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

[Chris Howden]

Whenever I hit this problem I add the minimum to all scores so they
now range from 0 and above. If necessary I can back transform.

As I haven't changed the ratio the parameters coefficients have the
same meaning, so interpretation is no problem. (Although the intercept
may now change and be difficult to interpret)

This will work if the scale is a human construct where negative and
positive numbers convey the same info, however if they mean different
things it may not work. For example some indices have different
meanings if negative.

Chris Howden
Founding Partner
Tricky Solutions
Tricky Solutions 4 Tricky Problems
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> On 27 Feb 2014, at 1:39, Jari Oksanen <jari.oksanen at oulu.fi> wrote:
>
> 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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