[R-sig-eco] RDA

[Gavin Simpson]

Yes, that is the appropriate citation for the software/implementation (and
in the case of capscale() the method, I think; there are other variants of
the idea around). `adonis()` is based on the permutational MANOVA
(PERMANOVA) references to the papers that introduced this method are in
`?adonis`, which you may choose to cite also.

HTH

Gavin

On 26 November 2015 at 14:13, Richards, Christina <clr at usf.edu> wrote:

> 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
>
> > 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 escribió:
> >> 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
>
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>



-- 
Gavin Simpson, PhD

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