Reduce code duplication by using more general functions in the back-end

[richelbilderbeek]

Feedback bjoelle:

Structure

• The structure is my main concern with this package, as it contains a lot of code duplication and many functions need to run through all possible types of a certain object to figure out what to do with it. I think this makes the package hard to maintain and to extend to additional models.

The main issue [...] (see #38)

Separating the different parameters (alpha, beta, gamma, etc) also leads to a lot of code duplication. It is useful for creating parameters as their default priors are different, but I would remove it for the other functions: the many functions is_%sth%_param(x) can be replaced by one function is_named_param(x, name) and the parameter_to_xml functions also have a lot of redundancy.

[richelbilderbeek]

For the is_*_param case: bjoelle has a point, see for example:

is_alpha_param <- function(
  x
) {
  if (!is_param(x)) return(FALSE)
  x$name == "alpha"
}

I do easily see that I can reduce those two lines to one, but I do not think it's worth it for three reasons:

1. the functions this applies to are still trivially simple
2. not all functions are as simple, for example:

is_kappa_1_param <- function(
  x
) {
  if (!is_param(x)) return(FALSE)
  if (x$name != "kappa_1") return(FALSE)

  if (!"lower" %in% names(x)) return(FALSE)
  if (!"value" %in% names(x)) return(FALSE)
  if (!"estimate" %in% names(x)) return(FALSE)
  TRUE
}

3. It reflects the current state of the package: not all parameters have a lower, upper, or estimate argument yet

I do predict in the future these is_*_param functions will get the same shape. At the current state, I think it's not worth it to refactor the is_*_param functions.

[richelbilderbeek]

Likewise for parameter_to_xml_*: it reflects the state of the package.

Note how this ties in with #45.

[richelbilderbeek]

I feel that bjoelle is right, yet it should and can be done as suggested if and only if the package is in a finished state. Because the package is not yet complete, this Issue must be moved to the future and potentially re-opened then.