Resolve package check warnings

[gfinak]

While I'm aware we're still in early development, the state of the package docs make it next to impossible to collaborate.
I've done a bit of work to clean it up, but there are still many issues visible via R CMD check.

• Undocumented code objects.
  • since we're using S3, do the S3 object specific methods even need to be exported? Can we just export the default methods and have those dispatch correctly?
• Undocumented parameters
  • signatures differ between many default methods and their object specific methods.
    • We need to make sure all of the parameters are documented correctly and unambiguously, and the appropriate usage sections are in place.
• No object documentation for S3 objects.
  how do the pieces fit together?

Addressing these now and keeping the docs up to date will save time and trouble later.