Vegan has PCoA in the capscale() function. If your community data are in data frame 'foo' then

ord <- capscale(foo ~ 1)

should take care of things. See the help page for details of extra arguments. Internally cmdscale() is used directly or indirectly depending on arguments used, but the resulting object works with all the rest of vegan's ordination functions.

G

Sent from my HTC

----- Reply message -----
From: "Alan Haynes" <aghaynes@gmail.com>
Date: Fri, Jun 22, 2012 08:38
Subject: [R-sig-eco] pooled versus averaged samples in diversityresult function
To: "Gian Maria Niccolò Benucci" <gian.benucci@gmail.com>
Cc: "r-sig-ecology@r-project.org" <r-sig-ecology@r-project.org>

Hi Gian,

when you do your stats you'll see that there isnt a significant difference
between the two types (very basic stats below). The assumptions dont look
bad either.
Perhaps the natural samples have a different community structure, based on
different species to the cultivated communities. Or some species are
"adapted" to cultivated conditions and dont survive in the natural systems.
A multivariate approach would probably be useful to you. PCA, PCoA, NMDS,
DCA, pick your favourite. Vegan has methods for all of them (except PCoA I
think, but thats available from ape or function cmdscale in the basic stats
package).

HTH

Alan




Sn <-c(5,2,3,3,5,4,4,4,2,2,5,2)
Sc <-c(5,3,5,3,3,2,4,3,5,3,3,5)

plot(Sn~SC)

S <- c(Sn, Sc)
trt <- factor(rep(c("n", "c"), each=12))

plot(trt, S)
aggregate(S, list(trt= trt), mean)
#   trt        x
# 1   c 3.666667
# 2   n 3.416667

anova(aov(S ~ trt))
# Response: S
# Df Sum Sq Mean Sq F value Pr(>F)
# trt        1  0.375  0.3750  0.2789 0.6027
# Residuals 22 29.583  1.3447

--------------------------------------------------
Email: aghaynes@gmail.com
Mobile: +41794385586
Skype: aghaynes


On 21 June 2012 22:34, Gian Maria Niccolò Benucci <gian.benucci@gmail.com>wrote:

> Hi Alan,
>
> You perfectly understand my question. I was indeed thinking to comment that
> pooled data gave an indication about the general diversity occurred in
> cultivated and natural communities, as you argued is like an *average
> diversity* because the function sums the data and then calculate the
> diversity, higher in natural site. This is in accordance with the richness,
> that is higher in the natural site (23) as could be normal to hypothesize.
> The *average* *diversity* is so higher in the natural community. But, if we
> look to the diversity *over all sites*, the cultivated sites are more
> diverse. And that is correct, because if we look to different replicates
> (see below the table) there are really have much more samples with more
> species in the cultivated community than in natural one. I detect more
> species in cultivated site if taken singularly, maybe the same species
> occurred more times, and make the average of the diversity higher. I surely
> will calculate standard deviation for those mean values.
> What do you think?
> Cheers,
>
> --
> Gian
>
>
>  natural cultivated  5 5  2 3  3 5  3 3  5 3  4 2  4 4  4 3  2 5  2 3  5 3
> 2 5  3.416667 3.666667
>
>
> On 21 June 2012 13:37, Alan Haynes <aghaynes@gmail.com> wrote:
>
> > Hi Gian,
> >
> > It depends what you want to look at.
> > My understanding of the pooled data is that it takes all replicates of
> > your cultivated samples and treats them as one big sample (same with the
> > natural samples). It tells you that *over all sites* cultivated sites are
> > more diverse, but the average site diversity is actually higher in
> natural
> > sites.
> > I think the mean is probably what you want.
> >
> > From a statistics point of view...you cant really compare the pooled data
> > - you only have 2 numbers, but you can compare the average diversity as
> you
> > have a diversity value per replicate...assuming you intend to carry out
> > further stats of course.
> >
> > HTH
> > Alan
> >
> > --------------------------------------------------
> > Email: aghaynes@gmail.com
> > Mobile: +41794385586
> > Skype: aghaynes
> >
> >
> > On 21 June 2012 10:44, Gian Maria Niccolò Benucci <
> gian.benucci@gmail.com>wrote:
> >
> >> Hallo ecologists,
> >>
> >> I know that this is not the right place where to post my help-request
> so I
> >> say sorry in advance. My question concern results of biodiversity
> indices
> >> with diversityresult() tha I used to describe the diversity of two
> >> different, comparable fungal communities.
> >> This is what I got:
> >>
> >>
> >> Averaged samples Pooled samples
> >> Cultivated Natural Cultivated Natural  ricnhess (S) 3.67
> >> 3.42
> >> 16 23  Simpson index (D) 0.58
> >> 0.49
> >> 0.83 0.91
> >>
> >> When I use pooled sample I obtain that the natural site is richer than
> the
> >> cultivated site wheraes when I try to do the average of the diversity
> >> results I have the opposite situation.
> >>
> >> My question is, which is the most correct approach to have a real
> picture
> >> of the diversiy and point the real differences between the two
> >> communities?
> >>
> >> Thanks a lot in advance,
> >>
> >> --
> >> Gian
> >>
> >>        [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> R-sig-ecology mailing list
> >> R-sig-ecology@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >>
> >
> >
>
>         [[alternative HTML version deleted]]
>
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
>

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