Authoring model data structures

The ready4class R package supports partially automated and standardised workflows for defining the data structures to be used in computational models.

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

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
TTUSynopsis TTU::TTUSynopsis() TTU TTUSynopsis FALSE
TTUReports TTU::TTUReports() TTU TTUReports FALSE
TTUProject TTU::TTUProject() TTU TTUProject FALSE
AusLookup aus::AusLookup() aus AusLookup FALSE
AusOrygen aus::AusOrygen() aus AusOrygen FALSE
AusHeadspace aus::AusHeadspace() aus AusHeadspace FALSE
AusProjections aus::AusProjections() aus AusProjections FALSE
AusTasmania aus::AusTasmania() aus AusTasmania FALSE
AusACT aus::AusACT() aus AusACT 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
POSIXt .POSIXct(NA_character\_) base .POSIXct NA_character\_ FALSE
CostlySource costly::CostlySource() costly CostlySource FALSE
CostlySeed costly::CostlySeed() costly CostlySeed FALSE
CostlyStandards costly::CostlyStandards() costly CostlyStandards FALSE
CostlyCorrespondences costly::CostlyCorrespondences() costly CostlyCorrespondences FALSE
CostlyCountries costly::CostlyCountries() costly CostlyCountries FALSE
CostlyCurrencies costly::CostlyCurrencies() costly CostlyCurrencies FALSE
dfidx dfidx::dfidx(dfidx()) dfidx dfidx dfidx() FALSE
Ready4Module Ready4Module() ready4 Ready4Module FALSE
Ready4Private Ready4Private() ready4 Ready4Private FALSE
Ready4Public Ready4Public() ready4 Ready4Public FALSE
ready4class_constructor ready4class::ready4class_constructor() ready4class ready4class_constructor TRUE
ready4class_pt_lup ready4class::ready4class_pt_lup() ready4class ready4class_pt_lup TRUE
ready4class_manifest ready4class::ready4class_manifest() ready4class ready4class_manifest TRUE
ready4fun_badges ready4fun_badges() ready4fun ready4fun_badges TRUE
ready4fun_abbreviations ready4fun_abbreviations() ready4fun ready4fun_abbreviations TRUE
ready4fun_objects ready4fun_objects() ready4fun ready4fun_objects TRUE
ready4fun_functions ready4fun_functions() ready4fun ready4fun_functions TRUE
ready4fun_executor ready4fun_executor() ready4fun ready4fun_executor TRUE
ready4fun_description ready4fun_description() ready4fun ready4fun_description TRUE
ready4fun_metadata_a ready4fun_metadata_a() ready4fun ready4fun_metadata_a TRUE
ready4fun_metadata_b ready4fun_metadata_b() ready4fun ready4fun_metadata_b TRUE
ready4fun_manifest ready4fun_manifest() ready4fun ready4fun_manifest TRUE
ready4fun_dataset ready4fun_dataset() ready4fun ready4fun_dataset 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
specific_models specific::specific_models() specific specific_models TRUE
specific_predictors specific::specific_predictors() specific specific_predictors TRUE
SpecificParameters specific::SpecificParameters() specific SpecificParameters FALSE
SpecificPrivate specific::SpecificPrivate() specific SpecificPrivate FALSE
SpecificShareable specific::SpecificShareable() specific SpecificShareable FALSE
SpecificResults specific::SpecificResults() specific SpecificResults FALSE
SpecificProject specific::SpecificProject() specific SpecificProject FALSE
SpecificInitiator specific::SpecificInitiator() specific SpecificInitiator FALSE
SpecificModels specific::SpecificModels() specific SpecificModels FALSE
SpecificPredictors specific::SpecificPredictors() specific SpecificPredictors FALSE
SpecificFixed specific::SpecificFixed() specific SpecificFixed FALSE
SpecificMixed specific::SpecificMixed() specific SpecificMixed FALSE
SpecificConverter specific::SpecificConverter() specific SpecificConverter FALSE
SpecificSynopsis specific::SpecificSynopsis() specific SpecificSynopsis FALSE
tbl_df tibble::tibble() tibble tibble FALSE
vicinity_parameters vicinity::vicinity_parameters() vicinity vicinity_parameters TRUE
vicinity_values vicinity::vicinity_values() vicinity vicinity_values TRUE
vicinity_abbreviations vicinity::vicinity_abbreviations() vicinity vicinity_abbreviations 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_points vicinity::vicinity_points() vicinity vicinity_points TRUE
vicinity_templates vicinity::vicinity_templates() vicinity vicinity_templates TRUE
vicinity_identifiers vicinity::vicinity_identifiers() vicinity vicinity_identifiers TRUE
vicinity_mapes vicinity::vicinity_mapes() vicinity vicinity_mapes TRUE
VicinityLookup vicinity::VicinityLookup() vicinity VicinityLookup FALSE
VicinityMacro vicinity::VicinityMacro() vicinity VicinityMacro FALSE
VicinityMesoRegion vicinity::VicinityMesoRegion() vicinity VicinityMesoRegion FALSE
VicinityMesoArea vicinity::VicinityMesoArea() vicinity VicinityMesoArea FALSE
VicinityMicro vicinity::VicinityMicro() vicinity VicinityMicro FALSE
VicinityProfile vicinity::VicinityProfile() vicinity VicinityProfile FALSE
VicinitySpaceTime vicinity::VicinitySpaceTime() vicinity VicinitySpaceTime FALSE
VicinityArguments vicinity::VicinityArguments() vicinity VicinityArguments FALSE
VicinityLocal vicinity::VicinityLocal() vicinity VicinityLocal FALSE
VicinityLocalRaw vicinity::VicinityLocalRaw() vicinity VicinityLocalRaw FALSE
VicinityLocalProcessed vicinity::VicinityLocalProcessed() vicinity VicinityLocalProcessed FALSE
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

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.

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.

Last modified February 2, 2024: more tidy-ups of model export (11ef896)