RDA
Hi Dr. Oksanen! Its very gracious of you to respond. On another important note, this is the citation suggested for the vegan package: Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H. (2015) vegan: Community Ecology Package. R package version 2.2-1. http://CRAN.R-project.org/package=vegan Is this the most appropriate for our purposes (using Adonis and capscale in Vegan)? 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: Jari Oksanen <jari.oksanen at oulu.fi>
Sent: Thursday, November 26, 2015 1:15 PM
To: Marcelino de la Cruz
Cc: Richards, Christina; r-sig-ecology at r-project.org; Robertson, Marta; Verhoeven, Koen; Alvarez, Mariano; Foust, Christy
Subject: Re: [R-sig-eco] RDA
Sent: Thursday, November 26, 2015 1:15 PM
To: Marcelino de la Cruz
Cc: Richards, Christina; r-sig-ecology at r-project.org; Robertson, Marta; Verhoeven, Koen; Alvarez, Mariano; Foust, Christy
Subject: Re: [R-sig-eco] RDA
> On 26 Nov 2015, at 20:05 pm, Marcelino de la Cruz <marcelino.delacruz at upm.es> wrote: > > El 26/11/2015 a las 16:27, Richards, Christina escribi?: >> Hello! >> >> That is very helpful and seems to work! Thank you!! >> >> I did not realize we could use raw data in capscale, > We could and we should! Currently, it is the only way to achieve it. > > is this true only because it is conditioning variables? > It seems that the current implementation of capscale only accepts a single *data.frame* for both explanatory and conditioning variables > Yes, this is true: current and *future* implementations of capscale/rda/cca (and future dbrda) will only have one data= argument. However, in addition to variables in the data frame given in data=, you can mix variables in the work environment in your formula. If you think you need to have several data frames for the data= argument, please consider cbind(). cheers, Jari Oksanen