[R-sig-eco] How to accommodate data with negative values for Canonical Correspondence Analysis in R using "vegan" Package

[Jari Oksanen]

It depends *where* to include negative values. Negative values are OK as constraints (environmental variables, right hand side of the model formula). However, all marginal sums of the response data (left hand side of the model formula) must be above zero. It is technically possible to have some negative entries in the response matrix as long as the marginal sums are positive, but you really should not have them. *CA family of methods were originally developed for non-negative data, and having negative entries usually indicates that your data are not at all suitable for the method. If you insist on the analysis, then you really must know what you are doing, but if you really know, you do not need ask in R-sig-ecology.

I still repeat: you can have negative data as constraints. If that fails, then something else is wrong with your data.

If you want to use CCA family of methods for negative response data, then RDA with equal scaling of variables is usable. Very commonly negative values also indicate that your response variables were measured in different scales and units, and therefore you must set scale=TRUE in the rda() call. Not knowing the data or any other details, this is a blind watchmaker recommendation.

Cheers, Jari Oksanen
________________________________________
From: r-sig-ecology-bounces at r-project.org [r-sig-ecology-bounces at r-project.org] on behalf of Ivailo [ubuntero.9161 at gmail.com]
Sent: 26 February 2014 16:23
To: Rajendra Mohan panda
Cc: r-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] How to accommodate data with negative values for Canonical Correspondence Analysis in R using "vegan" Package

On Wed, Feb 26, 2014 at 2:43 PM, Rajendra Mohan panda
<rmp.iit.kgp at gmail.com> wrote:
...
> I have temperature data with negative values which I am not able to include
> for my CCA ordination. ...

Rajendra, I am curious -- why are you not able to include the negative
values in the CCA ordination?

--
"The cure for boredom is curiosity. There is no cure for curiosity." --
Dorothy Parker

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