Rename GetPermuteMatrix -> getPermuteMatrix

grep -rl GetPermuteMatrix R/ | xargs \
  sed -i 's/GetPermuteMatrix/getPermuteMatrix/g'

and the same for man/. You don't want to do this recursiverly for .,
because that would mess with .git/index. T

This needs GNU grep, xargs and sed: did not work in MacOS (BSD).