I have a mixed effects model with 3 explanatory factors and a full interaction set (including 3 way interaction). This is the full model. Factor 1 is time and I am interested in the change in the response variable over time. Therefore, only factors or interactions where time is present are biologically relevant.

My questions are: 1) Is it better to begin model simplification by removing the highest order (3-way) interaction first, or by removing the least significant term first (which in this case is factor 2)? The 3 way interaction does actually have a relevant interpretation. I have seen both options proposed.

2)Is it okay to include interactions but remove their basic factors (IE include time x treatment when treatment alone is removed from the model)? Several of the basic factors make no sense when not interacting with time. IE measuring the effect of treatment when you are excluding time doesn't make much sense since starting conditions inside each treatment level are identical.

If my hypothesis is correct the final model should include several factor interactions but should not include basic factor 2 or 3 (as they make no sense in the absence of the time factor).

Thank you for your help. I am happy to clarify if my question is ambiguous.


Except in very unusual cases, you should not remove an effect and leave-in any effects that contain it. So if you find that the $AB$ interaction is significant, then don't throw out the main effects of $A$ or $B$. Similarly, don't keep $ABC$ and throw out $AB$, or $B$, or any other main effect or two-way interaction involving those three factors.

So, I recommend reading the ANOVA table from the bottom up. You can throw out stuff at the bottom to simplify the model, and work upward, keeping this effect hierarchy in mind.

To see, why, consider a simple illustration, where $A$ and $B$ both have two levels. Let $\mu_{ij}$ denote the expected response at the $i$th level of $A$ and the $j$th level of $B$. If you think that $A$ and $B$ interact, you are saying that the $A$ effects depend on $B$ and vice versa; and this is essentially the same as saying the the combinations of $A$ and $B$ should be regarded as levels of one factor (having 4 levels in this example). As such, the effects of this 4-level factor are quantified as contrasts $c_{11}\mu_{11}+c_{12}\mu_{12} + c_{21}\mu_{21} + c_{22}\mu_{22}$, where the $c_{ij}$ sum to zero. But if you exclude $A$ from the model, you are saying that the $A$ effect, $\{(\mu_{11}+\mu_{12}) - (\mu_{21}+\mu_{22})\}/2$ is equal to zero---thus limiting the contrasts you are willing to consider. Put another way, the four-level factor determined by the levels of $A$ and $B$ together has 3 degrees of freedom, but the interaction effect $AB$ has only 1 d.f.; the other two d.f. are covered by the $A$ and the $B$ main effects.

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  • $\begingroup$ I fully agree, but was hoping to see some account of the reasons for these rules in your answer. Although your (real-world) reputation lends weight to anything you might recommend, it is always better to appeal to objective reasons in support of any answer. $\endgroup$ – whuber Jan 6 '15 at 16:34
  • $\begingroup$ Thank you for the quick answer. Out of curiosity, in what situations would it be acceptable to remove main effects but retain interactions? $\endgroup$ – MANOVAboard Jan 6 '15 at 17:59
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    $\begingroup$ To @MANOVAboard, I put it that way because I naturally hedge on making absolute statements. I can't think of a good example right now, but I can imagine somebody has one. It'd be a case where there is an inherent meaning to some interaction effect independent of one or more of the main effects containing it. Perhaps some kind of synergistic scenario or something. $\endgroup$ – Russ Lenth Jan 6 '15 at 18:19
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    $\begingroup$ Well, I can see both sides. If you have a viable scientific theory, then that trumps any statistical convention. However, if your theory is even slightly approximate, you can get into a mess by following it literally. What comes to mind are instances where people fit regression lines through the origin, based on the theory that the trend should be zero at zero. However, if all the data are all way out in right field, that origin constraint has a huge amount of leverage -- and the fitted trend, viewed local to the data actually at hand, can be totally ridiculous. $\endgroup$ – Russ Lenth Jan 6 '15 at 19:08
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    $\begingroup$ Thank you both for the enlightening conversation. I have re-run the model taking out highest order (non-significant) interactions first and have settled on a model with a Time:Factor3 interaction. Interestingly Factor 2 dropped out of all interactions and eventually the main effect itself was removed. I arrived at a very different model this way but have more confidence in it. $\endgroup$ – MANOVAboard Jan 6 '15 at 19:51

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