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How about pool error term for RM factors?


When running a RMANOVA it seems like pool error term for RM factors is pre-checked. Could somebody enlighten me in which circumstances to check it and when NOT to have it checked? 🙄

Thank you for guidance:-)



  • The help file refers to Morey (2008) for details. I also Googled this and also found people who believe it is prudent not to pool the error term (e.g., I'll ask Johnny for his input.



  • Hi @PerPalmgren,

    The initial RM ANOVA model is a model where the error terms are pooled - this is simply how linear models are set up in these settings. As a consequence, the emmeans R-package (which we use for marginal means, contrasts, and posthoc tests) also works with the pooled error term (see the documentation here).

    You can read further about this in a previous thread:

    That's how the emmeans works: it operates based on the model you specify. In the ANOVA model, there is the assumption of equal variances, so that influences how emmeans handles the pairwise comparisons. We offer a workaround, where (for balanced designs only) in the RM ANOVA you can choose to use the non-pooled error term for RM factors. This basically comes down to running a series of paired samples t-tests.

    I am currently trying to have the anova be able to specify different types of models (i.e., gls), so that we can offer this possibility while still using the lovely emmeans package.

    see for instance

    I feel like the default behavior of emmeans ought to be respected (it makes sense to have pooled errors for followup tests if the original model is also using the pooled error term), hence the pooled error term is the default option. Does this clarify the issue for you?

    Kind regards,


  • Hi @JohnnyB ,

    Would you also advise pool error terms for simple main effects? E.g., in a RM ANOVA, you have a sig. interaction between the RM factor (A) and the between-subjects factor (B) and you follow-up this interaction with simple main effects in which A is the simple effect factor and B the moderator.



  • Hi Tomas,

    Yes, I would use the pooled error term by default, since that is in line with the anova model. Only if you have substantial grounds for doing otherwise, I would switch to unpooled.

    Kind regards


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