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tree diameter growth

3 messages · Bin Yue, Andrew Robinson, Drew Tyre

Original
2 days later
Andrew Robinson
# 
Dear Bin Yue,

you've described a pretty interesting modelling effort.  It's true
that determining what should be a fixed and what should be a random
effect is laregly up to the analyst, but different interpretations
will be available from these different choices.  You may find it worth
reading the Hierarchical Models chapter in my icebreakeR document
(freely available online), 

http://www.ms.unimelb.edu.au/~andrewpr/r-users/icebreakeR.pdf

or Chapter 7 of "Forest Analytics in R", both of which discuss fixed
and random effects fomr a forestry point of view.

I would tend to think that the following model is worth trying:

gr1 <- lmer(log(dbh.y)-log(dbh.x) ~ 
            scale(log(dbh.x)) + classsizedist + 
            (scale(log(dbh.x)) | spcode),
            data = livestem)

My reasoning is as follows.  First, the goal is to determine the
effect of different size-class distributions on growth.  I think that
you'd probably like to be able to represent these estimates and
discuss them.  To me it seems natural to make them fixed effects.

Second, one could argue for the species effect to be fixed or random.
Increasingly I see people fitting species as a random effect, and in
this case, it makes sense to me.  However, note that I'm allowing for
each species to have a different growth trajectory.  I would suspect
that there would be species-specific variation in the growth rates as
a function of size; this term will allow for that contingency.

I hope that these thoughts are useful to you.

Andrew
On Fri, Aug 19, 2011 at 04:46:41PM +0800, Bin Yue wrote:

  
    

      
      
    

  


  


      

    

    
2 days later

    

      
      

        


  

        

      Drew Tyre
    

    

      
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I would agree with Andrew's comments. In addition, there might be
phylogenetic effects - correlations between species due to the
relatedness, e.g. species in the same genus are more similar than
species in different genera. Package MCMCglmm can handle phylogenetic
correlations, although I've never had the opportunity to try it
myself.

What a wonderful dataset!

        
On Fri, Aug 19, 2011 at 3:46 AM, Bin Yue <byicymoon at 163.com> wrote: