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 *----- Do not print this email unless you really need to. Save paper and protect the environment! -----* On 8 February 2012 16:46, Ivailo <[email protected]> wrote: > On Wed, Feb 8, 2012 at 4:10 PM, Caroline Wallis <[email protected]> > 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. > > _______________________________________________ > R-sig-ecology mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > [[alternative HTML version deleted]]
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