Package 'safetyGraphics' reference manual

Title:	Interactive Graphics for Monitoring Clinical Trial Safety
Description:	A framework for evaluation of clinical trial safety. Users can interactively explore their data using the included 'Shiny' application.
Authors:	Jeremy Wildfire [cre, aut], Becca Krouse [aut], Preston Burns [aut], Xiao Ni [aut], James Buchanan [aut], Susan Duke [aut]
Maintainer:	Jeremy Wildfire <[email protected]>
License:	MIT + file LICENSE
Version:	2.1.1
Built:	2025-01-24 05:44:45 UTC
Source:	https://github.com/safetygraphics/safetygraphics

Startup code for shiny app

Description

Prepare inputs for safetyGraphics app - run before app is initialized.

Usage

app_startup(
  domainData = NULL,
  meta = NULL,
  charts = NULL,
  mapping = NULL,
  autoMapping = NULL,
  filterDomain = NULL,
  chartSettingsPaths = NULL,
  appName = NULL,
  hexPath = NULL,
  homeTabPath = NULL
)
app_startup(
  domainData = NULL,
  meta = NULL,
  charts = NULL,
  mapping = NULL,
  autoMapping = NULL,
  filterDomain = NULL,
  chartSettingsPaths = NULL,
  appName = NULL,
  hexPath = NULL,
  homeTabPath = NULL
)

Arguments

`domainData`	named list of data.frames to be loaded in to the app. Sample AdAM data from the safetyData package used by default
`meta`	data frame containing the metadata for use in the app. If no metadata is provided (default value is NULL), metatdata is generated by `makeMeta()`.
`charts`	list of charts in the format produced by safetyGraphics::makeChartConfig()
`mapping`	list specifying the initial mapping values for each data mapping for each domain (e.g. list(aes= list(id_col='USUBJID', seq_col='AESEQ')).
`autoMapping`	boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the `mapping` parameter overwrite automatically generated mappings when both are found. Defaults to true.
`filterDomain`	domain used for the data/filter tab. Demographics ("`dm`") is used by default. Using a domain that is not one record per participant is not recommended.
`chartSettingsPaths`	path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R). All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details.
`appName`	character string defining the name of the app (default = "safetyGraphics")
`hexPath`	path to image file with a hex or other logo. safetyGraphics hex used by default.
`homeTabPath`	path to html content to be used on the home page. default is a summary of the safetyGraphics framework.

Value

List of elements for used to initialize the shiny app with the following parameters

"meta" List of configuration metadata
"charts" List of charts
"domainData" List of domain level data sets
"mapping" Initial Data Mapping
"standards" List of domain level data standards

Server for a navbar tab

Description

Server for a navbar tab

Usage

chartsNav(input, output, session, chart, data, mapping)
chartsNav(input, output, session, chart, data, mapping)

Arguments

`input`	Input objects from module namespace
`output`	Output objects from module namespace
`session`	An environment that can be used to access information and functionality relating to the session
`chart`	list containing a safetyGraphics chart object like those returned by makeChartConfig.
`data`	named list of current data sets (Reactive).
`mapping`	tibble capturing the current data mappings (Reactive).

Adds a navbar tab that initializes the Chart Module UI

Description

Adds a navbar tab that initializes the Chart Module UI

Usage

chartsNavUI(id, chart)
chartsNavUI(id, chart)

Arguments

`id`	module id
`chart`	chart metadata

Server for chart module, designed to be re-used for each chart generated.

Description

Server for chart module, designed to be re-used for each chart generated.

Usage

chartsTab(input, output, session, chart, data, mapping, status)
chartsTab(input, output, session, chart, data, mapping, status)

Arguments

`input`	Input objects from module namespace
`output`	Output objects from module namespace
`session`	An environment that can be used to access information and functionality relating to the session
`chart`	list containing a safetyGraphics chart object like those returned by makeChartConfig.
`data`	named list of current data sets (Reactive).
`mapping`	tibble capturing the current data mappings (Reactive).
`status`	chart status (Reactive)

UI for chart module, designed to be re-used for each chart generated.

Description

UI for chart module, designed to be re-used for each chart generated.

Usage

chartsTabUI(id, chart)
chartsTabUI(id, chart)

Arguments

`id`	module id
`chart`	list containing chart specifications like those returned by makeChartConfig.

Detect the data standard used for a data set

Description

This function attempts to detect the clinical data standard used in a given R data frame.

Usage

detectStandard(data, domain = NULL, meta = NULL)
detectStandard(data, domain = NULL, meta = NULL)

Arguments

`data`	A data frame in which to detect the data standard - required.
`domain`	the domain to evaluate - should match a value of `meta$domain`. Uses the first value in `meta$domain` if no value is provided.
`meta`	the metadata containing the data standards.

Details

This function compares the columns in the provided "data" with the required columns for a given data standard/domain combination. The function is designed to work with the SDTM and ADaM CDISC(https://www.cdisc.org/) standards for clinical trial data by default. Additional standards can be added by modifying the "meta" data set included as part of this package.

Value

A data frame describing the detected standard for each "text_key" in the provided metadata. Columns are "domain", "text_key", "column" and "standard".

Examples

detectStandard(data=safetyData::adam_adae, meta=safetyCharts::meta_aes) 
detectStandard(data=safetyData::adam_adlbc,meta=safetyCharts::meta_labs, domain="labs" ) 

detectStandard(data=safetyData::adam_adae, meta=safetyCharts::meta_aes) 
detectStandard(data=safetyData::adam_adlbc,meta=safetyCharts::meta_labs, domain="labs" )

Evaluate a data set against a data standard

Description

Determines whether the required data elements in a data standard are found in a given data frame

Usage

evaluateStandard(data, meta, domain, standard)
evaluateStandard(data, meta, domain, standard)

Arguments

`data`	A data frame in which to detect the data standard
`meta`	the metadata containing the data standards.
`domain`	the domain to evaluate - should match a value of `meta$domain`
`standard`	standard to evaluate

Value

a list describing to what degree the data set matches the data standard. The "match" property describes compliance with the standard as "full", "partial" or "none". The "checks" property is a list of the data elements expected for the standard and whether they are "valid" in the given data set. "total_checks", "valid_checks" and "invalid_checks" provide counts of the specified checks. "match_percent" is calculated as valid_checks/total_checks. "mapping" is a data frame describing the detected standard for each "text_key" in the provided metadata. Columns are "text_key", "current" containing the name of the matched column or field value in the data and "match" a boolean indicating whether the data matches the standard.

Examples

# Match is TRUE
evaluateStandard(
 data=safetyData::adam_adlbc, 
 meta=safetyCharts::meta_labs, 
 domain="labs", 
 standard="adam"
) 

# Match is FALSE
evaluateStandard(
 data=safetyData::adam_adlbc, 
 meta=safetyCharts::meta_labs, 
 domain="labs", 
 standard="sdtm"
) 

# Match is TRUE
evaluateStandard(
 data=safetyData::adam_adlbc, 
 meta=safetyCharts::meta_labs, 
 domain="labs", 
 standard="adam"
) 

# Match is FALSE
evaluateStandard(
 data=safetyData::adam_adlbc, 
 meta=safetyCharts::meta_labs, 
 domain="labs", 
 standard="sdtm"
)

Server for the filter module in datamods::filter_data_ui

Description

Server for the filter module in datamods::filter_data_ui

Usage

filterTab(
  input,
  output,
  session,
  domainData,
  filterDomain,
  current_mapping,
  tabID = "Filtering",
  filterVars = NULL
)
filterTab(
  input,
  output,
  session,
  domainData,
  filterDomain,
  current_mapping,
  tabID = "Filtering",
  filterVars = NULL
)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`domainData`	list of data files for each domain
`filterDomain`	domain to use for filtering (typically "dm")
`current_mapping`	current data mapping
`tabID`	ID for the tab containing the filter UI (used for testing)
`filterVars`	Variables to use for filtering (used for testing)

Value

filtered data set

Checks for whether the current data and settings support a filter tab

Description

Checks for whether the current data and settings support a filter tab

Usage

filterTabChecks(domainData, filterDomain, current_mapping)
filterTabChecks(domainData, filterDomain, current_mapping)

Arguments

`domainData`	list of data files for each domain
`filterDomain`	domain to use for filtering (typically "dm")
`current_mapping`	current data mapping (REACTIVE)

Value

reactive that returns a boolean indicating whether the checks passed and filtering can be initialized

UI for the filter module in datamods::filter_data_ui

Description

UI for the filter module in datamods::filter_data_ui

Usage

filterTabUI(id)
filterTabUI(id)

Arguments

id

module id

Convert mapping data.frame to a list

Description

Convert mapping data.frame to a list

Usage

generateMappingList(settingsDF, domain = NULL, pull = FALSE)
generateMappingList(settingsDF, domain = NULL, pull = FALSE)

Arguments

`settingsDF`	data frame containing current mapping
`domain`	mapping domain to return (returns all domains as a named list by default)
`pull`	call pull() the value for each parameter - needed for testing only. default: FALSE

Server for the filter module in datamods::filter_data_ui

Description

Server for the filter module in datamods::filter_data_ui

Usage

homeTab(input, output, session, config)
homeTab(input, output, session, config)

Arguments

`input`	mod input
`output`	mod output
`session`	mod session

UI for the home module

Description

UI for the home module

Usage

homeTabUI(id)
homeTabUI(id)

Arguments

id

module id

Server for the chart loading module used in safetyGraphicsInit()

Description

Server for the chart loading module used in safetyGraphicsInit()

Usage

loadCharts(input, output, session, charts = makeChartConfig())
loadCharts(input, output, session, charts = makeChartConfig())

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`charts`	list containing chart specifications like those returned by makeChartConfig.

UI for the chart loading module used in safetyGraphicsInit()

Description

UI for the chart loading module used in safetyGraphicsInit()

Usage

loadChartsUI(id, charts = makeChartConfig())
loadChartsUI(id, charts = makeChartConfig())

Arguments

`id`	module id
`charts`	list containing chart specifications like those returned by makeChartConfig.

Server for the data loading module used in safetyGraphicsInit()

Description

Server for the data loading module used in safetyGraphicsInit()

Usage

loadData(input, output, session, domain)
loadData(input, output, session, domain)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`domain`	data domain to be loaded

UI for the data loading module used in safetyGraphicsInit()

Description

UI for the data loading module used in safetyGraphicsInit()

Usage

loadDataUI(id, domain = NULL)
loadDataUI(id, domain = NULL)

Arguments

`id`	module id
`domain`	character vector with domains to be loaded

Make Chart Config

Description

Converts YAML chart configuration files to an R list and binds workflow functions. See the vignette about creating custom charts for more details.

Usage

makeChartConfig(
  dirs,
  packages = "safetyCharts",
  packageLocation = "config",
  sourceFiles = FALSE
)
makeChartConfig(
  dirs,
  packages = "safetyCharts",
  packageLocation = "config",
  sourceFiles = FALSE
)

Arguments

`dirs`	path to one or more directories containing yaml config files (relative to working directory)
`packages`	installed packages names containing yaml config files in the /inst/packageLocation folder
`packageLocation`	inst folder where yaml config files (and possibly R functions referenced in yaml workflow) are located in `packages`
`sourceFiles`	boolean indicating whether to source all R files found in dirs.

Value

returns a named list of charts derived from YAML files. Each element of the list contains information about a single chart, and has the following parameters:

"env" Environment for the chart. Must be set to "safetyGraphics" or the chart is dropped.
"name" Name of the chart. Also the name of the element in the list - e.g. charts$aeExplorer$name is "aeExplorer"
"label" Short description of the chart
"type" Type of chart; options are: 'htmlwidget', 'module', 'plot', 'table', 'html' or 'plotly'.
"domain" Data domain. Should correspond to one or more domains in meta
"package" Primary package (if any). Other packages can be loaded directly in workflow functions.
"order" Integer order in which to display the chart. If order is a negative number, the chart is dropped.
"export" Logical flag indicating whether the chart can be exported to an html report. True by default, except for when type is module.
"path" Path to YAML file
"links" Named list of link names/urls to be shown in the chart header.
"workflow" List of functions names used to render chart. See vignette for details.
"functions" List of functions for use in chart renderering. These functions must be located in the global environment or package field of the YAML config. Function names must include either the name or workflow fields of the YAML config.

Make Chart Export

Description

Creates R code that allows chart to be exported

Usage

makeChartExport(chart, mapping)
makeChartExport(chart, mapping)

Arguments

`chart`	chart object like the one generated by makeChartConfig().
`mapping`	mapping object like the one generated by makeMapping().

Value

returns a character vector that can be saved as R code.

Make Chart Parameters

Description

Updates raw data and mapping for use with a specific chart

Usage

makeChartParams(data, chart, mapping)
makeChartParams(data, chart, mapping)

Arguments

`data`	list of domain-level data
`chart`	list containing chart specifications
`mapping`	data frame with current mapping

html chart summary

Description

makes a nicely formatted html summary for a chart object

Usage

makeChartSummary(
  chart,
  status = NULL,
  showLinks = TRUE,
  class = "chart-header"
)
makeChartSummary(
  chart,
  status = NULL,
  showLinks = TRUE,
  class = "chart-header"
)

Arguments

`chart`	list containing chart specifications
`status`	(optional) chart status from `getChartStatus`. Default is NULL.
`showLinks`	boolean indicating whether to include links
`class`	character to include as class

Create data mapping based on data standards and user input

Description

Create data mapping based on data standards and user input

Usage

makeMapping(domainData, meta, autoMapping, customMapping)
makeMapping(domainData, meta, autoMapping, customMapping)

Arguments

`domainData`	named list of data.frames to be loaded in to the app. Sample AdAM data from the safetyData package used by default
`meta`	data frame containing the metadata for use in the app.
`autoMapping`	boolean indicating whether the app should use `safetyGraphics::detectStandard()` to detect data standards and automatically generate mappings for the data provided. Values specified in the `customMapping` parameter overwrite auto-generated mappings when both are found. Defaults to true.
`customMapping`	optional list specifying initial mapping values within each data mapping (e.g. list(aes= list(id_col='USUBJID', seq_col='AESEQ')).

Value

List containing data standard information and mapping

"mapping" Initial Data Mapping
"standards" List of domain level data standards (or NULL if autoMapping is false)

Create a metadata object table for a set of charts

Description

Generates metadata object for a list of charts. makeMeta() looks for metadata in 3 locations for each chart object:

Domain-level metadata saved as meta_chart$name in the chart$package namespace
Chart-specific metadata saved as meta_chart$domain in the chart$package namespace
Chart-specific metadata saved directly to the chart object as chart$meta After checking all charts, all metadata files are stacked in to a single dataframe and returned. If duplicate metadata rows (domain + text_key) are found, an error is thrown.

Usage

makeMeta(charts)
makeMeta(charts)

Arguments

charts

list of safetyGraphics chart objects for which to create metadata

Value

tibble of metadata with the following columns:

domain: Data domain
text_key: Text key indicating the setting name. '--' delimiter indicates a field level data mapping
col_key: Key for the column mapping
field_key: Key for the field mapping (if any)
type: type of mapping - "field" or "column"
label: Label
description: Description
multiple: Mapping supports multiple columns/fields
standard_adam: Default values for the ADaM data standard
standard_sdtm: Default values for the SDTM data standard

Server that facilitates the mapping of a column data (and any associated fields)

Description

Server that facilitates the mapping of a column data (and any associated fields)

Usage

mappingColumn(input, output, session, meta, data)
mappingColumn(input, output, session, meta, data)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`meta`	metadata data frame for the object
`data`	current data file for the domain

Value

A reactive data.frame providing the current value for text_key associated with the selected column

UI that facilitates the mapping of a column data (and any associated fields)

Description

UI that facilitates the mapping of a column data (and any associated fields)

Usage

mappingColumnUI(id, meta, data, mapping = NULL)
mappingColumnUI(id, meta, data, mapping = NULL)

Arguments

`id`	module id
`meta`	metadata for the column (and related fields)
`data`	current data file for the domain
`mapping`	current data mapping for the column (and related fields)

Server that facilitates the mapping of a full data domain

Description

Server that facilitates the mapping of a full data domain

Usage

mappingDomain(input, output, session, meta, data)
mappingDomain(input, output, session, meta, data)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`meta`	metadata for the domain
`data`	clinical data for the domain

Value

A reactive data frame containing the mapping for the domain

UI that facilitates the mapping of a full data domain

Description

UI that facilitates the mapping of a full data domain

Usage

mappingDomainUI(id, meta, data, mapping = NULL)
mappingDomainUI(id, meta, data, mapping = NULL)

Arguments

`id`	module id
`meta`	metadata for the domain
`data`	data file for the domain
`mapping`	current data mapping

Server that facilitates the mapping of a single data element (column or field) with a simple select UI

Description

Server that facilitates the mapping of a single data element (column or field) with a simple select UI

Usage

mappingSelect(input, output, session)
mappingSelect(input, output, session)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object

Value

A reactive containing the selected column

UI that facilitates the mapping of a single data element (column or field) with a simple select UI

Description

UI that facilitates the mapping of a single data element (column or field) with a simple select UI

Usage

mappingSelectUI(id, label, choices = NULL, default = NULL)
mappingSelectUI(id, label, choices = NULL, default = NULL)

Arguments

`id`	unique id for the UI
`label`	label associated with the control
`choices`	a list of options for the control
`default`	default value for the control

Value

returns the selected value wrapped in a reactive().

Server for mapping tab covering of all data domains

Description

Server for mapping tab covering of all data domains

Usage

mappingTab(input, output, session, meta, domainData)
mappingTab(input, output, session, meta, domainData)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`meta`	metadata for all domains
`domainData`	clinical data for all domains

Value

list of mappings for all domains

UI for mapping tab covering of all data domains

Description

UI for mapping tab covering of all data domains

Usage

mappingTabUI(id, meta, domainData, mappings = NULL, standards = NULL)
mappingTabUI(id, meta, domainData, mappings = NULL, standards = NULL)

Arguments

`id`	module id
`meta`	metadata for all domains
`domainData`	list of data files for each domain
`mappings`	optional data frame containing stacked mappings for all domains
`standards`	optional list of data standards like the ones generated by `detectStandard()`

Prepare a chart object for safetyGraphics

Description

Sets default values and binds needed functions to a chart object based on chart type.

Usage

prepareChart(chart)
prepareChart(chart)

Arguments

chart

chart object like the one generated by makeChartConfig().

Value

returns the chart object with a new functions object added.

Server for the patient profile in safetyProfile::profile_server

Description

Server for the patient profile in safetyProfile::profile_server

Usage

profileTab(input, output, session, params)
profileTab(input, output, session, params)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`params`	reactive containing mapping and data
`current_id`	reactive containing currently selected participant

Value

current_id

UI for the profile module in safetyProfile::profile_ui

Description

UI for the profile module in safetyProfile::profile_ui

Usage

profileTabUI(id)
profileTabUI(id)

Arguments

id

module id

Run the core safetyGraphics App

Description

Run the core safetyGraphics App

Usage

safetyGraphicsApp(
  domainData = list(labs = safetyData::adam_adlbc, aes = safetyData::adam_adae, dm =
    safetyData::adam_adsl),
  meta = NULL,
  charts = NULL,
  mapping = NULL,
  autoMapping = TRUE,
  filterDomain = "dm",
  chartSettingsPaths = NULL,
  appName = "safetyGraphics",
  hexPath = system.file("resources/safetyGraphicsHex.png", package = "safetyGraphics"),
  homeTabPath = system.file("resources/safetyGraphicsHomeTab.html", package =
    "safetyGraphics"),
  launchBrowser = FALSE,
  runNow = TRUE
)
safetyGraphicsApp(
  domainData = list(labs = safetyData::adam_adlbc, aes = safetyData::adam_adae, dm =
    safetyData::adam_adsl),
  meta = NULL,
  charts = NULL,
  mapping = NULL,
  autoMapping = TRUE,
  filterDomain = "dm",
  chartSettingsPaths = NULL,
  appName = "safetyGraphics",
  hexPath = system.file("resources/safetyGraphicsHex.png", package = "safetyGraphics"),
  homeTabPath = system.file("resources/safetyGraphicsHomeTab.html", package =
    "safetyGraphics"),
  launchBrowser = FALSE,
  runNow = TRUE
)

Arguments

`domainData`	named list of data.frames to be loaded in to the app. Sample AdAM data from the safetyData package used by default
`meta`	data frame containing the metadata for use in the app. If no metadata is provided, metatdata is generated by `makeMeta()`.
`charts`	list of charts in the format produced by safetyGraphics::makeChartConfig()
`mapping`	list specifying the initial mapping values for each data mapping for each domain (e.g. list(aes= list(id_col='USUBJID', seq_col='AESEQ')).
`autoMapping`	boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the `mapping` parameter overwrite automatically generated mappings when both are found. Defaults to true.
`filterDomain`	domain used for the data/filter tab. Demographics ("`dm`") is used by default. Using a domain that is not one record per participant is not recommended.
`chartSettingsPaths`	path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R). All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details.
`appName`	character string defining the name of the app (default = "safetyGraphics")
`hexPath`	path to image file with a hex or other logo. safetyGraphics hex used by default.
`homeTabPath`	path to html content to be used on the home page. default is a summary of the safetyGraphics framework.
`launchBrowser`	boolean indicating whether to launch the app in a browser. default is false
`runNow`	Should the shiny app object created be run directly? Helpful when writing functions to dispatch to shinyapps, rsconnect, or shinyproxy.

App to select charts, load data and then initialize the core safetyGraphics app

Description

App to select charts, load data and then initialize the core safetyGraphics app

Usage

safetyGraphicsInit(
  charts = makeChartConfig(),
  delayTime = 1000,
  maxFileSize = NULL
)
safetyGraphicsInit(
  charts = makeChartConfig(),
  delayTime = 1000,
  maxFileSize = NULL
)

Arguments

`charts`	chart object
`delayTime`	time (in ms) between drawing app UI and starting server. Default set to 1000 (1 second), but could need to be higher on slow machine.
`maxFileSize`	maximum file size in MB allowed for file upload

Server for core safetyGraphics app including Home, Mapping, Filter, Charts and Settings modules.

Description

This function returns a server function suitable for use in shiny::runApp()

Usage

safetyGraphicsServer(
  input,
  output,
  session,
  meta,
  mapping,
  domainData,
  charts,
  filterDomain,
  config
)
safetyGraphicsServer(
  input,
  output,
  session,
  meta,
  mapping,
  domainData,
  charts,
  filterDomain,
  config
)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`meta`	data frame containing the metadata for use in the app.
`mapping`	current mapping
`domainData`	named list of data.frames to be loaded in to the app.
`charts`	list of charts to include in the app
`filterDomain`	domain used for the data/filter tab. Demographics ("`dm`") is used by default. Using a domain that is not one record per participant is not recommended.

UI for the core safetyGraphics app including Home, Mapping, Filter, Charts and Settings modules.

Description

UI for the core safetyGraphics app including Home, Mapping, Filter, Charts and Settings modules.

Usage

safetyGraphicsUI(id, meta, mapping, domainData, charts, standards, config)
safetyGraphicsUI(id, meta, mapping, domainData, charts, standards, config)

Arguments

`id`	module ID
`meta`	data frame containing the metadata for use in the app.
`mapping`	data.frame specifying the initial values for each data mapping. If no mapping is provided, the app will attempt to generate one via `detectStandard()`
`domainData`	named list of data.frames to be loaded in to the app.
`charts`	list of charts in the format produced by safetyGraphics::makeChartConfig()
`standards`	a list of information regarding data standards. Each list item should use the format returned by safetyGraphics::detectStandard.

Server for settings tab showing details for the charts loaded in the app

Description

Server for settings tab showing details for the charts loaded in the app

Usage

settingsCharts(input, output, session, charts)
settingsCharts(input, output, session, charts)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`charts`	list data frame summarizing the charts

UI for settings tab showing details for the charts loaded in the app

Description

UI for settings tab showing details for the charts loaded in the app

Usage

settingsChartsUI(id)
settingsChartsUI(id)

Arguments

id

module id

Server for settings tab providing code to re-start the app with current data/settings

Description

Server for settings tab providing code to re-start the app with current data/settings

Usage

settingsCode(input, output, session, mapping, charts, domainData)
settingsCode(input, output, session, mapping, charts, domainData)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`mapping`	mapping
`charts`	charts
`domainData`	data list

UI for settings tab providing code to re-start the app with current data/settings

Description

UI for settings tab providing code to re-start the app with current data/settings

Usage

settingsCodeUI(id)
settingsCodeUI(id)

Arguments

id

module ID

Server for settings tab showing current data

Description

Server for settings tab showing current data

Usage

settingsData(input, output, session, domains)
settingsData(input, output, session, domains)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`domains`	named list of the data.frames for each domain

UI for settings tab showing current data

Description

UI for settings tab showing current data

Usage

settingsDataUI(id)
settingsDataUI(id)

Arguments

id

module id

Server for settings tab showing current mapping

Description

Server for settings tab showing current mapping

Usage

settingsMapping(input, output, session, metadata, mapping)
settingsMapping(input, output, session, metadata, mapping)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`metadata`	Data mapping metadata used for initial loading of app
`mapping`	reactive data frame representing the current metadata mapping. columns = "domain", "text_id" and "current"

UI for settings tab showing current mapping

Description

UI for settings tab showing current mapping

Usage

settingsMappingUI(id)
settingsMappingUI(id)

Arguments

id

module id

Server for the setting page

Description

Server for the setting page

Usage

settingsTab(input, output, session, domains, metadata, mapping, charts)
settingsTab(input, output, session, domains, metadata, mapping, charts)

Arguments

`input`	Shiny input object
`output`	Shiny output object
`session`	Shiny session object
`domains`	domains
`metadata`	metadata
`mapping`	mapping
`charts`	charts

UI for the settings tab

Description

UI for the settings tab

Usage

settingsTabUI(id)
settingsTabUI(id)

Arguments

id

module ID

Package 'safetyGraphics'

Help Index

Startup code for shiny app

Description

Usage

Arguments

Value

Server for a navbar tab

Description

Usage

Arguments

Adds a navbar tab that initializes the Chart Module UI

Description

Usage

Arguments

Server for chart module, designed to be re-used for each chart generated.

Description

Usage

Arguments

UI for chart module, designed to be re-used for each chart generated.

Description

Usage

Arguments

Detect the data standard used for a data set

Description

Usage

Arguments

Details

Value

Examples

Evaluate a data set against a data standard

Description

Usage

Arguments

Value

Examples

Server for the filter module in datamods::filter_data_ui

Description

Usage

Arguments

Value

Checks for whether the current data and settings support a filter tab

Description

Usage

Arguments

Value

UI for the filter module in datamods::filter_data_ui

Description

Usage

Arguments

Convert mapping data.frame to a list

Description

Usage

Arguments

Server for the filter module in datamods::filter_data_ui

Description

Usage

Arguments

UI for the home module

Description

Usage

Arguments

Server for the chart loading module used in safetyGraphicsInit()

Description

Usage

Arguments

UI for the chart loading module used in safetyGraphicsInit()

Description

Usage

Arguments

Server for the data loading module used in safetyGraphicsInit()

Description

Usage

Arguments

UI for the data loading module used in safetyGraphicsInit()

Description

Usage

Arguments

Make Chart Config

Description