[R] Independent contrasts from lme with interactions

[Andrew Robinson]

Ken,

estimable in the gmodels package will help you.

Cheers

Andrew

On Mon, Apr 30, 2007 at 03:11:57PM -0700, Ken Nussear wrote:
> Hi All,
> 
> I've been searching the help archives but haven't found a workable  
> solution to this problem.
> 
> I'm running an lme model with the following call:
> 
>  >lme.fnl <- lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID)
>  > anova(lme.fnl)
>              numDF denDF   F-value p-value
> (Intercept)     1   168 19255.389  <.0001
> S               1   168     5.912  0.0161
> Tr              2   116    15.919  <.0001
> Yr              1   168    77.837  <.0001
> Tr:Yr           2   168    47.584  <.0001
> 
> 
>  >summary(lme.fnl)
> Linear mixed-effects model fit by REML
> Data: NULL
>         AIC      BIC    logLik
>    580.6991 613.5399 -281.3496
> 
> Random effects:
> Formula: ~1 | TID
>          (Intercept)  Residual
> StdDev:   0.3697006 0.5316062
> 
> Fixed effects: Max ~ S + Tr + Yr + Tr:Yr
>                  Value Std.Error  DF   t-value p-value
> (Intercept)  -13.5681  113.2623 168 -0.119793  0.9048
> SM             0.2187    0.0957 168  2.284605  0.0236
> TrT97       1375.5897  164.0060 116  8.387434  0.0000
> TrT98       2890.9462  455.3497 116  6.348848  0.0000
> Yr             0.0099    0.0567 168  0.174005  0.8621
> TrT97:Yr      -0.6883    0.0821 168 -8.384798  0.0000
> TrT98:Yr      -1.4463    0.2279 168 -6.347310  0.0000
> Correlation:
>           (Intr) SM     TrT97  TrT98  Yr     TT97:Y
> SM        0.067
> TrT97    -0.691 -0.049
> TrT98    -0.248 -0.001  0.171
> Yr       -1.000 -0.067  0.691  0.248
> TrT97:Yr  0.691  0.048 -1.000 -0.171 -0.691
> TrT98:Yr  0.248  0.001 -0.171 -1.000 -0.248  0.171
> 
> Standardized Within-Group Residuals:
>          Min          Q1         Med          Q3         Max
> -2.19017911 -0.58108001 -0.04983642  0.57323031  2.39811353
> 
> Number of Observations: 291
> Number of Groups: 119
> 
> 
> 
> I'm specifically interested in differences of  in the differences  
> between my treatment groups (3) and Year (Yr), and importantly in the  
> interaction. Normally I'm used to running independent contrast  
> analysis to explore these differences, but I'm not sure how to  
> extract this information using lme. Can anyone point me in the right  
> direction?
> 
> Thanks
> 
> Ken
> 
> 
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Andrew Robinson  
Department of Mathematics and Statistics            Tel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
http://www.ms.unimelb.edu.au/~andrewpr
http://blogs.mbs.edu/fishing-in-the-bay/