contrast coding error 3dLMEr

AFNI Message Board
2

A couple of issues may exist with your model specification:

  • Within-individual variable: Is Time_since_BL the only within-individual variable? If so, consider using the following model:

    -model 'Time_since_BL*education_group*ptau_status+Sex+TIV+scanner+(Time_since_BL|Subj)' \

  • Covariate selection: If your primary interest is in group differences in the effect of Time_since_BL, some included variables may not be justifiable. This blog post covers key considerations, and this paper provides a deeper discussion on covariate selection.

  • GLT specification: Update the following GLT codes:

    -gltCode TimeEdu 'Time_since_BL : education_group : 1*0 -1*1' \  
-gltCode TimePtau 'Time_since_BL : ptau_status : 1*1 -1*0' \  
-gltCode HighPosNeg 'Time_since_BL : education_group : 1*1 ptau_status : 1*1 -1*0' \  
-gltCode LowPosNeg 'Time_since_BL : education_group : 1*0 ptau_status : 1*1 -1*0' \  
-gltCode LowHighNeg 'Time_since_BL : education_group : 1*0 -1*1 ptau_status : 1*0' \  
-gltCode LowHighPos 'Time_since_BL : education_group : 1*0 -1*1 ptau_status : 1*1' \

    to

    -gltCode TimeEdu 'education_group : 1*0 -1*1 Time_since_BL :' \  
-gltCode TimePtau 'ptau_status : 1*1 -1*0 Time_since_BL :' \  
-gltCode HighPosNeg 'education_group : 1*1 ptau_status : 1*1 -1*0 Time_since_BL :' \  
-gltCode LowPosNeg 'education_group : 1*0 ptau_status : 1*1 -1*0 Time_since_BL :' \  
-gltCode LowHighNeg 'education_group : 1*0 -1*1 ptau_status : 1*0 Time_since_BL :' \  
-gltCode LowHighPos 'education_group : 1*0 -1*1 ptau_status : 1*1 Time_since_BL :' \

Gang Chen