switch to directly calculated growth rate and extend model options

[sbfnk]

This PR is meant to supersede #213 and #214. It

• finalises the work commenced in #214 to support three different models
• merges #214 into #213 and implements most of the suggestions made there by @hsbadr
• rebases #213 onto current master
• works with default options and a simple example (the README)

Things left to do:

• [ ] expose and document the model options and ensure the stan model options are set consistently
• [ ] more extensive testing
• [ ] update NEWS