We need to make sure all functions accept tbl_df objects

[Jason Vander Heiden]

I fixed a few bugs that appeared when dplyr::tbl_df object is passed into a function instead of a data.frame, but I'm sure there are many more waiting to be found.

[Jason Vander Heiden]

This basically means changing every instance of df[, column_name] to df[[column_name]]

[Namita Gupta]

Which can be easily addressed by searching for [, and [ , in all the .R files of shm

[Namita Gupta]

I think I fixed it, but currently can't check.

[Namita Gupta]

All examples still worked correctly with changes