What should the maximum number of parameters on {episoap} templates be?

[CarmenTamayo]

The transmissibility pipeline currently has 10 parameters that the user can modify. As more parameters are added, e.g., to select specific studies within the {epiparameter} database or to specify the source of data using {readapi}, the flexibility of the templates increases, but so does the complexity for the users.

This issue is to keep track of the discussions and decisions made about this topic in {episoap}.

For now, @Bisaloo and myself have agreed to keep the template as it is, in its somewhat more rigid format (when compared to other, more modular approaches), with the intention of providing a resource that's readily available for users to test and provide feedback.
The next step for deciding a manageable number of parameters is to check how many will be needed for the severity pipeline, and compare this number to that of the transmissibility pipeline.

[Bisaloo]

Two updates & new requirements on this:

• we should make sure parameter names are harmonized across templates
• we need to take into account "hidden" parameters, and also decide what to do with them. E.g., column names in

  episoap/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd

  Lines 306 to 311 in 0c525bd

  	date_var <- "date"
  	group_var <- "region"
  	# Leave count_var as NULL if the data is really a linelist / patient-level data.
  	# Update count_var to a character string with the name of the column if the data
  	# is already aggregated.
  	count_var <- NULL