Changed to package format

autogenerated by devtools::create
commented out contents

was breaking package loading. would be better as a demo
More package setup
Bug fixes:

-documentation error in GDMO.R
-negation wasn't working right in reproduce.R
-runscript.R:
  -changed `start` to `ancestors` for clarity
  -`ancestors` initialized as a list of lists
  -indexing was a bit weird