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Understanding variance components

Hi Gang,

Sorry that I so am late to the party, but in case you are still 
interested I will reply (and, of course, for the archive).

The answer is basically given in the old faq:
http://glmm.wikidot.com/faq#toc27

(1|site/block) = (1|site)+(1|site:block)

Which is exactly what is given in your output. A random intercept for 
Worker and a random intercept for each worker:Machine interaction.

To answer your questions. The random intercepts do not have base or 
reference levels. They are increments or decrements to the overall 
intercept for each level of Worker or the Machine:Worker combination. 
The reported variance is the estimated variance of these increments, 
which is most likely unequal to the actual variance you would obtain by 
calculating it from the estimated increments, which are sometimes called 
BLUPs (I wonder if a better term for those exist).

Hope that helps,
Henrik

PS: Belated Happy New Year to everyone.


Am 05.01.2017 um 17:28 schrieb Chen, Gang (NIH/NIMH) [C]: