adonis and distance metrics
Hi Wout, This is always tricky. There are so many different metrics out there that it can be really confusing to choose the "right one". Legendre and Legendre 1998 Numerical Ecology go at great length at describing many of them so that's a good place to start. The danger is that, not having any idea which one to choose a priori, it can become tempting to try them all and see which one gives you the results that you're the most happy with (a "fishing" expedition). Because, as you seem to have noticed, the metric can make a lot of difference. Personally, what I would recommend, and what I've done in the last papers where I've used such analyses, is to try a 3 different metrics that differ in their emphasis on pure shifts in composition (presence /absence) relative to shifts in abundance. This is because I've been heavily influenced by Anderson et al 2006 Ecology Letters (a recommended read), who make a compelling argument that one must be cautious at how a much a particular metric emphasizes shifts in composition (presence/absence) vs abundance. They propose a measure which is easy to interpret, which (confusingly enough) they call the modified-Gower distance. What I think is neat about it is that it is very clear what it does: with base 2, a doubling in abundance has the same weight as a shift from 0 to 1 (i.e. from absent to present). With base 10, then you need abundance to be 10x greater for it to be equal to a 0->1 shift, etc. The measure is available in vegdist: data(varespec) vare.dist <- vegdist(decostand(varespec, "log"), "altGower") # by default, base 2 vare.dist <- vegdist(decostand(varespec, "log", logbase = 10), "altGower") # base 10 But that's just me, and I'm sure others will have different opinions on the subject. For example, it's always easier to justify the very widely-used ones (e.g. Bray-Curtis) in a paper because every reviewer is familiar with them... Cheers Etienne Le vendredi 30 juillet 2010 ? 12:39 +0200, Opdekamp Wout a ?crit :
Dear R-sig users, In a full-factorial mesocosm experiment (80 mesocosms: three factors with two levels each and hence 10 replicates per treatment combination) we measured the aboveground biomass of 28 plant species that were sown in this experiment. Results are given as abundances (kg/m) in a (80 treatment-rows x 28 species-colums) dataframe. Apart from that PhospoLipicFattyAcids have also been analysed in the soil to characterise the microbial community. Results are given as peak heights in a (80 treatment-rows x 33 plfa-colums) dataframe, standardised per row. I used Adonis to analyse if and how the applied factors influence these floral and microbial communities. However, I am struggling a bit with the distance metric to use as the obtained results are somewhat differed on the metric applied. Any recommendations on which one to use or where I could find a comparison of the different metrics from an ecological point of view? Kind regards, Wout Wout Opdekamp, PhD student Ecosystem Management Research Group University of Antwerp, Belgium www.ua.ac.be/ecobe <BLOCKED::BLOCKED::BLOCKED::http://www.ua.ac.be/ecobe> P Please consider your environmental responsibility before printing this e-mail [[alternative HTML version deleted]]
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Etienne Lalibert? ================================ School of Forestry University of Canterbury Private Bag 4800 Christchurch 8140, New Zealand Phone: +64 3 366 7001 ext. 8365 Fax: +64 3 364 2124 www.elaliberte.info