> On 26 Nov 2015, at 17:27 pm, Richards, Christina <c...@usf.edu> wrote: > > Hello! > > That is very helpful and seems to work! Thank you!! > > I did not realize we could use raw data in capscale, is this true only > because it is conditioning variables? At any rate it recapitulates our > analysis using partial mantel in 2 species with 2 different results (one > significant, the other not), so I'm inclined to believe its doing something > similar. > If you supply raw community matrix (observations times species), capscale() will internally turn it into dissimilarities using specified distance= method (defaults “euclidean”). You should verify that the selected distance= method is the one you need. The variables on the right-hand-side of the formula must be in “raw” (observations times variables) format. They cannot be distances.
Cheers, Jari Oksanen > ___ > From: Marcelino de la Cruz <marcelino.delac...@upm.es> > Sent: Wednesday, November 25, 2015 3:28 AM > To: Richards, Christina; r-sig-ecology@r-project.org > Subject: Re: [R-sig-eco] RDA > > Hi Christina, > > I think this could work: > > You should combine the *raw* y and z (i.e.not the Euclidean matrices) in > the same data.frame (e.g. "yz"), and call capscale like this: > > capscale (x ~y1+y2+...+yn + Condition(z1+z2+...+z80), data=xy) > > > Cheers! > > Marcelino > > > > -- > Marcelino de la Cruz Rot > Depto. de Biología Y Geología > Universidad Rey Juan Carlos > Móstoles España > > > El 24/11/2015 a las 22:11, Richards, Christina escribió: >> >> >> Hello! >> >> >> We are trying to do a partial RDA with 3 matrices but our x matrix has a lot >> of missing data. We could use instead distance matrices which imputed >> missing data, but when we try to use capscale and the euclidean matrices, it >> seems we have to use the formula x~y + condition (z) and we cannot use a >> matrix of values for z. We would like to identify the the effect of y on x >> with z partitioned out where: >> >> >> x= dataframe of dna methylation with individuals listed in column 1 and 0/1 >> data across ~80 columns >> >> y= habitat for each individual >> >> z= dataframe of genetic loci with individuals listed in column 1 and 0/1 >> data across ~80 columns >> >> >> Christina Richards, Ph.D. >> University of South Florida >> Department of Integrative Biology >> 4202 East Fowler Avenue SCA 127 >> NES 107 (shipping) >> Tampa, FL 33620 >> (813)974-5090 >> (813)974-3263 FAX >> http://www.ecologicalepigenetics.com >> Twitter: @EcolEpig >> Facebook: Ecological Epigenetics >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-ecology mailing list >> R-sig-ecology@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >> > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
