# What is the intercept term in a mixed effects model using orthogonal polynomials to model time?

I'm using a mixed effects model (lmer) in R to model eye-tracking data using orthogonal polynomials (poly(time,3)) for time. The response variable is log(looks to target/looks to competitor). The fixed effects are condition, talker gender, accuracy, like so:

lmer(looks~(poly1+poly2+poly3)*condition*gender*accuracy+(1|stimulus)+(1|subject)


The polynomial time variables are of course, continuous (and centered), while the other factors are treatment coded so that each coefficient is compared to the baseline of the cells (where condition=0, gender=0, accuracy=0 (actually accuracy is recoded so that accurate trials are the baseline)). All of this is pretty much irrelevant because my question is more of a matter of mathematical interpretation.

I understand that the intercept reflects the estimate for the base level of each cell, but my question is-- what is the base level of the time polynomials? Mirman (2014) claims "For natural polynomials, the intercept term corresponds to the y-intercept [...] For orthogonal polynomials, the intercept term corresponds to the overall average [...] 'area under the curve'" (p. 48). While I don't claim to thoroughly understand mixed effects modeling (because matrix algebra!), it seems to me that the intercept should estimate a value for the zero points of the polynomials (so, at the midpoint of the linear time, at two points for the quadratic, and three points for the cubic, one of which is also the midpoint of the linear).

While it would be very convenient for me to pretend that this is the average, I can't make this claim while I am still confused about the math. Is there anyone who can explain to me whether my "5-point snapshot" hypothesis is correct, or if the intercept reflects the mean over time? I have no stake in which hypothesis is more accurate, but I don't want to misreport my results, and I would very much like to understand how mixed effects models work. Also, this is my first time posting a question here (though I've found many useful answers over the years), so please be kind even if you think I am completely stupid.

(Ref: Mirman, D. 2014. Growth Curve Analysis and Visualization Using R. CRC Press.)

• Take a look here: danmirman.org/gca May 15, 2017 at 18:36
• Here, again, Dan Mirman makes the claim that "With orthogonal polynomials, the intercept term reflects the average overall curve height, rather than the height at the left edge of the time window, so if you are interested in differences at the very beginning of the time window, you may be better off sticking with natural polynomials." But I don't understand how using orthogonal polynomials changes the intercept to reflect the mean over the entire time window, whereas raw polynomials follow the expected pattern of producing an intercept that represents the pattern at time zero. May 16, 2017 at 14:07

    lmer(looks~0+constant+(poly1+poly2+poly3)*condition*gender*accuracy+(1|stimulus)+(1|subject)

• This question does not seem to have anything to do with mixed models, right? If you kick out stimulus and subject random effects and use lm instead of lmer, your question about intercept would stay exactly the same. Mixed models might be just a complication that you are bringing in here. (I'm not saying that you should not be using mixed models! I am saying that they are irrelevant to the issue at hand.) Jun 16, 2017 at 7:16