Connect functions of DD with those of Shiny App

[fhoces]

So far the app and dynamic doc produce the same analysis, but that analysis is performed using a different function. So if something changes in the DD, it will not be reflected in the app.

To achieve a higher level of transparency and reproducibility we need to have both running on the same functions.

This will probably entail two big tasks:

• Make code from app more compact and readable.

• Wrap each step of the DD into a function. With the following structure:

dd_overall_chunk_functions{
    ...
    functions_in_common_dd_and_app{
        ...
    }
    ...
} 

• Make the relevant functions in the in the app with the following structure:

shiny_app_functions{
    ...
    functions_in_common_dd_and_app{
        ...
    }
    ...
}