[R-sig-ME] contrasts in lmer for a fix effect with 3 levels
Marcela A. Bustamante-Sanchez
mbustama at bio.puc.cl
Wed May 21 00:27:03 CEST 2008
thanks Federico I'll try this!
----- 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.
> 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
> 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
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