Custom function to compute contrasts in emmeans - r

Question

I want to create a custom contrast function in emmeans which could remove a given list of levels from the input vector and apply the built-in contrast method ("trt.vs.ctrl") on the remaining levels. An example dataset is available here. I am using the following R code for computing ANOVA and post hoc comparisons:
options(contrasts=c("contr.sum", "contr.poly"))
my_lm <- lm(D1 ~ C*R, data=df)
Anova(my_lm, type = "III")
#show Interaction effects using emmeans
emmip(my_lm, C ~ R )
emm = emmeans(my_lm, ~ C * R)
emm
contrast(emmeans(my_lm, ~ C * R), "consec", by = "C")
#compare 1st with next 3 groups (how to remove other three levels?)
contrast(emmeans(my_lm, ~ C * R), "trt.vs.ctrl", by = "R")
The built-in contrast option ("trt.vs.ctrl") compares the first level with everything that follows it (there are 7 factor levels in C, and I want to remove last 3 of them and compute the contrasts for the remaining 4). An example is provided in the official documentation to write a custom contrast function.
skip_comp.emmc <- function(levels, skip = 1, reverse = FALSE) {
if((k <- length(levels)) < skip + 1)
stop("Need at least ", skip + 1, " levels")
coef <- data.frame()
coef <- as.data.frame(lapply(seq_len(k - skip - 1), function(i) {
sgn <- ifelse(reverse, -1, 1)
sgn * c(rep(0, i - 1), 1, rep(0, skip), -1, rep(0, k - i - skip - 1))
}))
names(coef) <- sapply(coef, function(x)
paste(which(x == 1), "-", which(x == -1)))
attr(coef, "adjust") = "fdr" # default adjustment method
coef
}
However due to my limited understanding I am not very sure where to apply the modifications that I need to to customise the example. Any ideas?

Answer 1

Is this something you are going to want to do lots of times in the future? My guess is not, that you only want to do this once, or a few times at most; in which case it is way too much trouble to write a custom contrast function. Just get the contrast coefficients you need, and use that as the second argument in contrast.
Now, consider these results:
> con <- emmeans:::trt.vs.ctrl.emmc(1:7)
> con
2 - 1 3 - 1 4 - 1 5 - 1 6 - 1 7 - 1
1 -1 -1 -1 -1 -1 -1
2 1 0 0 0 0 0
3 0 1 0 0 0 0
4 0 0 1 0 0 0
5 0 0 0 1 0 0
6 0 0 0 0 1 0
7 0 0 0 0 0 1
From the description, I think you just want the first 3 sets of contrast coefficients. So use those columns:
contrast(emm, con[, 1:3], by = "R")
Update
StackOverflow can occasionally inspire developers to add software features. In this case, I decided it could be useful to add an exclude argument to most built-in .emmc functions in emmeans (all except poly.emmc()). This was fairly straightforward to do, and those features are now incorporated in the latest push to github -- https://github.com/rvlenth/emmeans. These features will be included in the next CRAN update as well.