title: GLM in R: Difference between estimates from glmer-summary and from effects-package
body: <p>I set up a GLMM in R using <code>glmer()</code> from <code>lme4</code> package. I used effects package for calculating estimates and CIs for fixed effects. 
  I'm new to GLMMs, so my question is how the estimates provided by the <code>effects</code> package are calculated and in which way they differ from log-means given in the <code>glmer</code>-summary?</p>
  
  <p>For example if I run</p>
  
  <pre><code>Model = glmer(response ~ fixed1 + fixed2 + (1 | random), data=df, family = poisson)
  </code></pre>
  
  <p>summary(Model) returns the following:</p>
  
  <pre><code>              Estimate      Std. Error      z value      Pr(&gt;|z|)
  (Intercept)     -0.1459        0.4863       -0.300        0.764
  fixed1_level2    0.3044        0.4479        0.680        0.497
  fixed2_level2    0.2298        0.3212        0.716        0.474
  fixed2_level3    0.3576        0.3368        1.062        0.288
  </code></pre>
  
  <p>Whereas summary(allEffects(Model)) returns this:</p>
  
  <pre><code>fixed1 effect
  
  fixed1_level1     fixed1_level2 
  1.125860          1.526514 
  
  fixed2 effect
  
  fixed2_level1     fixed2_level2     fixed2_level3
  1.115492          1.403738          1.594999
  </code></pre>