S4 class-based extension mechanism

[gustavdelius]

Make functions that extension packages may want to change into methods. This includes all functions whose first argument is either a MizerParams or a MizerSim object. Extension packages would then create subclasses of these classes to dispatch their own methods.

[gustavdelius]

I am not yet sure whether we want to use S4 or S3. Even though MizerParams and MizerSim are S4 classes, we can still dispatch via the S3 mechanism, as the following demonstrates:

library(mizer)

setGeneric("test", function(params) standardGeneric("test"))

setMethod("test", "MizerParams", function(params) {
    params@initial_n[1, 1]
})

test(NS_params)

setClass("testParams",
         contains = "MizerParams")

setTest <- function(params) {
    as(params, "testParams")
}

NS_params_test <- setTest(NS_params)

setMethod("test", "testParams", function(params) {
    summary(params)
})

test(NS_params_test)

[gustavdelius]

@SamikDatta has just illustrated to me in an email why we need to use method dispatch for the mizer extension mechanism: currently two expansion packages that define their own rate functions which in turn utilise the mizer rate functions do not compose. The example Samik gives is therMizer not working together with mizerMR