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. 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 ________________________________________ 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
