species scores for ordination in vegan
On Sun, 2013-02-24 at 11:22 +0400, Stas Malavin wrote:
Dear list readers, Please forgive me for asking trivial questions, but I've failed to find the exact answer by myself. I'm interested in how the species scores are calculated for ordination configuration in vegan package. It's written they are weighted averages (of sites scores?): vegan/html/metaMDS.html, vegan/html/wascores.html. My questions are: (1) Are all sites used for calculation of the average, or just those where the species presents?
As the weight for an absent species is 0 the contributions of those absent species at any given site are zero. So in one sense, they are not used, but the computations themselves certainly use them; their effect is just zero. Which way you want to think of this depends on what you mean by "calculated".
(2) What's used as weights: site totals, or the abundances of particular species which score is calculated?
The species abundances. The fitted species score for species i is the weighted average of the site scores for all sites k with weights given by the abundance of species i on those sites k. HTH G
Thank you in advance, Stas -------------------------------------------- Junior Res Asst Hydrobiology Lab Institute of Limnology Russian Academy of Sciences Sevastyanova 9 196105 Russia, St Petersburg http://www.limno.org.ru Phone: +7 (812) 387-80-60 Fax: +7 (812) 388-73-27 [[alternative HTML version deleted]]
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