I have two groups (A and B) each going through 5 repeated measures. I want to know how I can determine eta squared so that I can use it to calculate an a-priori sample size.
Before your study, estimate the effect size for your mixed ANOVA by reviewing similar research or using Cohen's conventions if no prior studies exist. Then, determine your sample size using G*Power, considering your desired power and significance level.
If you use the ezANOVA from the ez R package, you get the eta squared effect size. See the R script in attachment. It includes post hoc tests, nonparametric alternatives, and a figure.