How to run function on the deepest level only in a nested list?

We can recursively descend lst to find the maximum depth and then use that to recursively descend again applying unique only at the maximum depth. No packages are used.

maxDepth <- function(x, depth = 0) {
   if (is.list(x)) max(sapply(x, maxDepth, depth+1))
   else depth
}

lstUnique <- function(x, depth = maxDepth(x)) {
  if (depth == 0) unique(x)
  else if (is.list(x)) lapply(x, lstUnique, depth-1)
  else x
}

lstUnique(lst)

Variation using rapply

A variation of the above is to recursively add a class to each leaf equal to its depth. Then we can use rapply three times. First use rapply to extract the classes and take the maximum to find the maximum depth. second use rapply to apply unique on just the nodes having the maximum depth class. Third, remove any remaining classes that were not removed by unique because the node was not at maximum depth. (The third rapply, i.e. the last line of code below, could be omitted if it is ok to leave some leaves with the classes we added.)

addDepth <- function(x, depth = 0) {
  if (is.list(x)) lapply(x, addDepth, depth+1)
  else structure(x, class = format(depth))
}
lst2 <- addDepth(lst)

mx <- max(as.numeric(rapply(lst2, class))) # max depth
lst3 <- rapply(lst2, unique, classes = format(mx), how = "replace")
rapply(lst3, as.vector, how = "replace")

Note on rapply

Note that if you alternately wanted to run unique on all leaves rather than just on the maximum depth leaves then rapply in base R would work.

rapply(lst, unique, how = "replace")

data.tree

This alternative does require the use of a package. First we create a data.tree dt and then traverse it applying unique to the nodes that satisfy the filterFun.

library(data.tree)

dt <- as.Node(lst)
dt$Do(function(x) x$"1" <- unique(x$"1"), 
  filterFun = function(x) x$level == dt$height)
print(dt, "1")

rrapply

The rrapply package provides an enhancement to rapply which can also pass a position vector whose length equals the depth so we can use it first to calculate the maximum depth mx and then again to apply unique only at that depth. (Have updated rrapply call to use how = "unlist" as opposed to applying unlist afterwards as per suggestion in comments.)

library(rrapply)

mx <- max(rrapply(lst, f = function(x, .xpos) length(.xpos), how = "unlist"))
uniq_mx <- function(x, .xpos) if (length(.xpos) == mx) unique(x) else x
rrapply(lst, is.numeric, uniq_mx)