[R] rda variance partioning in vegan problems

David Winsemius dwinsemius at comcast.net
Thu May 2 06:17:17 CEST 2013

On May 1, 2013, at 8:37 PM, Thomas Parr wrote:

> This is not a request for coding help so there is no reproducible code,

So this is a general statistical problem? 

Perhaps you should try: CrossValidated.com

> rather I am trying to figure out if anyone had had a similar experience.
> My question is related to partitioning the variance in rda (vegan) results
> for multiple groups of variables.

Sounds like a question for authors of the package.

>  I have a  high dimensional dataset with
> 79 explanatory variables and 9 response variables. Within those 79
> explanatory variables there are ~8 groups (e.g. water chemistry, land cover,
> geography, surficial geology, etc).  To partition out their unique and
> binary interactive variance, I run the ~30 conditioned RDAs necessary to
> determine the "pure effects" of each group and the "pure binary
> interactions" of those groups with each other. 
> My method for partitioning the variance of binary interactions is as
> follows:
> Inertia of the interaction of water chemistry and geography = inertia of the
> combined effect (conditioned on the remaining groups) -  Inertia of just
> Waterchemistry - inertia of just geography.
> When I do this for each combination two problems arise:
> 1. I get small negative numbers when 0 should be the lowest possible number.
> Does this occur because of internal rounding in the RDA code, or is there
> something else going on?

And how exactly would one tell if there is no data? (or even results?)

> (If Total inertia is 9 and explainable inertia is
> 5.4, a "small negative number" for an interaction inertia might be -0.003
> after the above partitioning procedure.)
> 2. The sum of partitioned inertia is greater than the constrained inertia on
> the full model (in this case Total Inertia is 9, explainable inertia is
> 5.41, and the sum of partitioned inertia is 5.57). 
Again... with no data. How would one explain this?

> I have checked for coding errors.

David Winsemius
Alameda, CA, USA

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