Docs: Finding modules and sub-modules

Thu, 30 Nov 2023 00:00:00 +0000

This below section renders a vignette article from the ready4 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(ready4)

Motivation

When considering whether to use model modules, model developers and users will often want to see examples of each module’s application The ready4 package includes tools to allow a modelling project’s maintainers to perform automated searches for vignette examples of model modules and to output tabular summaries of these modules that are suitable for inclusion on documentation website pages.

Implementation

Details of how to search for themed collections of modules is described in another article. A table itemising individual model modules and sub-modules authored with ready4 can be generated using make_modules_tb. This function scrapes relevant data from the websites of module libraries that have been developed within a specified project’s GitHub organisation and may take a couple of minutes to execute. In this example, we are going to examine modules from a youth mental health model.

modules_tb <-  make_modules_tb(gh_repo_1L_chr = "ready4-dev/ready4")

A slightly quicker method to achieve a similar result is to use the get_modules_tb function. This function retrieves an archived version (and therefore potentially less up to date) of the modules summary table.

# Not run
# modules_tb <- get_modules_tb(gh_repo_1L_chr = "ready4-dev/ready4")

The modules_tb object itemises both ready4 modules (which always use R’s “S4” class type) and sub-modules (“S3” class type). To display a HTML summary of just ready4 modules, you can use the print_modules function.

print_modules(modules_tb, what_1L_chr = "S4")

Class	Description	Examples
AusACT	Meta data for processing ACT population projections
AusHeadspace	Meta data for constructing Headspace Centre geometries
AusLookup	Lookup tables for Australian geometry and spatial attribute data
AusOrygen	Meta data for constructing OYH Specialist Mental Health Catchment geometries
AusProjections	Meta data for constructing custom Australian population projections boundary
AusTasmania	Meta data for processing Tasmanian population projections
CostlyCorrespondences	Collection of input, standards definition and results datasets for projects to generate standardised costing datasets	1, 2
CostlyCountries	Collection of input, standards definition and results datasets for projects to generate standardised country data for use in costing datasets	1, 2
CostlyCurrencies	Collection of input, standards definition and results datasets for projects to generate standardised currency data for use in costing datasets	2
CostlySeed	Original (non-standardised) dataset (and metadata)	1, 2
CostlySource	Input dataset (and metadata) for generating standardised costing datasets
CostlyStandards	Dataset (and metadata) defining the allowable values of specified variables	1, 2
ScorzAqol6	A dataset and metadata to support implementation of an AQoL-6D scoring algorithm
ScorzAqol6Adol	A dataset and metadata to support implementation of a scoring algorithm for the adolescent version of AQoL-6D	3
ScorzAqol6Adult	A dataset and metadata to support implementation of a scoring algorithm for the adult version of AQoL-6D
ScorzEuroQol5	A dataset and metadata to support implementation of an EQ-5D scoring algorithm	4
ScorzProfile	A dataset to be scored, its associated metadata and details of the scoring instrument
SpecificConverter	Container for seed objects used for creating SpecificModels modules	5
SpecificFixed	Modelling project dataset, input parameters and complete fixed models results
SpecificInitiator	Modelling project dataset, input parameters and empty results placeholder
SpecificMixed	Modelling project dataset, input parameters and complete mixed models results
SpecificModels	Modelling project dataset, input parameters and model comparison results
SpecificParameters	Input parameters that specify candidate models to be explored
SpecificPredictors	Modelling project dataset, input parameters and predictor comparison results
SpecificPrivate	Analysis outputs not intended for public dissemination
SpecificProject	Modelling project dataset, parameters and results
SpecificResults	Analysis results
SpecificShareable	Analysis outputs intended for public dissemination
SpecificSynopsis	Input, Output and Authorship Data For Generating Reports
TTUProject	Input And Output Data For Undertaking and Reporting Utility Mapping Studies	6
TTUReports	Metadata to produce utility mapping study reports
TTUSynopsis	Input, Output and Authorship Data For Generating Utility Mapping Study Reports
VicinityArguments	Function arguments for constructing a spatial object
VicinityLocal	Object defining data to be saved in local directory
VicinityLocalProcessed	Object defining data to be saved in local directory in a processed (R) format
VicinityLocalRaw	Object defining data to be saved in local directory in a raw (unprocessed) format
VicinityLookup	Look up tables for spatiotemporal data
VicinityMacro	Macro level context
VicinityMesoArea	Meso level context - area
VicinityMesoRegion	Meso level context - region
VicinityMicro	Micro level context
VicinityProfile	Information to create a profiled area object
VicinitySpaceTime	Spatiotemporal environment
YouthvarsDescriptives	Metadata about descriptive statistics to be generated
YouthvarsProfile	A dataset and its associated dictionary, descriptive statistics and metadata	8
YouthvarsSeries	A longitudinal dataset and its associated dictionary, descriptive statistics and metadata	8

You can use the same function to display only ready4 sub-modules.

print_modules(modules_tb, what_1L_chr = "S3")

Class	Description	Examples
specific_models	Candidate models lookup table
specific_predictors	Candidate predictors lookup table
vicinity_abbreviations	ready4 S3 class for tibble object lookup table for spatial data abbreviations
vicinity_identifiers	ready4 S3 class for tibble object lookup table of unique feature identifiers used for different spatial objects
vicinity_mapes	ready4 S3 class for tibble object that stores spatial simulation parameters relating to Mean Absolute Prediction Errors
vicinity_parameters	ready4 S3 class for tibble object that stores simulation structural parameters relating to the spatial environment
vicinity_points	ready4 S3 class for tibble object lookup table of the longitude and latitude cordinates of sites of services / homes
vicinity_processed	ready4 S3 class for tibble object lookup table of meta-data for spatial data packs (imported and pre-processed data)
vicinity_raw	ready4 S3 class for tibble object lookup table of metadata about raw (un-processed) spatial data to import
vicinity_resolutions	ready4 S3 class for tibble object lookup table of the relative resolutions of different spatial objects
vicinity_templates	ready4 S3 class for tibble object lookup table for base file used in creation of certain spatial objects
vicinity_values	ready4 S3 class for tibble object that stores simulation parameter values for each iteration
youthvars_aqol6d_adol	youthvars ready4 sub-module (S3 class) for Assessment of Quality of Life Six Dimension Health Utility - Adolescent Version (AQoL6d Adolescent)	7
youthvars_bads	youthvars ready4 sub-module (S3 class) for Behavioural Activation for Depression Scale (BADS) scores	7
youthvars_chu9d_adolaus	youthvars ready4 sub-module (S3 class) for Child Health Utility Nine Dimension Health Utility - Australian Adolescent Scoring (CHU-9D Australian Adolescent)	7
youthvars_gad7	youthvars ready4 sub-module (S3 class) for Generalised Anxiety Disorder Scale (GAD-7) scores	7
youthvars_k10	youthvars ready4 sub-module (S3 class) for Kessler Psychological Distress Scale (K10) - US Scoring System scores	7
youthvars_k10_aus	youthvars ready4 sub-module (S3 class) for Kessler Psychological Distress Scale (K10) - Australian Scoring System scores	7
youthvars_k6	youthvars ready4 sub-module (S3 class) for Kessler Psychological Distress Scale (K6) - US Scoring System scores	7
youthvars_k6_aus	youthvars ready4 sub-module (S3 class)for Kessler Psychological Distress Scale (K6) - Australian Scoring System scores	7
youthvars_oasis	youthvars ready4 sub-module (S3 class) for Overall Anxiety Severity and Impairment Scale (OASIS) scores	7
youthvars_phq9	youthvars ready4 sub-module (S3 class) for Patient Health Questionnaire (PHQ-9) scores	7
youthvars_scared	youthvars ready4 sub-module (S3 class) for Screen for Child Anxiety Related Disorders (SCARED) scores	7
youthvars_sofas	youthvars ready4 sub-module (S3 class) for Social and Occupational Functioning Assessment Scale (SOFAS)	7

ready4 – Model - sub-modules

Docs: Finding modules and sub-modules

Motivation

Implementation