correct formatting for repeated measures ANOVA

abmayfield

I sat in on an interesting webinar by Jian Cao a few weeks ago on using the mixed model platform, during which I learned that you actually don't need to set up repeated measures ANOVA designs under MANOVA. This opens up more flexibility, so I wanted to try it. I have a series of corals ("pucks" in the attached data file) that were repeatedly measured (as color) over time, and I was interested in testing for the fixed effects of treatment (two temperatures), genotype (5-6 genotypes), time (calendar dates), and their interaction. I know how to do this under the MANOVA platform, but if I add the two fixed effects to the mixed model platform, then "Date" as the repeated measure, one of two things happens. It either ONLY gives the output of the fixed effects (i.e., NOT the effect of time), OR, if I include "Date" as a fixed factor as well, it causes it to crash, potentially since the software sees "Date" in two places. What Jian evidently did was trick JMP by calling "Date" something else in his example. I think he had "Time" (which was date x time) as the repeated measure and then "Date" (=date only) as a fixed factor. Surely I don't actually have to do recode a dummy variable like this every time?! I guess I could recode "Date" to "experiment day" and then have "date" be the repeated measure and "experiment day" be in the fixed factor model, but it seems like there must be a simpler way. In other words, how do I set it up under the mixed model platform to where I also get the time effect (as can be done under the MANOVA platform)? Or maybe interaction effects with the repeated measure are NOT possible under mixed model (and only with MANOVA)? 

May 2020 color scores.jmp

jiancao

Hi, Anderson,

 

You can use both Date as a fixed effect and as a repeated column in mixed models.  However, in your case, when you add Date, Treatment, Genotype and their interactions as fixed effect JMP warns that there are linear dependencies among the fixed effects ( I used Average column from your data as Y). This does not seem to have to do with the mixed models; you would receive the same warning when you just run a Standard Least Squares model as shown below.  If you only add the three main effects the mixed models will run.

I don’t know what exactly causes the linear dependencies, but I see you had an unbalanced design. In my repeated measures example from a balanced design, I have no problems running the model with the main effects and interactions using the calendar dates both as a fixed effect and a repeated column.  (Note that in my example I labeled the calendar date as Time.)

The trick you mentioned me saying is that when you select AR(1) as the repeated structure the repeated column must be continuous, so I created a continuous Days column from the original Time column.