ready4 Framework Blog

• Releases
• Dataset releases
• Framework taxonomies dataset releases
• Model datasets releases
• Datasets for modelling people releases
• Datasets for modelling places releases
• Synthetic (fake) datasets releases
• Posters dataset releases
• Executable releases
• Programs releases
• Subroutine releases
• Library releases
• Framework library releases
• Releases of module libraries
• People module library releases
• News About ready4
• Introducing ready4 framework modules and syntax
• ready4 software now archived on Zenodo
• Predicting Quality Adjusted Life Years in young people attending primary mental health services
• Modelling the mental health impacts of COVID-19
• readyforwhatsnext - conference posters now available

Releases

Dataset releases

All current and previous releases of framework, model, instructional and poster datasets.

Framework taxonomies dataset releases

Releases of the datasets of the taxonomies that support a consistent code house-style and automation of documentation autoring are described below.

Model datasets releases

All current releases of datasets to be used in conjunction with modules for modelling people (the Spring To Life model), places (the Springtides model), platforms (the First Bounce model) and programs (the On Target model).

Datasets for modelling people releases

Releases of the datasets that can be used with modules for modelling people are reproduced below.

Datasets for modelling places releases

Releases of the datasets that can be used with modules for modelling places are reproduced below.

Synthetic (fake) datasets releases

Releases of the datasets that are intended inputs or outputs of hypothetical applications of modules are reproduced below.

Posters dataset releases

Releases of the dataset of posters from academic conferences are reproduced below.

Executable releases

All current and previous releases of programs and subroutines.

Programs releases

Currently available (as at 18-Jan-2023) releases of analysis programs are described below.

Subroutine releases

Currently available (as at 18-Jan-2023) releases of subroutines are described below.

Library releases

All current and previous releases of framework and module libraries.

Framework library releases

Currently available (as at 18-Jan-2023) releases of framework libraries are described below.

Date	Package	Release	Description
13-Sep-2022		0.0.0.90985	ready4show provides tools for authoring technical documentation, analysis reports and scientific summaries to showcase insights generated by open, modular mental health system models.This release corrects citation information.
13-Sep-2022		0.0.0.92225	ready4use provides a set of tools for authoring and working with datasets when developing open source, modular mental health systems models.This release corrects package citation details.
13-Sep-2022		0.0.0.90981	ready4show provides tools for authoring technical documentation, analysis reports and scientific summaries to showcase insights generated by open, modular mental health system models.This release corrects citation information.
13-Sep-2022		0.0.0.9222	ready4use provides a set of tools for authoring and working with datasets when developping open source, modular mental health systems models.
13-Sep-2022		0.0.0.9098	ready4show provides tools for authoring technical documentation, analysis reports and scientific summaries to showcase insights generated by open, modular mental health system models.This release contains very minor updates.
13-Sep-2022		0.0.0.9102	ready4 provides the foundational elements (classes, generics, methods, functions) of a framework for implementing open source youth mental health systems modelling projects.This release includes a number of additional helper functions.
08-Sep-2022		0.0.0.92220	updated for fns_dmt_tb
08-Sep-2022		0.0.0.9221	updated for fns_dmt_tb
08-Sep-2022		0.0.0.90981	added fns_dmt_tb to release
08-Sep-2022		0.0.0.90980	added fns_dmt_tb to release
19-Apr-2022		0.0.0.9096	ready4show provides tools for authoring technical documentation, analysis reports and scientific summaries to showcase insights generated by open, modular mental health system models.This release references an updated R Markdown subroutine for generating scientific manuscripts.
15-Feb-2022		0.0.0.92201	ready4use provides a set of tools for authoring and working with datasets when developping open source, modular mental health systems models.This release corrects an error with the citation file.
15-Feb-2022		0.0.0.90951	ready4show provides tools for authoring technical documentation, analysis reports and scientific summaries to showcase insights generated by open, modular mental health system models.This release corrects an error in the citation file.
15-Feb-2022		0.0.0.90891	ready4 provides bare bones foundational elements (classes, generics, methods, functions) of a framework for ensuring that the computational model components of mental health systems modelling projects adhere to open science principles.This release fixes an error in the CITATION.cff file.
15-Feb-2022		0.0.0.9220	ready4use provides a set of tools for authoring and working with datasets when developing open source, modular mental health systems models.
15-Feb-2022		0.0.0.9095	ready4show provides tools for authoring technical documentation, analysis reports and scientific summaries to showcase insights generated by open, modular mental health system models.This release includes minor updates including addition of a CITATION.cff file.
15-Feb-2022		0.0.0.9089	ready4 provides bare bones foundational elements (classes, generics, methods, functions) of a framework for ensuring that the computational model components of mental health systems modelling projects adhere to open science principles.This release includes minor updates including new functions to generate CITATION.cff files and update the dictionary of recognised terms for the coding house-style.
14-Feb-2022		0.0.0.9088	Minor updates and fixes.
14-Jan-2022		0.0.0.9078	Release with first version of Framework syntax and foundational Ready4Module. Vignettes include details of initial applications of framework.
29-Oct-2021		Documentation	fix of write to repo fn
29-Oct-2021		0.0.0.9461	First release indexed with a Zenodo DOI.
28-Oct-2021		0.0.0.9022	Initial release of ready4 R package
26-Oct-2021		0.0.0.9048	Data release
26-Oct-2021		Doc_0.0	more s4 mthd dmtn fixes
08-Apr-2021		0.0.0.9122	This release includes some changed argument names and updated documentation.The user documentation ready4use_user_0.0.0.9122.pdf is the manual that is recommended for most package users as it lists only functions intended for use. There is an extended version of the manual ready4use_developer_0.0.0.9122.pdf) that provides a full list of all functions in the package (potentially including buggy, poorly tested in development functions or helper functions not meant for end-users), but this is only potentially useful for developers who want a quick guide to what’s under the hood.
07-Apr-2021		0.0.0.9120	This release addresses a build failure in the previous release due to a improper class creation.The user documentation ready4use_user_0.0.0.9120.pdf is the manual that is recommended for most package users as it lists only functions intended for use. There is an extended version of the manual ready4use_developer_0.0.0.9120.pdf that provides a full list of all functions in the package (potentially including buggy, poorly tested in development functions or helper functions not meant for end-users), but this is only potentially useful for developers who want a quick guide to what’s under the hood.
07-Apr-2021		0.0.0.9119	This release addresses a build failure in the previous release due to a problematic dependency.The user documentation ready4use_user_0.0.0.9119.pdf is the manual that is recommended for most package users as it lists only functions intended for use. There is an extended version of the manual ready4use_developer_0.0.0.9119.pdf that provides a full list of all functions in the package (potentially including buggy, poorly tested in development functions or helper functions not meant for end-users), but this is only potentially useful for developers who want a quick guide to what’s under the hood.
07-Apr-2021		0.0.0.9193	This release includes updated dependencies to address potential build problems.The user documentation ready4class_user_0.0.0.9193.pdf is the manual that is recommended for most package users as it lists only functions intended for use. There is an extended version of the manual ready4class_developer_0.0.0.9193.pdf that provides a full list of all functions in the package (potentially including buggy, poorly tested in development functions or helper functions not meant for end-users), but this is only potentially useful for developers who want a quick guide to what’s under the hood.
07-Apr-2021		0.0.0.9289	Updates from previous release include adding an internal helper function for removing labels from dataframes that replaces a dependency that was causing build fails on Mac installs.The user documentation ready4fun_user_0.0.0.9289.pdf is the manual that is recommended for most package users as it lists only functions intended for use. There is an extended version of the manual ready4fun_developer_0.0.0.9289.pdf that provides a full list of all functions in the package (potentially including buggy, poorly tested in development functions or helper functions not meant for end-users), but this is only potentially useful for developers who want a quick guide to what’s under the hood.
07-Apr-2021		0.0.0.9189 (Initial)	This is the initial release of the ready4class package.The user documentation ready4class_user_0.0.0.9189.pdf is the manual that is recommended for most package users as it lists only functions intended for use. There is an extended version of the manual ready4class_developer_0.0.0.9189.pdf that provides a full list of all functions in the package (potentially including buggy, poorly tested in development functions or helper functions not meant for end-users), but this is only potentially useful for developers who want a quick guide to what’s under the hood.
07-Apr-2021		0.0.0.9279	Updates from previous release include (another) bug fix for the write_links_for_website function.The user documentation ready4fun_user_0.0.0.9279.pdf is the manual that is recommended for most package users as it lists only functions intended for use. There is an extended version of the manual ready4fun_developer_0.0.0.9279.pdf that provides a full list of all functions in the package (potentially including buggy, poorly tested in development functions or helper functions not meant for end-users), but this is only potentially useful for developers who want a quick guide to what’s under the hood
06-Apr-2021		0.0.0.9187	updated v nbr
06-Apr-2021		0.0.0.9186	updates to authoring workflow
01-Apr-2021		0.0.0.9278	Updates from previous release include bug fixes for the write_links_for_website.The user documentation (ready4fun_user_0.0.0.9278.pdf) is the manual that is recommended for most package users as it lists only functions intended for use. There is an extended version of the manual (ready4fun_developer_0.0.0.9278.pdf) that provides a full list of all functions in the package (potentially including buggy, poorly tested in development functions or helper functions not meant for end-users), but this is only potentially useful for developers who want a quick guide to what’s under the hood.
01-Apr-2021		0.0.0.9276	Updates from previous release includes some function and argument renaming (to improve self-documentation), improvements to the write_links_for_website function and reduction of the number of functions listed in the default user manual. This release comes bundled with two versions of package documentation. The user documentation (ready4fun_user_0.0.0.9276.pdf) is the manual that is recommended for most package users as it lists only functions intended for use. There is an extended version of the manual (ready4fun_developer_0.0.0.9276.pdf) that provides a full list of all functions in the package (potentially including buggy, poorly tested in development functions or helper functions not meant for end-users), but this is only potentially useful for developers who want a quick guide to what’s under the hood.
30-Mar-2021		0.0.0.9270 (Initial)	Initial releaseThis initial release of the ready4fun package includes functions that have been successfully deployed to help author other packages in the ready4 suite. However, only self-authored documentation (i.e. documentation created by the functions contained in ready4fun) is available in this release. We intend expanding on this very basic documentation in future releases.

Releases of module libraries

All current releases of modules for modelling people (the Spring To Life model), places (the Springtides model), platforms (the First Bounce model) and programs (the On Target model).

People module library releases

Currently available (as at 18-Jan-2023) releases of module libraries for modelling people are reproduced below.

Date	Package	Release	Description
27-Oct-2022		0.0.0.9015	migrated in fns from updated analysis program
17-Oct-2022		0.0.0.9014	Model youth choices using the ready4 framework.Tools for modelling the choice behaviours of young people relating to their mental health. Implements the ready4 framework for open and modular youth mental health systems models. Supports standardised workflows for the design and analysis of Discrete Choice Experiments. This development version of the youthu package has been made available as part of the process of testing and documenting the package.
13-Sep-2022		0.0.0.91125	Tools for mapping measures routinely collected in youth mental health services to Quality Adjusted Life Years (QALYs). Part of the First Bounce model of primary youth mental health services. This development version of the youthu package has been made available as part of the process of testing and documenting the package.This release corrects package citation information.
13-Sep-2022		0.0.0.93465	Tools for developing, reporting and sharing Transfer To Utility (TTU) mapping algorithms that predict health utility from other health measures. This development version of the TTU package has been made available as part of the process of testing and documenting the package.This release corrects package citation information.
13-Sep-2022		0.0.0.90835	Tools to standardise the formalising and solving of inverse problems as part of the development of open and modular mental health systems. This development version of the specific package has been made available as part of the process of testing and documenting the package.This release corrects package citation information.
13-Sep-2022		0.0.0.90535	Tools to summarise questionnaire responses from youth mental health collections in a single index measure. The main motivation for this package is to facilitate automated scoring, using published publicly available scoring algorithms, of measures relevant to mental health systems models.This release corrects package citation information.
13-Sep-2022		0.0.0.91085	Tools to describe and quality assure types of data commonly present in youth mental health collections. The main motivation for this package is to facilitate automated data integrity checks, ensure that methods are applied to the appropriate data structures and streamline reporting of descriptive statistics.This release corrects package citation information.
13-Sep-2022		0.0.0.9112	Tools for mapping measures routinely collected in youth mental health services to Quality Adjusted Life Years (QALYs). Part of the First Bounce model of primary youth mental health services. This development version of the youthu package has been made available as part of the process of testing and documenting the package.
13-Sep-2022		0.0.0.9346	Tools for developing, reporting and sharing Transfer To Utility (TTU) mapping algorithms that predict health utility from other health measures. This development version of the TTU package has been made available as part of the process of testing and documenting the package.
13-Sep-2022		0.0.0.9083	Tools to standardise the formalising and solving of inverse problems as part of the development of open and modular mental health systems. This development version of the specific package has been made available as part of the process of testing and documenting the package.
13-Sep-2022		0.0.0.9053	Tools to summarise questionnaire responses from youth mental health collections in a single index measure. The main motivation for this package is to facilitate automated scoring, using published publicly available scoring algorithms, of measures relevant to mental health systems models.
13-Sep-2022		0.0.0.9108	Tools to describe and quality assure types of data commonly present in youth mental health collections. The main motivation for this package is to facilitate automated data integrity checks, ensure that methods are applied to the appropriate data structures and streamline reporting of descriptive statistics.
08-Sep-2022		0.0.0.90532	updated dpcys
08-Sep-2022		0.0.0.90531	updated dpcys
08-Sep-2022		0.0.0.91081	updated dpcys
21-Feb-2022		0.0.0.9338	Tools for developing, reporting and sharing Transfer To Utility (TTU) mapping algorithms that predict health utility from other health measures. This development version of the TTU package has been made available as part of the process of testing and documenting the package.
21-Feb-2022		0.0.0.9111	Tools for mapping measures routinely collected in youth mental health services to Quality Adjusted Life Years (QALYs). Part of the First Bounce model of primary youth mental health services. This development version of the youthu package has been made available as part of the process of testing and documenting the package.
21-Feb-2022		0.0.0.9111	edits to work with new mdl_ingredients_ls
21-Feb-2022		0.0.0.9337	Tools for developing, reporting and sharing Transfer To Utility (TTU) mapping algorithms that predict health utility from other health measures. This development version of the TTU package has been made available as part of the process of testing and documenting the package.Updates in this release include new TTUSynopsis class.
21-Feb-2022		0.0.0.9079	Tools to standardise the formalising and solving of inverse problems as part of the development of open and modular mental health systems. This development version of the specific package has been made available as part of the process of testing and documenting the package.
17-Feb-2022		0.0.0.9335	Tools for developing, reporting and sharing Transfer To Utility (TTU) mapping algorithms that predict health utility from other health measures.
17-Feb-2022		0.0.0.9334	changed dpcy pkgs
17-Feb-2022		0.0.0.9333	Increment version number to 0.0.0.9333
17-Feb-2022		0.0.0.9332	updated dpcys
17-Feb-2022		0.0.0.90780	Tools to standardise the formalising and solving of inverse problems as part of the development of open and modular mental health systems.
17-Feb-2022		0.0.0.9078	Tools to standardise the formalising and solving of inverse problems as part of the development of open and modular mental health systems.
16-Feb-2022		0.0.0.9077	fix of transform fn
16-Feb-2022		0.0.0.9331	removed all migrated out fns
16-Feb-2022		0.0.0.9076	updated investigate methds
15-Feb-2022		0.0.0.9330	added TTUReports class and author method
15-Feb-2022		0.0.0.9075	Tools to standardise the formalising and solving of inverse problems as part of the development of open and modular mental health systems.This release includes updated author and share methods.
15-Feb-2022		0.0.0.9074	Tools to standardise the formalising and solving of inverse problems as part of the development of open and modular mental health systems.
15-Feb-2022		0.0.0.9048	Tools to summarise questionnaire responses from youth mental health collections in a single index measure. The main motivation for this package is to facilitate automated scoring, using published publicly available scoring algorithms, of measures relevant to mental health systems models.
15-Feb-2022		0.0.0.9104	Tools to describe and quality assure types of data commonly present in youth mental health collections. The main motivation for this package is to facilitate automated data integrity checks, ensure that methods are applied to the appropriate data structures and streamline reporting of descriptive statistics.This release includes updates to plot functions.
04-Nov-2021		0.0.0.9072	Version implemented following significant redevelopment of package dependencies.
07-Aug-2021		0.9095	Some minor updates to functions and vignettes.For most users the most appropriate manual will be youthu_0.0.0.9095_user.pdf. Developers may prefer to use the more comprehensive version:youthu_0.0.0.9095_developer.pdf
04-Aug-2021		0.9061	This release combines changes to the naming conventions of variables included in the example data dictionary, some additional functions migrated in from TTU and an additional vignette.Most users should refer to this manual: youthvars_user_0.0.0.9061.pdfA manual intended for developers is also available: youthvars_developer_0.0.0.9061.pdf. Note the developer version of the manual lists all functions in the package, including helper functions and poorly tested, partially working in development functions that are not intended for end-users.
12-May-2021		0.0.0.9044	This release includes a number of new functions, some of which have been migrated from previous versions of the TTU package.Most users should refer to this manual: youthvars_user_0.0.0.9044.pdfA manual intended for developers is also available: youthvars_developer_0.0.0.9044.pdf. Note the developer version of the manual lists all functions in the package, including helper functions and poorly tested, partially working in development functions that are not intended for end-users.A number of vignettes are also available
09-Apr-2021		0.0.0.9065	This is the initial release of the youthu (Youth OUtcomes To Health Utility) modelling toolkit.Bundled with this release are vignettes youthu_vignettes.zip which give worked examples of applying the tools in this package and two versions of a manual describing the functions and datasets included in the package.Most users should refer to the end-user version of the manual: youthu_user_0.0.0.9065.pdf.A more extensive manual intended for developers is also available: youthu_developer_0.0.0.9065.pdf. Note the developer version of the manual lists all functions in the package, including helper functions and poorly tested, partially working in development functions that are not intended for end-users.
08-Apr-2021		0.0.0.9018	updated dpcy
08-Apr-2021		0.0.0.9017	This release includes a number of naming convention changes and improvements to the algorithm generated manual.Most users should refer to this manual: youthvars_user_0.0.0.9017.pdfA manual intended for developers is also available: youthvars_developer_0.0.0.9017.pdf. Note the developer version of the manual lists all functions in the package, including helper functions and poorly tested, partially working in development functions that are not intended for end-users.A number of vignettes are also available

News About ready4

Introducing ready4 framework modules and syntax

The ready4 framework has reached a major milestone with the launch of tools to implement modular models that use a simple and consistent syntax.

Development version software to implement and extend the ready4 framework has been publicly available for over a year now. However, the way that this code was limited has limited its potential utility as a toolkit for developing transparent and modular mental health systems models. The latest release of the ready4 R package addresses these limitations with two important innovations:

• introducing the concept of modules, to facilitate consistent application of an Object Oriented Programming approach throughout the ready4 software suite;

• codifying a simple and consistent syntax for use in all programs that implement configurations of models developed with the ready4 framework.

To view or cite the archive copy of the version of the ready4 package which introduced these innovations use https://doi.org/10.5281/zenodo.5847544. To view or cite the most recently archived copy of the ready4 package use https://doi.org/10.5281/ZENODO.5606250. The latest documentation for the package is available at https://ready4-dev.github.io/ready4/

ready4 software now archived on Zenodo

The software that we create to implement the ready4 framework and the models developed with that framework will from this point forward be archived on Zenodo.

Zenodo is an open science platform developed by CERN and using it as a repository for archiving our software has a number of advantages:

• it creates a permanent copy of each software item, thus making these items appropriate for citation in peer-reviewed journal articles (unlike software stored in impermanent development code repositories such as GitHub);
• it create DOI identifiers for each archived software item, minting a new DOI for each version of a software item sent for archiving as well as providing a catch all DOI that can apply to all versions of the software;
• it provides a simple workflow to integrate with GitHub repositories (where our most up to date development code is stored);
• it automatically submites archived items for indexing on OpenAire; and
• it includes easy to use citation tools to help generate appropriate citations for software in multiple output formats.

We have established a ready4 community within Zenodo, in which all our code is stored.

Predicting Quality Adjusted Life Years in young people attending primary mental health services

We applied our youthvars and TTU modules to developing a dataset of transfer to utility models that can be used to predict adolescent weighted AQoL-6D health utility from a range of psychological distress, depression, anxiety and functioning predictors. Vignettes from the youthu R package illustrate (using fake data) how these models can be used to derive Quality Adjusted Life Year predictions. A preprint describing this study is now available at: https://www.medrxiv.org/content/10.1101/2021.07.07.21260129v3. The three toolkits, the dataset and the pre-print are outputs of the Spring To Life model of people.

Modelling the mental health impacts of COVID-19

Combined Springtides and University of Sydney model predictions

One of the preliminary applications of the Springtides model was to provide initial predictions, early in the COVID-19 pandemic about the potential mental health impacts of the pandemic in the absence of government intervention. That original analysis was undertaken in May 2020 in collaboration with colleagues at the University of Sydney and was subject to media coverage, both at the time and in December 2020.

Code-libraries and datasets for Springtides will be publicly released in the future, but a brief overview of the modelling approach is described from the 55 minute mark of the below webinar.

readyforwhatsnext - conference posters now available

readyforwhatsnext spatial systems dynamics model poster

International academic conference poster presentations relating to the readyforwhatsnext project have been made available in the project’s scientific summaries dataset https://doi.org/10.7910/DVN/QBZFQV. The two posters that have been uploaded summarise the project’s conceptual model and how its systems dynamics model was adapted to develop the Springtides spatial epidemiology simulator.

readyforwhatsnext resilience conceptual model poster