Docs: Installing tools for authoring computational models

Wed, 28 Jan 2026 00:00:00 +0000

Before you install

If you are a coder planning on using ready4 to author computational models, then you may wish to install the ready4class, ready4fun and ready4pack libraries.

However, please note that none of these libraries are yet available as a production release. You should therefore understand the limitations of using ready4 software development releases before you make the decision to install this software. Although we use these authoring tools intensively to help us write highly standardised model modules, we feel that these tools are only likely to be helpful to others once much more comprehensive documentation and training resources become available. Without this training and support, these packages are unlikely to appear to be very user-friendly. Furthermore, the initial burden of complying with house-style, file-naming and directory structure requirements of these packages is only likely to be worthwhile if you plan on developing multiple ready4 module libraries. If you still think these tools could be useful to you, consider contacting us first to discuss what additional information may be most helpful to you.

Installation

As ready4class and ready4fun are bundled as dependencies of ready4pack, you can install all three from our GitHub organisation using one command.

devtools::install_github("ready4-dev/ready4pack")

Configuration

To use these computational model authoring tools, you will need to have set-up and appropriately configured your own accounts in:

GitHub (you will need write permissions to a GitHub organisation and to then enable GitHub actions and GitHub pages support for the repositories you create in that organisation);
Zenodo (you will need to have linked each GitHub repository used for your ready4 projects to your Zenodo account); and
Codecov (linked to your GitHub organisation).

The machine onto which you install ready4pack will also need to be securely storing your GitHub credentials (i.e. the value for the GITHUB_PAT token).

Try it out!

It should be noted that the development workflow supported by our computational model authoring tools is not yet well documented. We don’t recommend undertaking R package development with these tools until this has been rectified. However, if you still want to try these tools out, the best place to start is review the examples in the ready4class, ready4fun and ready4pack vignettes.

Docs: Authoring model data structures

Wed, 28 Jan 2026 00:00:00 +0000

This below section renders a vignette article from the ready4class library. You can use the following links to:

view the vignette on the library website (adds useful hyperlinks to code blocks)
view the source file from that article, and;
edit its contents (requires a GitHub account).

library(ready4class)
library(ready4show)
library(ready4use)

Motivation

The ready4 framework uses object oriented programming (OOP) to implement modular approaches to computational models of mental health systems. That means that a standardised approach to developing modules (S4 classes) and sub-modules (S3 classes) is required. ready4class provides the tools to implement this workflow.

Workflow

Prototyes, constructor and manifest

The main classes exported as part of ready4class are readyclass_manifest and ready4class_constructor. ready4class_pt_lup is a tibble based ready4 sub-module, which contains metadata on the prototypes of classes that can be used as sub-components of ready4 modules and sub-modules (for example a tibble based class can be used as a slot in an S4 class). When authoring ready4 R packages, you will create a ready4class_pt_lup instance and store it in an online repository that you have write permissions to. As you create new ready4 modules and sub-modules using ready4class tools, your ready4class_pt_lup object will be updated so that these classes can be made available to any future modules or sub-modules that you author. The ready4class_pt_lup sub-module recently used in workflows for authoring ready4 modules is reproduced below.

x <- ready4use::Ready4useRepos(gh_repo_1L_chr = "ready4-dev/ready4",
                               gh_tag_1L_chr = "Documentation_0.0") %>%
  ingest(fls_to_ingest_chr = "prototype_lup",
         metadata_1L_lgl = F) 
x %>%
  exhibit(scroll_box_args_ls = list(width = "100%"))

Class Prototypes Lookup Table
Class	Value	Namespace	Function	Default	Is Old Class
AusACT	aus::AusACT()	aus	AusACT		FALSE
AusHeadspace	aus::AusHeadspace()	aus	AusHeadspace		FALSE
AusLookup	aus::AusLookup()	aus	AusLookup		FALSE
AusOrygen	aus::AusOrygen()	aus	AusOrygen		FALSE
AusProjections	aus::AusProjections()	aus	AusProjections		FALSE
AusTasmania	aus::AusTasmania()	aus	AusTasmania		FALSE
POSIXt	.POSIXct(NA_character\_)	base	.POSIXct	NA_character\_	FALSE
character	NA_character\_	base		NA_character\_	FALSE
data.frame	data.frame()	base		data.frame()	FALSE
integer	NA_integer\_	base		NA_integer\_	FALSE
list	list(list())	base	list	list()	FALSE
logical	NA	base		NA	FALSE
numeric	NA_real\_	base		NA_real\_	FALSE
function	function() NULL	base		function() NULL	FALSE
CostlyCorrespondences	costly::CostlyCorrespondences()	costly	CostlyCorrespondences		FALSE
CostlyCountries	costly::CostlyCountries()	costly	CostlyCountries		FALSE
CostlyCurrencies	costly::CostlyCurrencies()	costly	CostlyCurrencies		FALSE
CostlySeed	costly::CostlySeed()	costly	CostlySeed		FALSE
CostlySource	costly::CostlySource()	costly	CostlySource		FALSE
CostlyStandards	costly::CostlyStandards()	costly	CostlyStandards		FALSE
dfidx	dfidx::dfidx(dfidx())	dfidx	dfidx	dfidx()	FALSE
Period	lubridate::period()	lubridate	period		FALSE
Ready4Module	ready4::Ready4Module()	ready4	Ready4Module		FALSE
Ready4Private	ready4::Ready4Private()	ready4	Ready4Private		FALSE
Ready4Project	ready4::Ready4Project()	ready4	Ready4Project		FALSE
Ready4Public	ready4::Ready4Public()	ready4	Ready4Public		FALSE
ready4class_constructor	ready4class::ready4class_constructor()	ready4class	ready4class_constructor		TRUE
ready4class_manifest	ready4class::ready4class_manifest()	ready4class	ready4class_manifest		TRUE
ready4class_pt_lup	ready4class::ready4class_pt_lup()	ready4class	ready4class_pt_lup		TRUE
ready4fun_abbreviations	ready4fun::ready4fun_abbreviations()	ready4fun	ready4fun_abbreviations		TRUE
ready4fun_badges	ready4fun::ready4fun_badges()	ready4fun	ready4fun_badges		TRUE
ready4fun_dataset	ready4fun::ready4fun_dataset()	ready4fun	ready4fun_dataset		TRUE
ready4fun_description	ready4fun::ready4fun_description()	ready4fun	ready4fun_description		TRUE
ready4fun_executor	ready4fun::ready4fun_executor()	ready4fun	ready4fun_executor		TRUE
ready4fun_functions	ready4fun::ready4fun_functions()	ready4fun	ready4fun_functions		TRUE
ready4fun_manifest	ready4fun::ready4fun_manifest()	ready4fun	ready4fun_manifest		TRUE
ready4fun_metadata_a	ready4fun::ready4fun_metadata_a()	ready4fun	ready4fun_metadata_a		TRUE
ready4fun_metadata_b	ready4fun::ready4fun_metadata_b()	ready4fun	ready4fun_metadata_b		TRUE
ready4fun_objects	ready4fun::ready4fun_objects()	ready4fun	ready4fun_objects		TRUE
ready4pack_manifest	ready4pack::ready4pack_manifest()	ready4pack	ready4pack_manifest		TRUE
ready4show_authors	ready4show::ready4show_authors()	ready4show	ready4show_authors		TRUE
ready4show_institutes	ready4show::ready4show_institutes()	ready4show	ready4show_institutes		TRUE
ready4show_correspondences	ready4show::ready4show_correspondences()	ready4show	ready4show_correspondences		TRUE
Ready4showPaths	ready4show::Ready4showPaths()	ready4show	Ready4showPaths		FALSE
Ready4showSynopsis	ready4show::Ready4showSynopsis()	ready4show	Ready4showSynopsis		FALSE
ready4use_distributions	ready4use::ready4use_distributions()	ready4use	ready4use_distributions		TRUE
ready4use_dataverses	ready4use::ready4use_dataverses()	ready4use	ready4use_dataverses		TRUE
ready4use_imports	ready4use::ready4use_imports()	ready4use	ready4use_imports		TRUE
ready4use_mapes	ready4use::ready4use_mapes()	ready4use	ready4use_mapes		TRUE
ready4use_dictionary	ready4use::ready4use_dictionary()	ready4use	ready4use_dictionary		TRUE
Ready4useFiles	ready4use::Ready4useFiles()	ready4use	Ready4useFiles		FALSE
Ready4useRaw	ready4use::Ready4useRaw()	ready4use	Ready4useRaw		FALSE
Ready4useProcessed	ready4use::Ready4useProcessed()	ready4use	Ready4useProcessed		FALSE
Ready4useArguments	ready4use::Ready4useArguments()	ready4use	Ready4useArguments		FALSE
Ready4useDyad	ready4use::Ready4useDyad()	ready4use	Ready4useDyad		FALSE
Ready4useIngest	ready4use::Ready4useIngest()	ready4use	Ready4useIngest		FALSE
Ready4useRepos	ready4use::Ready4useRepos()	ready4use	Ready4useRepos		FALSE
Ready4usePointer	ready4use::Ready4usePointer()	ready4use	Ready4usePointer		FALSE
Ready4useRecord	ready4use::Ready4useRecord()	ready4use	Ready4useRecord		FALSE
ScorzProfile	scorz::ScorzProfile()	scorz	ScorzProfile		FALSE
ScorzAqol6	scorz::ScorzAqol6()	scorz	ScorzAqol6		FALSE
ScorzAqol6Adol	scorz::ScorzAqol6Adol()	scorz	ScorzAqol6Adol		FALSE
ScorzAqol6Adult	scorz::ScorzAqol6Adult()	scorz	ScorzAqol6Adult		FALSE
ScorzEuroQol5	scorz::ScorzEuroQol5()	scorz	ScorzEuroQol5		FALSE
sf	sf::st_sf(sf::st_sfc())	sf	st_sf	sf::st_sfc()	FALSE
SpecificConverter	specific::SpecificConverter()	specific	SpecificConverter		FALSE
SpecificFixed	specific::SpecificFixed()	specific	SpecificFixed		FALSE
SpecificInitiator	specific::SpecificInitiator()	specific	SpecificInitiator		FALSE
SpecificMixed	specific::SpecificMixed()	specific	SpecificMixed		FALSE
SpecificModels	specific::SpecificModels()	specific	SpecificModels		FALSE
SpecificParameters	specific::SpecificParameters()	specific	SpecificParameters		FALSE
SpecificPredictors	specific::SpecificPredictors()	specific	SpecificPredictors		FALSE
SpecificPrivate	specific::SpecificPrivate()	specific	SpecificPrivate		FALSE
SpecificProject	specific::SpecificProject()	specific	SpecificProject		FALSE
SpecificResults	specific::SpecificResults()	specific	SpecificResults		FALSE
SpecificShareable	specific::SpecificShareable()	specific	SpecificShareable		FALSE
SpecificSynopsis	specific::SpecificSynopsis()	specific	SpecificSynopsis		FALSE
specific_models	specific::specific_models()	specific	specific_models		TRUE
specific_predictors	specific::specific_predictors()	specific	specific_predictors		TRUE
tbl_df	tibble::tibble()	tibble	tibble		FALSE
tbl_ts	tsibble::tsibble()	tsibble	tsibble		FALSE
TTUProject	TTU::TTUProject()	TTU	TTUProject		FALSE
TTUReports	TTU::TTUReports()	TTU	TTUReports		FALSE
TTUSynopsis	TTU::TTUSynopsis()	TTU	TTUSynopsis		FALSE
VicinityArguments	vicinity::VicinityArguments()	vicinity	VicinityArguments		FALSE
VicinityLocal	vicinity::VicinityLocal()	vicinity	VicinityLocal		FALSE
VicinityLocalProcessed	vicinity::VicinityLocalProcessed()	vicinity	VicinityLocalProcessed		FALSE
VicinityLocalRaw	vicinity::VicinityLocalRaw()	vicinity	VicinityLocalRaw		FALSE
VicinityLookup	vicinity::VicinityLookup()	vicinity	VicinityLookup		FALSE
VicinityMacro	vicinity::VicinityMacro()	vicinity	VicinityMacro		FALSE
VicinityMesoArea	vicinity::VicinityMesoArea()	vicinity	VicinityMesoArea		FALSE
VicinityMesoRegion	vicinity::VicinityMesoRegion()	vicinity	VicinityMesoRegion		FALSE
VicinityMicro	vicinity::VicinityMicro()	vicinity	VicinityMicro		FALSE
VicinityProfile	vicinity::VicinityProfile()	vicinity	VicinityProfile		FALSE
VicinitySpaceTime	vicinity::VicinitySpaceTime()	vicinity	VicinitySpaceTime		FALSE
vicinity_abbreviations	vicinity::vicinity_abbreviations()	vicinity	vicinity_abbreviations		TRUE
vicinity_identifiers	vicinity::vicinity_identifiers()	vicinity	vicinity_identifiers		TRUE
vicinity_mapes	vicinity::vicinity_mapes()	vicinity	vicinity_mapes		TRUE
vicinity_parameters	vicinity::vicinity_parameters()	vicinity	vicinity_parameters		TRUE
vicinity_points	vicinity::vicinity_points()	vicinity	vicinity_points		TRUE
vicinity_processed	vicinity::vicinity_processed()	vicinity	vicinity_processed		TRUE
vicinity_raw	vicinity::vicinity_raw()	vicinity	vicinity_raw		TRUE
vicinity_resolutions	vicinity::vicinity_resolutions()	vicinity	vicinity_resolutions		TRUE
vicinity_templates	vicinity::vicinity_templates()	vicinity	vicinity_templates		TRUE
vicinity_values	vicinity::vicinity_values()	vicinity	vicinity_values		TRUE
youthvars_aqol6d_adol	youthvars::youthvars_aqol6d_adol()	youthvars	youthvars_aqol6d_adol		TRUE
youthvars_chu9d_adolaus	youthvars::youthvars_chu9d_adolaus()	youthvars	youthvars_chu9d_adolaus		TRUE
youthvars_phq9	youthvars::youthvars_phq9()	youthvars	youthvars_phq9		TRUE
youthvars_bads	youthvars::youthvars_bads()	youthvars	youthvars_bads		TRUE
youthvars_gad7	youthvars::youthvars_gad7()	youthvars	youthvars_gad7		TRUE
youthvars_oasis	youthvars::youthvars_oasis()	youthvars	youthvars_oasis		TRUE
youthvars_scared	youthvars::youthvars_scared()	youthvars	youthvars_scared		TRUE
youthvars_k6	youthvars::youthvars_k6()	youthvars	youthvars_k6		TRUE
youthvars_k6_aus	youthvars::youthvars_k6_aus()	youthvars	youthvars_k6_aus		TRUE
youthvars_k10	youthvars::youthvars_k10()	youthvars	youthvars_k10		TRUE
youthvars_k10_aus	youthvars::youthvars_k10_aus()	youthvars	youthvars_k10_aus		TRUE
youthvars_sofas	youthvars::youthvars_sofas()	youthvars	youthvars_sofas		TRUE
YouthvarsDescriptives	youthvars::YouthvarsDescriptives()	youthvars	YouthvarsDescriptives		FALSE
YouthvarsProfile	youthvars::YouthvarsProfile()	youthvars	YouthvarsProfile		FALSE
YouthvarsSeries	youthvars::YouthvarsSeries()	youthvars	YouthvarsSeries		FALSE
MimicAlgorithms	MimicAlgorithms()	mimic	MimicAlgorithms		FALSE
MimicInputs	MimicInputs()	mimic	MimicInputs		FALSE
MimicRepos	MimicRepos()	mimic	MimicRepos		FALSE
MimicConfiguration	MimicConfiguration()	mimic	MimicConfiguration		FALSE

ready4class_constructor is another tibble based ready4 sub-module that summarises the desired features of the ready4 modules and sub-modules that you are authoring. An instance of ready4class_constructor is combined with a ready4fun_manifest sub-module to create a ready4class_manifest sub-module. Instances of ready4class_constructor are most efficiently created using the make_pt_ready4class_constructor function.

y <- make_pt_ready4class_manifest(ready4fun::ready4fun_manifest(),
                                  constructor_r3 = ready4class_constructor()) %>%
  ready4class_manifest()

Typical use

The most important method included in ready4class is the author method for the ready4class_manifest sub-module, that enhances the author method defined for the ready4fun_manifest so that consistently documented R package classes are also generated.

## Not run
author(y)

Examples

ready4class sub-modules and methods are not intended for independent use, but instead should be deployed as part of ready4pack R package authoring workflow.

Future documentation

It should be noted that some ready4class methods require files of a standardised format to be saved in specific sub-directories of the package data-raw directory. Detailed instructions on how to prepare these files are not yet available, but will be outlined in documentation to be released in 2022.

ready4 – Software - libraries (ready4class)