[R] calculate length of gradient ?

[Jari Oksanen]

On 29 Mar 2004, at 16:54, Andreas Plank wrote:on=2.63
> my question is about ordination technics:
> To decide using a linear model response or a unimodal model response,
> in Canoco (software for ordination technics)
> you can calculate a so-called "length of gradient".
>
> (from Canoco Help file:)
>> The length of gradient is a measure of how unimodal the species
>> responses are along an ordination axis. It is the range of the
>> sample scores divided by the average within-species standard
>> deviation along the axis. The gradient length is expressed in
>> standard deviation units of species turnover (SD).
>
> The function  cca in package vegan and other functions give many
> outputs, but I didn't find anything about "length of gradient". Is
> there a possibility to calculate this in R? If yes how can I
> calculate this?

You cannot get this scaling in the cca function. However, function 
decorana() gives you "axis lengths". Cajo ter Braak suggested a linear 
approximation to Mark Hill's "sd scaling" that would be easy to 
implement in cca (actually, in summary.cca(), since no scaling is done 
until your request one), but I haven't bothered to do that. By the way, 
I disagree with the recommendation: CA is in general better than PCA, 
even with "short gradients" so  you don't need axis lengths.

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cheers, jari oksanen
--
Jari Oksanen, Oulu, Finland