[R-sig-eco] question about appropriate model for abundance studies

[Nicholas Lewin-Koh]

Hi Sacha,
A few things:
1) If counts are large, a normal error structure may be fine as an
approximation,
   large counts means conditional on the covariates, the counts in each
 cell are relatively 'large'. if there are not many 0's a log
 transformation
 might be appropriate. This will be a lot easier if you want to start
 adding
 spatial covariance structure. However, without seeing your particular
 data
 it is hard to say what is an appropriate assumption.
2) Spatial Poisson models are tricky. You have to be a bit careful 
   in the specification. In a mixed model context, ie normal random
   effects
   I suspect the problems that you get in a Poisson auto regressive
   model are not the same. In the Poisson spatial auto regressive model
   on a finite lattice 
   you can only get negative correlation.
3) The bell shaped abundance distribution is the old idea that a single
species
   will have a Gaussian or unimodal distribution of abundance along
   a continuous environmental gradient, with the mode at the optimum.
   The species-abundance distribution is a different beast and tend
   to be highly skewed, the classic distribution is the lognormal
   but there are many others, see Engen, or many other references.
4) You are talking about empirical modelling of species abundance in a
survey,
   so all the theoretical mumbo-jumbo above may not be that relevant,
   depending
   upon the goals of the study and interpretation of the data. So you
   have to
   think about how the survey was conducted, and construct your model
   according
   to the data collection process, some of the theoretical constructs
   can be tested
   as part of the systematic component of your model.

Hoping this helps,

Nicholas 



> Message: 1
> Date: Fri, 18 Mar 2011 14:14:12 +0100
> From: Sacha Viquerat <tweedie-d at web.de>
> To: r-sig-ecology at r-project.org
> Subject: [R-sig-eco] question about appropriate model for abundance
> 	studies
> Message-ID: <4D835AA4.40706 at web.de>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
> 
> hello! I did a count survey on a tropical fish species! Well, I didnt do 
> it, Im just helping at the statistics-stage. We recorded some water 
> parameters alogside each catch, such as no3, no2, po4 etc. as the data 
> are count data (and require error terms due to spatial 
> pseudoreplication), the glm with poisson error structure should be the 
> method of choice. however, I do fear that in doing so, I will not be 
> able to model fish abundance correctly. In my opinion (and, as far as I 
> remember, in the opinion of those who gave ecology classes), the 
> abundance of species should be sort of bell shaped, since there will 
> always be, for example, an optimal temperature, pH-level and so forth. 
> However, I have not yet seen such a discussion arise on one of the many 
> forums. Am I missing the obvious??
> 
> 
>