Expose missing methods defaultMethod and valueOf0 (#118)

* fix: expose defaultMethod and valueof0 * bump version * update codemeta * re-knit README * add news entry * add PR number * fix: typo
hsloot · Apr 18, 2024 · 801723b · 801723b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rmo
 Title: A package for the Marshall-Olkin distribution
-Version: 0.8.7
+Version: 0.8.8
 Authors@R:
   person(given = "Henrik",
     family = "Sloot",

diff --git a/NAMESPACE b/NAMESPACE
@@ -12,6 +12,7 @@ export(ParetoBernsteinFunction)
 export(PoissonBernsteinFunction)
 export(ScaledBernsteinFunction)
 export(SumOfBernsteinFunctions)
+export(defaultMethod)
 export(exIntensities)
 export(exQMatrix)
 export(intensities)
@@ -23,9 +24,11 @@ export(rpextmo)
 export(stieltjesDensity)
 export(uexIntensities)
 export(valueOf)
+export(valueOf0)
 exportClasses(BernsteinFunction)
 exportClasses(CompleteBernsteinFunction)
 exportClasses(LevyBernsteinFunction)
+exportMethods(defaultMethod)
 exportMethods(exIntensities)
 exportMethods(exQMatrix)
 exportMethods(intensities)
@@ -34,6 +37,7 @@ exportMethods(show)
 exportMethods(stieltjesDensity)
 exportMethods(uexIntensities)
 exportMethods(valueOf)
+exportMethods(valueOf0)
 importFrom(Rcpp,sourceCpp)
 importFrom(Rdpack,reprompt)
 importFrom(checkmate,assert)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,7 @@
 # rmo 0.9
 
+- Improve extensibility by exposing `defaultMethod` and `valueOf0` (#118)
+
 - Review and improve documentation (#116)
 
 - Re-organize S4 code and documentation (#117)

diff --git a/R/s4-AlphaStableBernsteinFunction.R b/R/s4-AlphaStableBernsteinFunction.R
@@ -192,9 +192,13 @@ setMethod(
   }
 )
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
 #' @include s4-valueOf0.R
 #' @importFrom checkmate assert qassert check_numeric check_complex
-#' @keywords internal
+#' @export
 setMethod(
   "valueOf0", "AlphaStableBernsteinFunction",
   function(object, x, cscale = 1, ...) {

diff --git a/R/s4-BernsteinFunction.R b/R/s4-BernsteinFunction.R
@@ -192,20 +192,6 @@ setClass("BernsteinFunction", # nolint
 #' @docType methods
 NULL
 
-
-#' @include s4-valueOf0.R s4-valueOf.R
-#' @importFrom methods setMethod
-#' @keywords internal
-setMethod(
-  "valueOf0", "BernsteinFunction",
-  function(object, x, cscale = 1, ...) {
-    valueOf(
-      object, x,
-      difference_order = 0L, n = 1L, k = 0L, cscale = cscale, ...
-    )
-  }
-)
-
 #' @rdname hidden_aliases
 #'
 #' @inheritParams uexIntensities

diff --git a/R/s4-CompositeScaledBernsteinFunction.R b/R/s4-CompositeScaledBernsteinFunction.R
@@ -88,6 +88,19 @@ setMethod( # nocov start
   }
 ) # nocov end
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
+#' @include s4-valueOf0.R
+#' @export
+setMethod(
+  "valueOf0", "CompositeScaledBernsteinFunction",
+  function(object, x, cscale = 1, ...) {
+    valueOf(object, x, cscale = cscale)
+  }
+)
+
 #' @rdname hidden_aliases
 #'
 #' @inheritParams valueOf

diff --git a/R/s4-ConstantBernsteinFunction.R b/R/s4-ConstantBernsteinFunction.R
@@ -99,6 +99,19 @@ setMethod( # nocov start
   }
 ) # nocov end
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
+#' @include s4-valueOf0.R
+#' @export
+setMethod(
+  "valueOf0", "ConstantBernsteinFunction",
+  function(object, x, cscale = 1, ...) {
+    valueOf(object, x, cscale = cscale)
+  }
+)
+
 #' @rdname hidden_aliases
 #'
 #' @inheritParams valueOf

diff --git a/R/s4-ConvexCombinationOfBernsteinFunctions.R b/R/s4-ConvexCombinationOfBernsteinFunctions.R
@@ -135,6 +135,19 @@ setMethod( # nocov start
   }
 ) # nocov end
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
+#' @include s4-valueOf0.R
+#' @export
+setMethod(
+  "valueOf0", "ConvexCombinationOfBernsteinFunctions",
+  function(object, x, cscale = 1, ...) {
+    valueOf(object, x, cscale = cscale)
+  }
+)
+
 #' @rdname hidden_aliases
 #'
 #' @inheritParams valueOf

diff --git a/R/s4-ExponentialBernsteinFunction.R b/R/s4-ExponentialBernsteinFunction.R
@@ -181,17 +181,25 @@ setMethod(
   }
 )
 
-#' @keywords internal
+#' @rdname hidden_aliases
+#'
+#' @inheritParams defaultMethod
+#'
+#' @export
 setMethod(
   "defaultMethod", "ExponentialBernsteinFunction",
   function(object) {
     "stieltjes"
   }
 )
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
 #' @include s4-valueOf0.R
 #' @importFrom checkmate assert qassert check_numeric check_complex
-#' @keywords internal
+#' @export
 setMethod(
   "valueOf0", "ExponentialBernsteinFunction",
   function(object, x, cscale = 1, ...) {

diff --git a/R/s4-GammaBernsteinFunction.R b/R/s4-GammaBernsteinFunction.R
@@ -193,9 +193,13 @@ setMethod(
   }
 )
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
 #' @include s4-valueOf0.R
 #' @importFrom checkmate assert qassert check_numeric check_complex
-#' @keywords internal
+#' @export
 setMethod(
   "valueOf0", "GammaBernsteinFunction",
   function(object, x, cscale = 1, ...) {

diff --git a/R/s4-InverseGaussianBernsteinFunction.R b/R/s4-InverseGaussianBernsteinFunction.R
@@ -203,9 +203,13 @@ setMethod(
   }
 )
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
 #' @include s4-valueOf0.R
 #' @importFrom checkmate assert qassert check_numeric check_complex
-#' @keywords internal
+#' @export
 setMethod(
   "valueOf0", "InverseGaussianBernsteinFunction",
   function(object, x, cscale = 1, ...) {

diff --git a/R/s4-LevyBernsteinFunction.R b/R/s4-LevyBernsteinFunction.R
@@ -55,8 +55,12 @@ setClass("LevyBernsteinFunction",
   contains = c("BernsteinFunction", "VIRTUAL")
 )
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
 #' @include s4-defaultMethod.R
-#' @keywords internal
+#' @export
 setMethod(
   "defaultMethod", "LevyBernsteinFunction",
   function(object) {
@@ -173,9 +177,13 @@ setMethod(
   }
 )
 
-#' @include s4-valueOf0.R s4-valueOf.R
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
+#' @include s4-valueOf0.R s4-valueOf.R s4-defaultMethod.R
 #' @importFrom methods setMethod
-#' @keywords internal
+#' @export
 setMethod(
   "valueOf0", "LevyBernsteinFunction",
   function(object, x, cscale = 1, method = defaultMethod(object), ...) {

diff --git a/R/s4-LinearBernsteinFunction.R b/R/s4-LinearBernsteinFunction.R
@@ -98,6 +98,19 @@ setMethod( # nocov start
   }
 ) # nocov end
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
+#' @include s4-valueOf0.R
+#' @export
+setMethod(
+  "valueOf0", "LinearBernsteinFunction",
+  function(object, x, cscale = 1, ...) {
+    valueOf(object, x, cscale = cscale)
+  }
+)
+
 #' @rdname hidden_aliases
 #'
 #' @inheritParams valueOf

diff --git a/R/s4-ParetoBernsteinFunction.R b/R/s4-ParetoBernsteinFunction.R
@@ -165,10 +165,14 @@ setMethod(
   }
 )
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
 #' @include s4-valueOf0.R
 #' @importFrom checkmate assert qassert check_numeric check_complex
 #' @importFrom stats pgamma
-#' @keywords internal
+#' @export
 setMethod(
   "valueOf0", "ParetoBernsteinFunction",
   function(object, x, cscale = 1, ...) {

diff --git a/R/s4-PoissonBernsteinFunction.R b/R/s4-PoissonBernsteinFunction.R
@@ -136,9 +136,13 @@ setMethod(
   }
 )
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
 #' @include s4-valueOf0.R
 #' @importFrom checkmate assert qassert check_numeric check_complex
-#' @keywords internal
+#' @export
 setMethod(
   "valueOf0", "PoissonBernsteinFunction",
   function(object, x, cscale = 1, ...) {

diff --git a/R/s4-ScaledBernsteinFunction.R b/R/s4-ScaledBernsteinFunction.R
@@ -88,6 +88,19 @@ setMethod( # nocov start
   }
 ) # nocov end
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
+#' @include s4-valueOf0.R
+#' @export
+setMethod(
+  "valueOf0", "ScaledBernsteinFunction",
+  function(object, x, cscale = 1, ...) {
+    valueOf(object, x, cscale = cscale)
+  }
+)
+
 #' @rdname hidden_aliases
 #'
 #' @inheritParams valueOf

diff --git a/R/s4-SumOfBernsteinFunctions.R b/R/s4-SumOfBernsteinFunctions.R
@@ -77,6 +77,19 @@ setMethod( # nocov start
   }
 ) # nocov end
 
+#' @rdname hidden_aliases
+#'
+#' @inheritParams valueOf0
+#'
+#' @include s4-valueOf0.R
+#' @export
+setMethod(
+  "valueOf0", "SumOfBernsteinFunctions",
+  function(object, x, cscale = 1, ...) {
+    valueOf(object, x, cscale = cscale)
+  }
+)
+
 #' @rdname hidden_aliases
 #'
 #' @inheritParams valueOf

diff --git a/R/s4-defaultMethod.R b/R/s4-defaultMethod.R
@@ -1,5 +1,21 @@
+#' Default method for approximating Bernstein function differences
+#'
+#' @description
+#' Evaluating Bernstein function differences is usually not numerically stable.
+#' Consequently, various alternative approaches are used dependent on the class
+#' of the Bernstein function. This method returns a String indicating the
+#' default method used for the approximation.
+#'
+#' @param object An object deriving from the class [BernsteinFunction-class].
+#'
+#' @return
+#' A String indicating the default method used for the approximation.
+#'
+#' @family Bernstein function generics
 #' @importFrom methods setGeneric
-#' @keywords internal
+#' @export
+#' @examples
+#' defaultMethod(AlphaStableBernsteinFunction(alpha = 0.7))
 setGeneric(
   "defaultMethod",
   function(object) {

diff --git a/R/s4-valueOf.R b/R/s4-valueOf.R
@@ -1,4 +1,4 @@
-#' Evaluate Bernstein Functions
+#' Evaluate Bernstein Function differences
 #'
 #' Calculate the values for a Bernstein function and its higher-order,
 #' alternating iterated forward differences, possibly scaled by a binomial
@@ -11,12 +11,9 @@
 #' numerically stable. Consequently, the various alternative approaches are used
 #' dependent on the class of the Bernstein function.
 #'
-#' @param object An object deriving from the class [BernsteinFunction-class].
-#' @param x A nonnegativ numeric vector at which the iterated difference of
-#'   the Bernstein function is evaluated.
+#' @inheritParams valueOf0
 #' @param difference_order A nonnegative integer with the order of the
 #'   alternating iterated forward differences taken on the Bernstein function.
-#' @param cscale A positive number for the *composite scaling factor*.
 #' @param n,k Nonnegative numbers for the binomial factor.
 #' @param ... Pass-through parameter.
 #'

diff --git a/R/s4-valueOf0.R b/R/s4-valueOf0.R
@@ -1,5 +1,20 @@
+#' Evaluate Bernstein functions
+#'
+#' @description
+#' Calculate the values for a Bernstein function function.
+#'
+#' @param object An object deriving from the class [BernsteinFunction-class].
+#' @param x A nonnegativ numeric vector at which the iterated difference of
+#'   the Bernstein function is evaluated.
+#' @param cscale A positive number for the *composite scaling factor*.
+#' @param ... Pass-through parameter.
+#'
+#' @family Bernstein function generics
 #' @importFrom methods setGeneric
-#' @keywords internal
+#' @export
+#' @examples
+#' bf <- AlphaStableBernsteinFunction(alpha = 0.7)
+#' valueOf0(bf, 1:5)
 setGeneric(
   "valueOf0",
   function(object, x, cscale = 1, ...) {

diff --git a/README.md b/README.md
@@ -7,13 +7,13 @@
 
 ![minimal R
 version](https://img.shields.io/badge/R%3E%3D-3.4.0-6666ff.svg)
-![packageversion](https://img.shields.io/badge/Package%20version-0.8.3-orange.svg?style=flat-square)
+![packageversion](https://img.shields.io/badge/Package%20version-0.8.8-orange.svg?style=flat-square)
 [![Project Status: WIP – Initial development is in progress, but there
 has not yet been a stable, usable release suitable for the
 public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
-[![Last-changedate](https://img.shields.io/badge/last%20change-2024--04--02-yellowgreen.svg)](/commits/master)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2024--04--17-yellowgreen.svg)](/commits/master)
 [![R build
 status](https://github.com/hsloot/rmo/workflows/check-full/badge.svg)](https://github.com/hsloot/rmo/actions)
 [![Codecov test