cosmetic/cleanup

[bbolker]

This will be a catch-all for minor cosmetic/methods issues. It can be updated by ~crossing off~ items in the list, or by commenting.

• make sure state vars are factorized consistently in an appropriate order
• write_params should save descriptions where available (stored in attr(.,"description"))
• set up a dictionary definition and better labels for graphs (e.g. "D" -> "Deaths")
• pretty-print parameters:
  • e.g. detect "1/" in description and format as sprintf("1/%f",1/x)
  • describe_params should have an option to display mean stage durations rather than rates
• include starting dates as metadata where appropriate (E0 is conditional on a starting date)
• make param_timevar less fussy about capitalization etc. of columns (tolower() everything?)
• clean up and document date formats: anything allowed but y-m-d preferred