In klmr/roxydoxy: Documentation for non-package R code

knitr::opts_chunk$set(comment = "#>", collapse = TRUE)

The package NAMESPACE is one of the most confusing parts of building a package. Roxygen2 aims to make it as easy as possible to build a package that is a well-behaved member of the R ecosystem. This is a little frustrating at first, but soon becomes second-nature.

Exports

For a function to be usable outside of your package, you must export it. By default roxygen2 doesn't export anything from your package. If you want an object to be publically available, you must explicitly tag it with @export.

Use the following guidelines to decide what to export:

Functions: export functions that you want to make available. Exported functions must be documented, and you must be cautious when changing their interface.
Datasets: all datasets are publicly available. They exist outside of the package namespace and should not be exported.
S3 classes: if you want others to be able to create instances of the class @export the constructor function.
S3 generics: the generic is a function so @export if you want it to be usable outside the package
S3 methods: every S3 method must be exported, even if the generic is not. Otherwise the S3 method table will not be generated correctly and internal generics will not find the correct method.
S4 classes: if you want others to be able to extend your class, @export it. If you want others to create instances of your class, but not extend it, @export the constructor function, but not the class.

```R # Can extend and create #' @export setClass("A")

# Can extend, but constructor not exported #' @export B <- setClass("B")

# Can create, but not extend #' @export C C <- setClass("C")

# Can create and extend #' @export D #' @exportClass D D <- setClass("D") ```
S4 generics: @export if you want the generic to be publicly usable.
S4 methods: you only need to @export methods for generics that you did not define. But @exporting every method is a good idea as it will not cause problems and prevents you from forgetting to export an important method.
RC classes: the same principles apply as for S4 classes. @export will only export the class.

Imports

The NAMESPACE also controls which functions from other packages are made available to your package. Only unique directives are saved to the NAMESPACE file, so you can repeat them as needed to maintain a close link between the functions where they are needed and the namespace file.

If you are using just a few functions from another package, the recommended option is to note the package name in the Imports: field of the DESCRIPTION file and call the function(s) explicitly using ::, e.g., pkg::fun(). Alternatively, though no longer recommended due to its poorer readability, use @importFrom, e.g., @importFrom pgk fun, and call the function(s) without ::.

If you are using many functions from another package, use @import package to import them all and make available without using ::.

If you want to add a new method to an S3 generic, import it with @importFrom pkg generic.

If you are using S4 you may also need:

@importClassesFrom package classa classb ... to import selected S4 classes.
@importMethodsFrom package methoda methodb ... to import selected S4 methods.

To import compiled code from another package, use @useDynLib

@useDynLib package imports all compiled functions.
@useDynLib package routinea routineb imports selected compiled functions.
Any @useDynLib specification containing a comma, e.g. @useDynLib mypackage, .registration = TRUE will be inserted as is into the the NAMESPACE, e.g. useDynLib(mypackage, .registration = TRUE)