Dear Caroline,

I agree with Ivailo, maybe the problem is the data format, you should
provide a community data format or at least manage data in that format
(columns are variables and rows are samples).

About the Errrors: rowSums (x, na.rm=TRUE)

I am not sure but I think you're producing some NA values maybe becuse you
have unequal sample sizes among different SFT. That's is only and hypotheis
I am not sure about that, an please anyone to correct me!

Have a good day,

Gian



-- 
Gian Maria Niccolò Benucci, Ph.D.
Department of Applied Biology
University of Perugia


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On 8 February 2012 16:46, Ivailo <ubuntero.9161@gmail.com> wrote:

> On Wed, Feb 8, 2012 at 4:10 PM, Caroline Wallis <c.wallis@worc.ac.uk>
> wrote:
> > I am trying to use the 'adonis' function in the 'vegan' package to
> assess differences in water depth and water velocity between areas of a
> river channel categorised by surface flow type (6 types in total, unequal
> sample sizes).
> >
> > Sample Data (LB):
> >
> > SFT     Depth   Vel
> > BSW     0.18    1.2
> > BSW     0.16    1.03
> > BSW     0.16    0.98
> > BSW     0.22    0.53
> > BSW     0.11    0.668
> > BSW     0.14    0.432
> > BSW     0.12    0.391
> > BSW     0.16    0.647
> > BSW     0.2     0.903
> > BSW     0.3     0.594
> > BSW     0.37    0.429
> > ....
> >
> > The dependent data was used in data frame format, rather than a
> dissimilarity matrix.
> >
> > Using the call
> 'adonis(formula=SFT~Depth*Vel,data=LB,permutations=999,method="canberra",strata=NULL)'
> I get the following error:
> >
> > Error in rowSums (x, na.rm=TRUE)
> > 'x' must be an array of at least two dimensions
> >
> > I examined the adonis code to find 'x'. It first appears at the
> permutation stage:
> >
> > if (missing(strata))
> >        strata <- NULL
> >    p <- sapply(1:permutations, function(x) permuted.index(n,
> >        strata = strata))
> >    tH.s <- lapply(H.s, t)
> >    tIH.snterm <- t(I - H.snterm)
> >    f.perms <- sapply(1:nterms, function(i) {
> >        sapply(1:permutations, function(j) {
> >            f.test(tH.s[[i]], G[p[, j], p[, j]], df.Exp[i], df.Res,
> >                tIH.snterm)
> >
> > However I'm no closer to understanding what 'x' is or how to correct the
> error. If anyone could offer any advice or help I'd be very grateful.
> >
> > I also tried transposing the data but this generated a different error!
> >
> > Regards,
> >
> > Caroline Wallis
>
> Dear Caroline,
>
> you need to provide a community table (i.e. species x samples data
> frame) to adonis, but you have provided a single categorical variable.
> Therefore I am not sure if the adonis() function would be appropriate
> for the analysis you're trying to perform.
>
> Cheers,
> Ivailo
> --
> UBUNTU: a person is a person through other persons.
>
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