nlme model specification and estimation of empty cells using emmeans

Question

I have a data set with 20 users who were exposed to three levels and two variants (except the low level was only exposed to one variant). There are two measurements for each combination. Below are example data for one user:

I know the two measurements are correlated for the same user, level and variant (not in this example data) so I'm imposing an AR1 structure. Below is the lme model and estimation of interactions I'm interested in using the emmeans package.

Two questions:

1. Am I specifying the correlation structure correctly given I expect scores within user, level, and variant to be correlated?
2. How does the emmeans function produce an estimate for level = low and variant = B when that combination is not even in the data.

Full code for reproducibility:

library(tidyverse)
library(nlme)
library(emmeans)

NUM_USERS=20
save_list=list()

for(i in 1:NUM_USERS){
  
  user=paste0("ID_",i)
  save_list[[i]]=tibble(user,level=c(rep("high",4),rep('med',4),rep("low",2)),
                         variant=c(rep(c("A","B"),times=2,each=2),"A","A"),
             score_num=rep(c("one","two"),5),score=rnorm(10,20,5))
  
}

a1 = bind_rows(save_list) 

fit=lme(score~score_num*level+variant*score_num,random=~1|user,
         correlation=corAR1(form=~1|user/level/variant),data=a1)

emmeans(fit,pairwise~score_num|variant*level)

Answer 1

The answer to your second question is that those two factors do not interact in your model. Therefore the effects of those two factors are additive, meaning that we are assuming that the interaction effect between them is equal to zero. if your model had included the interaction between variant and level, then that missing combination would not have been estimable. Try it and see!