[R-sig-eco] Do I have to standardise my explanatory data before doing a RDA?

[francois gillet]

Dear Connie,

1. Explanatory variables are automatically standardized when you perform an RDA and there is no need to do it before calling the vegan's rda() function. This is not the case for the response variables (usually the species), which are not standardized by default unless you specify scale = TRUE, but this not advised for species abundances.

2. Various scalings may be applied to an RDA triplot (with argument scaling in the call of the plot() function). Scaling 1 preserves distances among sites and scaling 2 preserves angles among species arrows. If you get close results for both scalings 1 and 2 (the default) and if you want to have both species and sites spread in the triplot, you can apply scaling 3. You can also arbitrarily multiply species scores by a constant to increase the length of the projected vectors without changing the interpretation of the triplot. This option is used in our function triplot.rda(), an appendix to the book "Numerical Ecology with R". Note that the plot() function as applied in vegan to an rda object represents species as points, which is misleading and not recommended.

Best wishes,

François Gillet

----- Mail original -----
De: "Constanze Keye" <constanze_keye using hotmail.com>
À: r-sig-ecology using r-project.org
Envoyé: Mardi 12 Janvier 2021 10:43:35
Objet: [R-sig-eco] Do I have to standardise my explanatory data before doing a RDA?

Dear list members,

I struggle over a few things whilst doing a RDA for the last couple of days. Could please somebody enlighten me?

  1.  Do I have to standardise my explanatory data before doing a RDA (function rda, vegan)?
  2.
I know that�s a normal procedure before RDA, but I found this post in the r-sig forum: https://stat.ethz.ch/pipermail/r-sig-ecology/2010-April/001196.html
Now, I'm not sure if I can/should skip standardisation before RDA using the vegan package, or if I did understand something wrong here?

2.  Why are all my species always clustered in the very middle of my RDA plot ? If I use function 'triplot.rda' from https://raw.githubusercontent.com/zdealveindy/anadat-r/master/scripts/NumEcolR2/triplot.rda.R , they are much more spaced around the plot and some of them seem to correlate well with my explanatory variables...

Sorry, if these questions are a bit basic, but I�m still trying to get my head around the whole subject of RDA.

Cheers,
Conny


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