Authoring model algorithms

library(ready4)
library(ready4fun)

Motivation

The ready4 framework uses an object-oriented programming (OOP) approach to implement computational health economic models. One motivation for using OOP is the concept of “abstraction” - making things as simple as possible for end-users of ready4 modules by exposing the minimal amount of code required to implement each method.

However, some users of the ready4 modules will want to “look under the hood” and examine the code that implements module algorithms in much more detail. Reasons to do so include to:

• gain detailed insight into how methods are implemented;
• test individual sub-components of methods as part of code verification and model validation checks;
• re-use sub-components of existing methods when authoring new methods.

To help facilitate achieving these objectives, methods associated with ready4 modules can be de-composed into functions that can be used independent of ready4 modules. However, these functions need to be documented and will be easier to comprehend if they adopt a consistent house style (e.g. naming conventions). ready4fun provides workflow tools (classes, methods, functions and datasets) to achieve these goals.

ready4fun function authoring taxonomies, abbreviations and workflow

The ready4fun package uses taxonomy and abbreviation datasets to ensure standardised function code style and documentation.

Function names begin with a meaningful verb

Consistent with a naming convention popular in the R development community, all functions authored with the ready4 framework need to begin with a verb. Furthermore, the choice of verb is meaningful - it communicates something about the type of task a function implements. For example, all functions beginning with the word “fit” will fit a model of a specified type to a dataset. The definitions of all meaningful verbs used in functions authored for a ready4 framework model implementation can be retrieved using get_fn_types(), which by default returns a dataset instance of the ready4fun_functions submodule.

x <- get_fn_types(gh_repo_1L_chr = "ready4-dev/ready4")
class(x)
#> [1] "ready4fun_functions" "tbl_df"              "tbl"                 "data.frame"

exhibit(x,select_int = 1:2, scroll_box_args_ls = list(width = "100%"))

Function inputs and outputs have meaningful suffices

The type of input (arguments) required and output (return) produced by a function can be efficiently communicated by using meaningful suffices. For example all objects ending in “_chr” are character vectors and all objects ending in “_int” are integer vectors. Definitions of all meaningful suffices used in functions authored for a ready4 framework model implementation can be retrieved using get_obj_types(), which by default returns a dataset instance of the ready4fun_objects submodule.

y <- get_obj_types(gh_repo_1L_chr = "ready4-dev/ready4")
class(y)
#> [1] "ready4fun_objects" "tbl_df"            "tbl"               "data.frame"

exhibit(y, select_int = 1:2, scroll_box_args_ls = list(width = "100%"))

Consistent use of abbreviations

Further information about the purpose of a function and the nature of its inputs and outputs can be encoded by using naming conventions that make consistent use of abbreviations. A master table of the abbreviations used in a ready4 framework model implementation can be retrieved using get_abbrs(), which by default returns a dataset instance of the ready4fun_abbreviations submodule.

z <- get_abbrs(gh_repo_1L_chr = "ready4-dev/ready4")
class(z)
#> [1] "ready4fun_abbreviations" "tbl_df"                  "tbl"                     "data.frame"

exhibit(z %>% head(50), select_int = 1:2, scroll_box_args_ls = list(width = "100%"))

The ready4fun_abbreviations submodule is searchable. It is therefore possible to see if an abbreviation has been defined for an existing word or phrase…

procure(z,"template")
#> # A tibble: 2 × 3
#>   short_name_chr long_name_chr plural_lgl
#>   <chr>          <chr>         <lgl>     
#> 1 tmpl           template      FALSE     
#> 2 tmpls          templates     TRUE

…and to look-up the meaning of an abbreviation…

procure(z,"org",type_1L_chr = "extension")
#> # A tibble: 2 × 3
#>   short_name_chr long_name_chr plural_lgl
#>   <chr>          <chr>         <lgl>     
#> 1 org            organisation  FALSE     
#> 2 orgs           organisations TRUE

…or whether a potential abbreviation has already been defined.

procure(z,"org", type_1L_chr = "extension", what_1L_chr = "string")
#> [1] "org"  "orgs"

Workflow

Manifest

The main class exported as part of ready4fun is the ready4 sub-module ready4fun_manifest which is used to specify metadata (including details of the repository in which the fn_types_lup, seed_obj_lup_tb and abbreviations_lup objects are stored) for the functions being authored and the R package that will contain them.

x <- ready4fun_manifest()

Typical Usage

A ready4fun_manifest object is most efficiently created with the aid of the make_pkg_desc_ls and make_manifest functions rather than a direct call to the ready4fun_manifest() function.

## Not run
x <- ready4fun::make_pkg_desc_ls(
  pkg_title_1L_chr = "Your Package Title",
  pkg_desc_1L_chr = "Your Package Description.",
  authors_prsn = c(
    utils::person("Author 1 Name",
      role = c("aut", "cre")
    ),
    utils::person("Author 2 Name", role = c("cph"))
  ),
  urls_chr = c(
    "Package website url",
    "Package source code url",
    "Project website"
  )
) %>%
  ready4fun::make_manifest(
    copyright_holders_chr = "Organisation name",
    custom_dmt_ls = ready4fun::make_custom_dmt_ls(user_manual_fns_chr = c("Functions to be included in main user manual are itemised here")),
    dev_pkgs_chr = c("Any development package dependencies go here"),
    path_to_pkg_logo_1L_chr = "Local path to package logo goes here",
    piggyback_to_1L_chr = "GitHub Release Repository to which supporting files will be uploaded",
    ready4_type_1L_chr = "authoring",
    zenodo_badge_1L_chr = "DOI badge details go here"
  )

The main method defined for ready4fun_manifest is author which, assuming the raw undocumented function files are saved in the appropriate directories, will author an R package in which all functions are consistently documented.

## Not run
author(x)

Examples

The ready4fun_manifest sub-module and its methods along with the make_pkg_desc_ls and make_manifestfunctions are designed to be used as part of the ready4pack R package authoring workflow. That vignette includes links to two examples of where the ready4pack workflow has been used to author R package. To illustrate how readyfun tools used as part of that workflow are used to document functions, we are just going to focus on the program used to create the ready4show package.

That program makes use of ready4fun tools that read all undocumented package functions, performs automated checks to ensure that these functions appropriately use the taxonomies and abbreviations mentioned previously (prompting authors to make specific amendments if they do not) and then rewrites these functions to the package R directory, appending tags (with the aid of the sinew package) that will generate meaningful documentation.

For example, one of the functions to be documented is the knit_from_tmpl, which is transformed to a version with tags. The tags added to all functions are then used to generate the package documentation, including the package manual. Two versions of the ready4show package manual are generated - a slimmed down version for end-users and a more detailed inventory of contents intended for developers.

Future documentation

Detailed guidance for how to apply ready4fun workflow tools has yet to be prepared but is planned for 2024.