Methods to Enrich R Objects with Extra Components

Provides the "enrich" method to enrich list-like R objects with new, relevant components. The current version has methods for enriching objects of class 'family', 'link-glm', 'lm' and 'glm'. The resulting objects preserve their class, so all methods associated with them still apply. The package also provides the 'enriched_glm' function that has the same interface as 'glm' but results in objects of class 'enriched_glm'. In addition to the usual components in a `glm` object, 'enriched_glm' objects carry an object-specific simulate method and functions to compute the scores, the observed and expected information matrix, the first-order bias, as well as model densities, probabilities, and quantiles at arbitrary parameter values. The package can also be used to produce customizable source code templates for the structured implementation of methods to compute new components and enrich arbitrary objects.

Methods to enrich list-like R objects with extra components

Get the development version from github with

# install.packages("devtools")

Suppose you developed a piece of statistical methodology that relies on a component that a list-like R object object_x of a certain class could potentially have but doesn't.

The aim of enrichwith is to:

  • produce customisable source code templates for the structured implementation of methods to compute new components
  • provide generic methods for the easy enrichment of the object with those components

Specifically, once the methods for the components have been implemented, object_x can be enriched with the components corresponding to the option enrichment_option through the following simple call.

enrich(object_x, with = enrichment_option)

The main objectives of enrichwith is to allow users and developers to directly use the enrichment options that other developers have provided, minimising the need of adapting source code of others.

Objects of class link-glm have as components functions to compute the link function (linkfun), the inverse link function (linkinv), and the 1st derivative of the link function (mu.eta).

enrichwith comes with a built-in template with the methods for the enrichment of link-glm objects with the 2nd and 3rd derivatives of the inverse link function.

The get_enrichment_options method can be used to check what enrichment options are available for objects of class link-glm.

standard_link <-"probit")
# [1] "link-glm"
# -------
# Option: d2mu.deta
# Description: 2nd derivative of the inverse link function
#   component  compute_function
# 1 d2mu.deta compute_d2mu.deta
# -------
# Option: d3mu.deta
# Description: 3rd derivative of the inverse link function
#   component  compute_function
# 1 d3mu.deta compute_d3mu.deta
# -------
# Option: inverse link derivatives
# Description: 2nd and 3rd derivative of the inverse link function
#   component  compute_function
# 1 d2mu.deta compute_d2mu.deta
# 2 d3mu.deta compute_d3mu.deta
# -------
# Option: all
# Description: all available options
#   component  compute_function
# 1 d2mu.deta compute_d2mu.deta
# 2 d3mu.deta compute_d3mu.deta

According to the result of get_enrichment_options, the object standard_link can be enriched with the 2nd and 3rd derivative of the inverse link function through the option "inverse link derivatives".

enriched_link <- enrich(standard_link, with = "inverse link derivatives")
# [1] "link-glm"
cat(format(enriched_link$d2mu.deta), sep = "\n")
# function (eta)
# {
#     -eta * pmax(dnorm(eta), .Machine$double.eps)
# }
cat(format(enriched_link$d3mu.deta), sep = "\n")
# function (eta)
# {
#     (eta^2 - 1) * pmax(dnorm(eta), .Machine$double.eps)
# }

enriched_link is now an "enriched" link-glm object, which, as per the enrichment options above, has the extra components d2mu.deta and d3mu.deta, for the calculation of 2nd and 3rd derivatives of the inverse link function with respect to eta, respectively.

The implemention of enrichment options is streamlined into 3 steps:

  1. Use create_enrichwith_skeleton to produce an enrichwith template.
  2. Edit the compute_* functions by adding the specific code that calculates the components.
  3. Finalise the documentation and/or include more examples.

The first step results in a template that includes all necessary functions to carry out the enrichment. The second step is where the user edits that template and implements the calculation of the components that the object will be enriched with. Specifically, each compute_* function takes as input the object to be enriched and returns the corresponding new component to be added to the object.

Everything else (for example, mapping between the enrichment options and the components that the enriched object will have, checks that an enrichment option exists, listing enrichment options, enriching the object, and so on) is taken care of by the methods in enrichwith.

Developers can either put their enrichwith templates in their packages or are welcome to contribute their template to enrichwith, particularly if that extends core R objects.


enrichwith 0.2

  • Fixed an issue with the example in ?enrich.glm
  • Minor codebase imporvements
  • Harmonised the output of the functions in the auxiliary_functions component of enriched glm objects
  • More detailed descriptions for the enrichment options for glm objects
  • Included a vignette on ohw bias-reduction for GLMs can be implemented using enriched glm objects

enrichwith 0.1

  • First release

Reference manual

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0.0.4 by Ioannis Kosmidis, 17 days ago

Browse source code at

Authors: Ioannis Kosmidis [aut, cre]

Documentation:   PDF Manual  

GPL-2 | GPL-3 license

Suggests whisker, SuppDists, brglm, ggplot2, knitr, rmarkdown

Imported by brglm2.

Depended on by mbrglm.

See at CRAN