[R-pkg-devel] Question on proper methods documentation for R package with multiple S4 classes

[Ioana Bouros]

Hello,


We are trying to build an R package with more than two S4 classes that have common methods. However, when checking the methods part of the documentation for the second class, we see only the definition of the generic of the first class.


For illustration, we can call these two classes `Myclass` and `Mynewclass` which have similarly named methods `parameters` and `parameters<-`


```

#' Example docstring of Myclass

#'

#' @slot parameters_names names of the parameters which are used by the

#'     model.

#' @slot parameters parameters which are used by the

#'     model.

#'

#' @import tidyverse

#' @import reshape2

#' @importFrom methods new

#' @export Myclass

#'

Myclass <- setClass('Myclass',

                    # slots

                    slots = c(

                      parameters_names = 'list',

                      parameters = 'list'

                    ),



                    # prototypes for the slots, automatically set output and param

                    # names

                    prototype = list(

                      parameters_names = list('a', 'b'),

                      parameters = vector(mode = "list", length = 2)

                    )

)


# Setter and getter methods for parameters


#' Retrieves parameters Myclass.

#'

#' @param object An object of the class Myclass.

#'

#' @return parameter values of Myclass.

#' @export

setGeneric('parameters',

           function(object) standardGeneric('parameters'))


#' @describeIn Myclass Retrieves parameters Myclass.

#'

#' @param object An object of the class Myclass.

#'

#' @return parameter values of Myclass.

#' @aliases parameters,ANY,ANY-method

#' @export

setMethod('parameters', 'Myclass',

          function(object) object using parameters)


#' Sets parameters of Myclass,

#'

#' @param object An object of the class Myclass

#' @param value a named list of (a, b).

#'

#' @return Updated version of Myclass.

#' @export

setGeneric(

  'parameters<-',

  function(object, value){

    standardGeneric('parameters<-')

  })


#' @describeIn Myclass Sets parameters of Myclass.

#'

#' @param object An object of the class Myclass.

#' @param value a named list of (a, b).

#'

#' @return Updated version of Myclass.

#' @aliases parameters<-,ANY,ANY-method

#' @export

setMethod(

  'parameters<-', 'Myclass',

  function(object, value) {

    a = value$a

    b = value$b

    ic <- list(a, b)

    # if all above tests are passed, assign the ic namelist to the object

    object using parameters <- ic



    return(object)

  })

```

 and


```

#' Example docstring of Mynewclass

#'

#' @slot parameters_names names of the parameters which are used by the

#'     model.

#' @slot parameters parameters which are used by the

#'     model.

#'

#' @import tidyverse

#' @import reshape2

#' @importFrom methods new

#' @export Mynewclass

#'

Mynewclass <- setClass('Mynewclass',

                    # slots

                    slots = c(

                      parameters_names = 'list',

                      parameters = 'list'

                    ),



                    # prototypes for the slots, automatically set output and param

                    # names

                    prototype = list(

                      parameters_names = list('a', 'b', 'c'),

                      parameters = vector(mode = "list", length = 3)

                    )

)


# Setter and getter methods for parameters


#' @describeIn Mynewclass Retrieves parameters Mynewclass.

#'

#' @param object An object of the class Mynewclass.

#'

#' @return parameter values of Mynewclass.

#' @aliases parameters,ANY,ANY-method

#' @export

setMethod('parameters', 'Mynewclass',

          function(object) object using parameters)


#' @describeIn Mynewclass Sets parameters of Mynewclass.

#'

#' @param object An object of the class Mynewclass.

#' @param value a named list of (a, b, c).

#'

#' @return Updated version of Mynewclass.

#' @aliases parameters<-,ANY,ANY-method

#' @export

setMethod(

  'parameters<-', 'Mynewclass',

  function(object, value) {

    a = value$a

    b = value$b

    c = value$c

    ic <- list(a, b, c)

    # if all above tests are passed, assign the ic namelist to the object

    object using parameters <- ic



    return(object)

  })

```


It might be worth mentioning that keeping the generics for both classes led to problems in the `devtools::document()` command, as seen in the following StackOverflow question [https://stackoverflow.com/questions/68113799/how-can-you-create-multiple-s4-classes-with-similarly-named-methods-in-r]


How could we solve this issue without having to give different names for the methods?


Many thanks,

Ioana


PS. The link to the relevant branch of the Github repository is below:

[https://github.com/Como-DTC-Collaboration/como-models/tree/i4-age-structure]


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