Interpreting results from generalized linear mixed model

Comments

• EJ

  January 23

  I've asked the experts!

  Cheers,

  E.J.
• mercator88

  January 25

  Thanks! I'm at a standstill until I get guidance on the above.
• František

  January 26

  Hi Andrew,

  The contrast coding can be indeed a bit confusing. We added a more detailed explanation to the help file that summarizes what are the differences and reasons for using the sum contrasts (where the fixed effects are not readily interpretable vs. the dummy coding--default in R):

  The analysis uses sum contrast encoding for categorical (nominal and ordinal) predictors (R uses dummy encoding by default). This scheme is used for better interpretability of models with interactions. However, the fixed and random effects estimates will differ from those obtained from R with default settings. We advise using the 'Estimated marginal means' section for obtaining mean estimates at individual factor levels. For comparing the mean estimates, use the contrasts option.

  Let me know if this explains the issue!

  Frantisek
• mercator88

  January 26

  Frantisek,

  
  

  I'm still a bit confused. The estimate I'm getting using the contrasts option is exactly the same as the marginal mean for Phase (1). Maybe I'm doing the contrasts wrong; I set the contrasts to 0 for Phase = 0 and 1 for Phase = 1.

  
  

  I didn't know there was a help file. How do I access it?
• František

  January 28

  Dear Andrew,

  I'm slightly confused about your question now. When you have a factor with two levels, the sum contrast creates (-1, 1) coding for the levels (i.e., contr.sum(2)). In other words, the fixed effect estimate corresponds to half the difference. You can find more detailed information about sum contrasts e.g., here https://rpubs.com/monajhzhu/608609 (Linear Models with Sum Contrast).

  The JASP help file can be opened by clicking the "i" icon:

  

  Which opens the corresponding pop-up window.

  Cheers,

  Frantisek
• mercator88

  January 30

  Frantisek,

  Thanks for directing me to the Help pages.

  I apologize for the confusion. My contrast was (0, 1) not (-1, 1), and here is what I got:

   

  Estimate SE df Lower Upper z p†

  Contrast 1 0.136 0.045 inf. 0.048 0.224 3.039 0.002

  Is it correct to assume an odds ratio of exp(0.136)?

  Thanks!!!

  Andrew
• František

  January 31

  Hi Andrew,

  You can get OR from the contrasts only if you don't use the "Outcome scale" option. Otherwise, the contrast is a difference in the probabilities of those two outcomes.

  Glad I could help,

  Frantisek