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
PhD student
University of Worcester
Tel: 01905 542441
Mobile: 07811 384641
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