You could use the enhanced dcast function from the data.table package for that where you can select multiple value variables. With setDT(mydf) you convert your dataframe to a datatable and with [, idx := 1:.N, by = ID] you add a index by ID which you use subsequently in the dcast formula:
library(data.table)
dcast(setDT(mydf)[, idx := 1:.N, by = ID], ID ~ idx, value.var = c("x","y"))
Or with the development version of data.table (v1.9.7+), you can use the new rowid function:
dcast(setDT(mydf), ID ~ rowid(ID), value.var = c("x","y"))
gives:
ID x_1 x_2 x_3 y_1 y_2 y_3
1: a 1 1 2 2 4 3
2: b 1 3 NA 3 2 NA
3: c 2 NA NA 4 NA NA
4: d 1 NA NA 3 NA NA
Used data:
mydf <- structure(list(x = c(1L, 1L, 2L, 1L, 1L, 3L, 2L), y = c(2L, 3L,
4L, 3L, 4L, 2L, 3L), ID = structure(c(1L, 2L, 3L, 4L, 1L, 2L,
1L), .Label = c("a", "b", "c", "d"), class = "factor")), .Names = c("x",
"y", "ID"), class = "data.frame", row.names = c(NA, -7L))
