Extracting elements from output in of mixed-effects model using nlme
<p>I am trying to extract individual elements from the random effects table contained within the object created by the summary call of a mixed-effects model. Specifically I want to extract each of the level-2 random effects.</p>

<p>Toy data:</p>

<pre><code>set.seed(1234)
score &lt;- c(rnorm(8, 20, 3), rnorm(8, 35, 5))
rep &lt;- rep(c(0,1,2,3), each = 8)
group &lt;- rep(0:1, times = 16)
id &lt;- factor(rep(1:8, times = 4))

df &lt;- data.frame(id, group, rep, score)
</code></pre>

<p>Now create a model</p>

<pre><code>require(nlme)

modelLME &lt;- summary(lme(score ~ group*rep, data = df, random = ~ rep|id))

modelLME
</code></pre>

<p>When we call it we get the output</p>

<pre><code>Linear mixed-effects model fit by REML
 Data: df 
       AIC      BIC    logLik
  219.6569 230.3146 -101.8285

Random effects:
 Formula: ~rep | id
 Structure: General positive-definite, Log-Cholesky parametrization
            StdDev       Corr  
(Intercept) 2.664083e-04 (Intr)
rep         2.484345e-05 0     
Residual    7.476621e+00       

Fixed effects: score ~ group * rep 
                Value Std.Error DF   t-value p-value
(Intercept) 22.624455  3.127695 22  7.233587  0.0000
group       -1.373324  4.423229  6 -0.310480  0.7667
rep          2.825635  1.671823 22  1.690152  0.1051
group:rep    0.007129  2.364315 22  0.003015  0.9976
 Correlation: 
          (Intr) group  rep   
group     -0.707              
rep       -0.802  0.567       
group:rep  0.567 -0.802 -0.707

Standardized Within-Group Residuals:
        Min          Q1         Med          Q3         Max 
-1.86631781 -0.74498367  0.03515508  0.76672652  1.91896578 

Number of Observations: 32
Number of Groups: 8 
</code></pre>

<p>Now I can extract the residuals from the random effects table above via</p>

<pre><code>modelLME$sigma
</code></pre>

<p>But I can't find the values in the <code>(Intercept)</code> and <code>rep</code> rows of the <code>StdDev</code> column of the random effects table in this output (<code>2.664083e-04</code> and <code>2.484345e-05</code> respectively) It must be there somewhere and I looked via searching <code>str(modelLME)</code> but I can't find it.</p>