Can someone point me to where I can see how differences of LSMEANS are calculated in GLIMMIX using the DIFF option?
TDIFF is the t-value of the test to see if the LSMEANS are different. PDIFF is the probability associated with the t-value.
LSMEANS calculations: https://documentation.sas.com/?docsetId=statug&docsetTarget=statug_glm_details41.htm&docsetVersion=1...
Essentially, Least Squares Means tries to adjust for different number of observations in cells, which can bias the calculation of regular old means.
First you calculate the individual LSMEANS and then you do a subtraction to get a DIFF.
The formula for Fisher's LSD is here: https://www.statisticshowto.com/how-to-calculate-the-least-significant-difference-lsd/
So I believe that FIsher's LSD uses the difference of actual factor means while LSMEANS uses the difference of least-squares means. So the difference between two means won't even agree.
I don't understand what you are saying.
Here's a worked example: https://support.sas.com/kb/24/984.html
TDIFF is the t-value of the test to see if the LSMEANS are different. PDIFF is the probability associated with the t-value.
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