Things to change/tidy

[OJWatson]

• Tidy passing of parameters from create_r_model through the param list creation, i.e. don't have any params specified outside of through model_param_list ellipsis parse - OJ
• Remove the c versions as not being used - OJ
• Vignettes for functionality - OJ make 1 files, Ettie others
• Tidy up outputs of equilibrium_init_create (that's a silly list that is being returned). - Ettie (S_eq)
• equilibrium_init_create remove irrelevant code and comments - OJ

[OJWatson]

the state output of create_r_model can be edited to chnage the iniitial. THis should be done by the user with custom functions etc, rather than something internal to create_r_model. This should be documented and vignetted

[OJWatson]

Tests (testthat)

• Check intiial sooultion outputs against BM - Ettie DONE waiting to push
• Check adding new parmeters to model_param_list_create - OJ
• Basic funcitionality, does it break tests - OJ

[OJWatson]

Tidy up the versions of the odin models that are in the inst/extdata, Should really just have 2 to begin with:

1. The main one
2. A demo dummy one to show how to extend an odin model

These should be described in a vignette/wiki what they are for.

Then when someone has written an etension to the model, e.g. Hannah's IVM, this can then be pushed to inst/extdata when it's finished and we can update the wiki. Idea being that someone who arrives at the repo should read the vignette to know what all the odin models do:

1. odiin_model.R - base version
2. odin_model_dummy.R - demo dummy
3. odin_model_IVM - Extensions to the base model for modelling ivermectin, published in xxx etc.

[OJWatson]

Travis set up

[ettieunwin]

When edit how generator is written in generator_utils.R. Made sure age in equilibrium-init-create.R returns age not age_vector.

[ettieunwin]

wy does .data$value not work in run_model

[ettieunwin]

I think this issue can now be closed as all written as individual issues for easier tracking completion.