Мы можем использовать Map
для этого
Map(merge, mylist_a, mylist_b, MoreArgs = list(by = 0))
data
mylist_a <- list(aa = structure(list(D1 = c(52L, 103L, 15L, 3L, 1L, 0L),
D2 = c(41L, 111L, 12L, 2L, 1L, 0L), D3 = c(55L, 104L, 16L,
0L, 0L, 2L)), class = "data.frame", row.names = c("a", "b",
"c", "d", "e", "f")))
mylist_b <- list(aa = structure(list(D1 = c(0.68659264, 0.02358574, 1, 1,
1, 1), D2 = c(1, 0.0007992743, 1, 1, 1, 1), D3 = c(1, 0.3253237,
1, 1, 1, 1)), class = "data.frame", row.names = c("a", "b", "c",
"d", "e", "f")))