I have been often using GEE for complex panel analyses. However, it occurs to me that in many cases GLM would have provided similar results.

What is the main conceptual difference between the two?

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    $\begingroup$ When you use the GLM and think that response variable is not independent, add the GEE to GLM to deal with incorporate the correlation into the model. $\endgroup$ – user158565 May 29 '17 at 17:46
  • $\begingroup$ I think you will find the information you need in the linked thread. Please read it. If it isn't what you want / you still have a question afterwards, come back here & edit your question to state what you learned & what you still need to know. Then we can provide the information you need without just duplicating material elsewhere that already didn't help you. $\endgroup$ – gung - Reinstate Monica May 31 '17 at 12:43