replace use of subset() throughout package with standard subsetting functions

[atn38]

According to subset() documentation and general R programming resources, subset() is better used interactively than in programs. This is due to its non-standard evaluation (need to understand more what it means).

Replace use of subset() in the package with [ and [[. $ is also not ideal, as it allows partial matching.

[atn38]

in progress. ditto with dollar sign subsetting $