M-x ess-fix-miscellaneous
M-x ess-MM-fix-src

(query-replace ".Uminus" "-" nil nil nil)
(query-replace-regexp "^###" "##=" nil nil nil)

use builtin "pi" instead of "PI <- 3.14159"

added ^L after the main function

s/null()/NULL/
s/S-plus/S/

Comment out  x <- as.matrix(x, ncol = 1)
## It's unnecessary and  R does not allow `ncol' in as.matrix()

.Machine$single..  replaced by explicit numeric constants valid for IEEE arithm

Replace quite a few ' (single quotes) by " (double q.) or '..' by `..'