Dear Caroline, It seems that you response (community-like) data are Depth and Velocity. Than a dataframe with these two variables should be on the left hand side of the formula, while SFT on the right hand side. Something like adonis(LB[,2:3] ~ SFT, data=LB, method="canberra") should work. Cheers, Vit
> 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 Niccol? 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]] > > _______________________________________________ > R-sig-ecology mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > _______________________________________________ R-sig-ecology mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
