[R] Interaction term in lmer

From: emine özgür Bayman <eozgur10_at_hotmail.com>
Date: Fri, 01 Jun 2007 18:01:02 +0000


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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Received on Fri 01 Jun 2007 - 18:05:26 GMT

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