Testing different approaches for replacing characters with integers. https://stackoverflow.com/q/65227663/1270695

65227663.R

## If your replacement is just a sequence of integers the length of the unique values being factored,
##   you can create a function like this which should be quite fast.
fac2int <- function(x, levels, labels = levels, exclude = NA, ordered = is.ordered(x), nmax = NA) {
  as.integer(factor(x, levels, labels, exclude, ordered, nmax))
}

### DIFFERENT APPROACHES TO TEST

fun_datamatrix <- function() {
  df[] <- data.matrix(as.data.frame(lapply(df, factor, levels = df2$Group)))
  df
}
fun_match <- function() {
  df[] <- df2$Value[match(unlist(df), df2$Group)]
  df
}
fun_lapply <- function() {
  df[] <- lapply(df, function(x) 
    as.integer(as.character(factor(x, levels = df2$Group, labels = df2$Value))))
  df
}
fun_matrix <- function() {
  df[] <- as.integer(as.character(factor(as.matrix(df), levels = df2$Group, 
                                         labels = df2$Value)))
  df
}
fun_dplyr <- function() {
  df <- df %>% mutate(across(.fns = ~df2$Value[match(., df2$Group)]))
  df
}
fun_fac2int <- function() {
  df[] <- lapply(df, fac2int, levels = df2$Group)
  df
}

### MAKE SOME LARGER SAMPLE DATA
                 
nrow <- 10000
ncol <- 100
set.seed(1)
df <- setNames(data.frame(replicate(ncol, sample(c(sample(c(letters, LETTERS), 20), NA), nrow, TRUE), 
                          simplify = FALSE)), paste0("V", sequence(ncol)))
df2 <- data.frame(Group = c(letters, LETTERS), Value = 1:52)

### BENCHMARK THE DIFFERENT APPROACHES
                 
bench::mark(fun_datamatrix(), fun_match(), fun_lapply(), fun_matrix(), fun_dplyr(), fun_fac2int())
# # A tibble: 6 x 13
#   expression            min   median `itr/sec` mem_alloc `gc/sec` n_itr  n_gc
#   <bch:expr>       <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl> <int> <dbl>
# 1 fun_datamatrix() 809.35ms 809.35ms     1.24     77.5MB     4.94     1     4
# 2 fun_match()         1.86s    1.86s     0.538   103.6MB     1.62     1     3
# 3 fun_lapply()     689.02ms 689.02ms     1.45     38.9MB     1.45     1     1
# 4 fun_matrix()     915.66ms 915.66ms     1.09    111.4MB     3.28     1     3
# 5 fun_dplyr()       284.5ms 326.96ms     3.06     19.8MB     1.53     2     1
# 6 fun_fac2int()     99.83ms 184.53ms     5.97     31.3MB     4.48     4     3
# # … with 5 more variables: total_time <bch:tm>, result <list>, memory <list>,
# #   time <list>, gc <list>