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The model lmer(Y ~ 0 + A + B + C + (0 + B | A) does indeed have three fixed effects and a single random slope. I would write this model (using a vectorized notation) as $$ Y = \beta_{a} A + (\beta_b …

I have a different way of looking at the problem. I think you can use binom.test here, but you have not invoked the command correctly. You should use x = 214 (the number of heads observed in the exper …

lme fits linear mixed models, not non-linear ones. For certain types of non-linear mixed models, you can use nlme. If area is nested in the levels of id, you can use the code model = lme(dv ~ inte …

Gene is a factor with three levels. You can confirm this by checking levels(factor(data$gene)). The reference level is rolled into the intercept term, and the coefficients corresponding to the other t …

Add more protected names pi <- 3 should probably not be allowed.

Bring data.table like syntax to data.frame data.table's syntax (DT[i, j, by]) is so useful and such a faithful extension of data.frame that it should just be built in at this point. (If we are willing …

The help page for R's aov function states: The default ‘contrasts’ in R are not orthogonal contrasts, and aov and its helper functions will work better with such contrasts: see the examples for how to …

The default optimization criterion of lme is restricted maximum likelihood (REML). REML is not compatible with likelihood ratio tests. You need to refit your models with maximum likelihood, method = " …