[R-sig-ME] contrasts in lmer for a fix effect with 3 levels

[Marcela A. Bustamante-Sanchez]

thanks Federico I'll try this!
m
----- Original Message ----- 
From: "Federico Calboli" <f.calboli at imperial.ac.uk>
To: "Marcela A. Bustamante-Sanchez" <mbustama at bio.puc.cl>
Cc: <r-sig-mixed-models at r-project.org>
Sent: Tuesday, May 20, 2008 5:56 PM
Subject: Re: [R-sig-ME] contrasts in lmer for a fix effect with 3 levels


> On 20 May 2008, at 22:16, Marcela A. Bustamante-Sanchez wrote:
> 
>> Dears lmers!
>> I have a field experiment with a split plot design. I have blocks  
>> in three different types of shurblands. In each shurbland-plot I  
>> set up two sub-plots, with two types of cover vegetation (open and  
>> close) and in each sub plot I sowed 20 seeds of a species of tree.  
>> My response variable is the probability of germination. So, I have  
>> two fixed factors: shurbland and cover, and one random factor block/ 
>> shrubland. The following is my model:
>>
>>
>>
>> modela<-lmer(cbind(success, failures) ~ shrubland* cover+ (1 |  
>> block/shrubland), family="binomial", data=Tod07)
>>
>> shrubland: tree levels (Bb, Bp, R)
>>
>> cover: two levels (open, close)
>>
>>
>>
>> I want to know if someone can explain or indicate me how to make  
>> the contrasts or comparisons for the three levels in the shurbland  
>> factor? I'm nwe using R so I have no idea how to make the  
>> comparisons using these mixed models.
> 
> try:
> 
> contrasts(Tod07$shrubland)
> 
> this should give you the contrasts set for the levels in shrubland.  
> If you want different contrasts you need to build a new matrix of  
> contrasts (of the very same dimensions of the original contrasts matrix.
> 
> contrasts(Tod07$shrubland) = your.matrix
> 
> Obviously you need to know what kind of contrasts you want before...  
> look around for orthogonal contrasts, I think that would be a good  
> starting point.
> 
> Finally, this question is a general R question, it applies to lm()  
> and similar functions outside the libraries lme4/nlme
> 
> HTH
> 
> F
> 
> --
> Federico C. F. Calboli
> Department of Epidemiology and Public Health
> Imperial College, St. Mary's Campus
> Norfolk Place, London W2 1PG
> 
> Tel +44 (0)20 75941602   Fax +44 (0)20 75943193
> 
> f.calboli [.a.t] imperial.ac.uk
> f.calboli [.a.t] gmail.com
> 
> 
> 
>