Move functions from Rmd to trias package

[damianooldoni]

As @amyjsdavis noticed, it's time to move some functions she uses in her modelling to trias package.
This means:

1. make functions robust
2. document them
3. test them

First thing to do, @amyjsdavis, is list them before deciding which ones are worth to be moved and which ones are just very small help functions which can be left in the Rmd.

I can provide assistance on all these steps.