Replace missing values in a matrix with 1/2 of the minimum value of each row (in R)

impute_half_minimum.R

library(checkmate)

# Replace missing values in a matrix with 1/2 of the minimum value of each row
m <- matrix(1:9, ncol = 3)
m[1, 3] <- NA
m[3, 1] <- NA
m

impute_half_minimum <- function(m, verbose = TRUE) {
  checkmate::assert_matrix(m)
  checkmate::assert_flag(verbose)
  na_positions <- is.na(m)
  if (any(na_positions)) {
    replacement_val <- apply(m, 1, min, na.rm = TRUE) / 2
    # rows without valid values yield an Inf replacement_val, reset those to NA
    replacement_val[!is.finite(replacement_val)] <- NA
    # look up the replacement value for each row
    insert_val <- replacement_val[row(m)[na_positions]]
    # if there are any valid replacement values, insert them
    n_valid_insert_val <- sum(!is.na(insert_val))
    if (isTRUE(verbose) & n_valid_insert_val > 0) {
      message("Replacing ", n_valid_insert_val, " missing measurements",
              " with 50% of the smallest observed value for that row." )
    }
    m[na_positions] <- insert_val
  }
  return(m)
}

n <- impute_half_minimum(m)
stopifnot(n[1, 3] == 0.5)
stopifnot(n[3, 1] == 3)