Hi, Yes, I know there are issues about using residuals as response variable, and contrasting opinions about that.
However, what I attempt to do is to perform an indicator species analysis (ISA) with these residuals. I want to see if I can find species which are indicators for different environmental conditions, but first I would like to remove the differences in species composition due to the study region (which accounts in fact for a big part of the differences in species composition). I am using the packages indicspecies and labdsv for ISA but in none of the cases did I found a way of including this as, for example, a block variable, that's what I attempt to get the residuals. Cheers, Alicia -- Alicia Valdés Université de Picardie Jules Verne Unité EDYSAN (Ecologie et Dynamique des Systèmes Anthropisés) 1, rue des Louvels F-80037 Amiens Cedex France tel:+33 322825775 alicia.val...@u-picardie.fr http://www.u-picardie.fr/edysan/ 2014-03-18 15:43 GMT+01:00 Cade, Brian <ca...@usgs.gov>: > You ought to be very careful about using residuals from one analysis as > the response variable in another analysis as the inferences about the > second analysis will almost certainly be flawed. Best to try and do this > another way if at all possible. > > Brian > > Brian S. Cade, PhD > > U. S. Geological Survey > Fort Collins Science Center > 2150 Centre Ave., Bldg. C > Fort Collins, CO 80526-8818 > > email: ca...@usgs.gov <brian_c...@usgs.gov> > tel: 970 226-9326 > > > > On Tue, Mar 18, 2014 at 5:53 AM, Alicia Valdés <aliciavaldes1...@gmail.com > > wrote: > >> Hi, >> >> I am using the adonis function in the vegan package to determine effects >> of >> different environmental factors in forest plant community composition in >> different regions. I would like to first use adonis to remove the region >> effect, this is, to fit a model like >> >> adonis_region<- adonis(community ~ region,permutations=999,method="bray") >> >> Where community is a presence/absence data matrix of species in forest >> patches belonging to different regions. >> >> Then I would like to use the residuals of this model as the response >> variable for some other analyses. I know I could use strata to model >> region >> as a block variable, but this does not interest me, as afterwards I want >> to >> perform another kind of analysis where I would like the region effect to >> be >> removed. >> >> My problem is that I cannot figure out how to get residual values from the >> adonis model. >> >> Any hint of some other kind of multivariate analysis that could solve this >> problem is very welcome. >> >> Thanks in advance, >> >> -- >> Alicia Valdés >> Université de Picardie Jules Verne >> Unité EDYSAN (Ecologie et Dynamique des Systèmes Anthropisés) >> 1, rue des Louvels >> F-80037 Amiens Cedex >> France >> tel:+33 322825775 >> alicia.val...@u-picardie.fr >> http://www.u-picardie.fr/edysan/ >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> R-sig-ecology mailing list >> R-sig-ecology@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >> >> > [[alternative HTML version deleted]]
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