Document the full description of the methods towards a wider audience

[njtierney]

Write up a vignette that walks through the entire process and motivation for how conmat creates the contact matrices.

This should be written up in a way that is aimed at people who might not be as familiar with epidemiology. So, it will go into detail on what each of the steps in the model fitting does, what the polymod data is, and answer questions like:

• "What is a contact matrix"
• "How do I adjust contact matrices for my age population"
• "How do I estimate the impact of vaccination on spread"

This will involve fixing and simplifying the README, which is #35.

[njtierney]

Some thoughts on sections / topics to address

README

• [x] Why should we use conmat?
• [x] How do we use conmat?

Topics to address in a vignette called, "implementation details", which goes into greater depth of explaining various parts of the data analysis

• [x] What is a contact matrix?
• [x] Why are contact matrices used?
• [x] What is a contact survey? Provide details of what get_polymod_setting_data() and get_polymod_population() do
• [x] What is the goal of the example analysis in the README? Do we want to understand the number of people who might get COVID? What exactly does this type of analysis do
• [x] What does the fit_setting_contacts() function do? How does it do it? What does it use? Why do we use a GAM? Why are we predicting the number of contacts?
• [x] What does predict_setting_contacts() do? More clearly walking through that process of model fitting based on other models.
• [x] What does the final output of plot_setting_matrices() do? What do we learn from these matrices? What is the interpretation of these figures?
• [x] What does the next generation matrix do? What does generate_ngm() do? Why would we want to use it?
• [x] Why would we want to use:
  • [x] get_age_population_function()
  • [x] get_household_size_distribution()
  • [x] get_per_capita_household_size()
• [x] What does apply_vaccination() do?

[njtierney]

done in #78