[R] Interaction term in lmer

[Martin Henry H. Stevens]

HI Emine,
The parentheses specify a variable as random or fixed. You are using  
center for random intercepts, but fixed for interactions.
You may want
> mer(cbind( yvect, nvect-yvect) ~ trt   + ( 1 | center) + (1 |  
> trt:center),
>   family = binomial, niter = 25, method = "Laplace", control = list 
> (usePQL =
> FALSE) )

Cheers,
Hank

On Jun 1, 2007, at 2:01 PM, emine özgür Bayman wrote:

> Dear R users,
> I'm pretty new on using lmer package. My response is binary and I  
> have fixed
> treatment effect (2 treatments) and random center effect (7  
> centers). I want
> to test the effect of treatment by fitting 2 models:
>
> Model 1: center effect (random) only
> Model 2: trt (fixed) + center (random) + trt*center interaction.
>
> Then, I want to compare these 2 models with Likelihood Ratio Test.  
> Here are
> my lmer codes that I don't feel comfortable about their correctness.
>
> model1 <- try(lmer(cbind( yvect, nvect-yvect) ~ 1 + (1 | center),
>   family = binomial, niter = 25, method = "Laplace", control = list 
> (usePQL =
> FALSE) ))
>
> model2 <- try(lmer(cbind( yvect, nvect-yvect) ~ trt*center  + ( 1 |  
> center)
> ,
>   family = binomial, niter = 25, method = "Laplace", control = list 
> (usePQL =
> FALSE) ))
>
>
> (I have attached outputs below)
> What I don't understand is; I thought in model2 I have defined  
> center effect
> as a random effect. Then how come I got center effects and trt*center
> interactions under the fixed effects list on the output? Probably I  
> didn't
> understand how to set up these models in lmer. Could anyone help me  
> about
> this?
>
> Thanks a lot for your help...
>
> Emine
>
> model1 <- try(lmer(cbind( yvect, nvect-yvect) ~ 1 + (1 | center),
>   family = binomial, niter = 25, method = "Laplace", control = list 
> (usePQL =
> FALSE) ))
>
>> summary(model1)
> Generalized linear mixed model fit using Laplace
> Formula: cbind(yvect, nvect - yvect) ~ 1 + (1 | center)
> Family: binomial(logit link)
>      AIC      BIC    logLik deviance
> 236.817 238.0951 -116.4085  232.817
> Random effects:
> Groups Name        Variance Std.Dev.
> center (Intercept) 0.088127 0.29686
> number of obs: 14, groups: center, 7
>
> Estimated scale (compare to 1)  0.2672612
>
> Fixed effects:
>             Estimate Std. Error z value Pr(>|z|)
> (Intercept) -0.32084    0.14709 -2.1812  0.02917 *
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>
>
> ##################
> model2 <- try(lmer(cbind( yvect, nvect-yvect) ~ trt*center  + ( 1 |  
> center)
> ,
>   family = binomial, niter = 25, method = "Laplace", control = list 
> (usePQL =
> FALSE) ))
>
>> summary(model2)
> Generalized linear mixed model fit using Laplace
> Formula: cbind(yvect, nvect - yvect) ~ trt * center + (1 | center)
> Family: binomial(logit link)
> AIC      BIC        logLik     deviance
>   30 39.58586 -1.547024e-07 3.094048e-07
> Random effects:
> Groups Name        Variance Std.Dev.
> center (Intercept) 5e-10    2.2361e-05
> number of obs: 14, groups: center, 7
>
> Estimated scale (compare to 1)  0.2672612
>
> Fixed effects:
>               Estimate Std. Error  z value Pr(>|z|)
> (Intercept)  -1.060869   0.065372 -16.2282  < 2e-16 ***
> trt2          1.118029   0.086842  12.8743  < 2e-16 ***
> center2      -0.325428   0.504256  -0.6454  0.51869
> center3      -0.325440   0.504258  -0.6454  0.51868
> center4       0.655407   0.413449   1.5852  0.11292
> center5      -0.325433   0.504256  -0.6454  0.51869
> center6      -0.325421   0.504255  -0.6454  0.51870
> center7       0.655422   0.413448   1.5853  0.11291
> trt2:center2  0.673737   0.651313   1.0344  0.30094
> trt2:center3 -0.137183   0.651314  -0.2106  0.83318
> trt2:center4 -0.307083   0.583845  -0.5260  0.59891
> trt2:center5 -0.137203   0.651314  -0.2107  0.83316
> trt2:center6  1.654555   0.712419   2.3224  0.02021 *
> trt2:center7  0.673705   0.651311   1.0344  0.30096
> ---
>
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Dr. Hank Stevens, Assistant Professor
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Botany Department
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