using Adonis for zero data
On Mon, 2010-06-21 at 15:45 +0100, Emma Stone wrote:
Dear All, I am running a multivariate ANOVA based on dissimilarities using the adonis function in the VEGAN package in R. I have trying to assess the number and types of bat mitigation used at sites as a function of three predictors. The predictors are : number of bats (nobats= continuous), impact (factor with 3 categories) and roost type(rtype = factor with 5 categories). There are three responses which are count data: number of boxes, number of barns and number of lofts. The problem is that I have a lot of zeros in the data and they are not all integers. I have been running the following code using euclidean distances but I am not sure that it is ok to use Euclidean distances for count data with zeros.
Are you interested in the magnitude - should abundant species dominate the dissimilarity? - differences? Euclidean could be OK if you were magnitude focussed but there are often better dissimilarities for ecological data where absolute difference rather than squared differences are used.
adonis(resp~Impact+nobats+rtype,data=pred,method=euclidean,permutation=500)
Is that exactly how you ran this in R? If so it is incorrect; argument 'method' is supposed to be passed a character which is the name of the dissimilarity coefficient you want to use, one provided by vegdist(). See ?vegdist for the available options.
I have read that you can transform the distances with the following code dis <- vegdist(decostand(resp, "norm"), "euclid")
I doubt it, if you are interested in normalising the species as MARGIN = 1 be default for that method and that refers to rows. But it depends on what you hope to achieve by transforming the sites/samples. If you want the species to all have the same mean and variance, then dis <- vegdist(scale(resp), "euclidean") should do it but then the analysis will be focussed on the relative abundance to some extent.
so have done this and I do get a very difference result, but again I am not sure that this is suitable. I have tried running the model with different distance measures but it will only run with the euclidean distance method.
Given that the default for 'method' is "bray" and vegan passes R CMD check on a large number of systems, that comment is patently *not* true.
Any help would be most appreciated.
If this doesn't sort your problem out, can you past back exactly the commands you used and the output from R so we can diagnose what is going on? HTH G
Thanks Emma ---------------------- Emma Stone Postgraduate Researcher Bat Ecology and Bioacoustics Lab & Mammal Research Unit School of Biological Sciences, University of Bristol, Woodland Road, Bristol, BS8 1UG Email: emma.stone at bristol.ac.uk
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