>
> >> ##    some data to play with, 20 sites by 30 spp
> >> data(dune)
> >>
> >> ##    calculate distance, making it a matrix
> >> dune.dist <- as.matrix(vegdist(dune,method=
> >> "bray"))
> >>
> >> ##    take average distance
> >> dune.avg <- apply(dune.dist,1,mean)
> >> dune.avg
> >>
> >> not sure what the gurus of dissimilarity analysis might think of this.
> >> good luck,
> >> andy
> >>
> >> On Tue, Nov 23, 2010 at 5:43 PM,
> >> <Steve_Friedman@nps.gov<mailto:Steve_Friedman@nps.gov>> wrote:
> >> Burak
> >>
> >> You should explore the use of non-metric multidimensional scaling.
> >>
> >> ?cmdscale
> >>
> >> Steve Friedman Ph. D.
> >> Ecologist  / Spatial Statistical Analyst Everglades and Dry Tortugas
> >> National Park
> >> 950 N Krome Ave (3rd Floor)
> >> Homestead, Florida 33034
> >>
> >> Steve_Friedman@nps.gov<mailto:Steve_Friedman@nps.gov>
> >> Office (305) 224 - 4282
> >> Fax     (305) 224 - 4147
> >>
> >>
> >>
> >>             "Pekin, Burak K"
> >>             <bpekin@purdue.ed
> >>             u>
> To
> >>             Sent by:
> >> "'r-sig-ecology@r-project.org<mailto:r-sig-ecology@r-project.org>'"
> >>             r-sig-ecology-bou
> >> <r-sig-ecology@r-project.org<mailto:r-sig-ecology@r-project.org>>
> >>             nces@r-project.or<mailto:nces@r-project.or>
> >> cc
> >>             g
> >>
> Subject
> >>                                       [R-sig-eco] Dissimilarity ranking
> >>             11/23/2010 03:09
> >>             PM
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Hello, I want to rank the dissimilarity of sites based on their
> >> species composition. For example, I would like to be able to say that
> >> site A is less similar in composition to the other sites than site B
> >> is similar to the other sites. I could do a cluster analysis and look
> >> at which sites are less closely clustered.
> >>
> >> It would be even better if I could come up with a quantitative scale
> >> rather than a relative ranking that would give a value for each site
> >> based on its relative dissimilarity to the rest of the sites. So site
> >> A might receive a
> >> 90 out of 100, whereas site B and C might receive a 60 and a 50
> >> indicating the rank as well as 'relative quantity' of dissimilarity
> >> for each site.
> >>
> >> Thanks,
> >> Burak
> >>
> >> --------------------------
> >>
> >> Burak K. Pekin, PhD
> >> Postdoctoral Research Associate
> >> Purdue University
> >>
> >>
> >>             [[alternative HTML version deleted]]
> >>
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> >>
> >> _______________________________________________
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> >> R-sig-ecology@r-project.org<mailto:R-sig-ecology@r-project.org>
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> >>
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
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> >> R-sig-ecology@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >
>
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-- 
In God we trust, all others bring data.

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