| Title: | Interactive Graphics for Monitoring Clinical Trial Safety |
| Version: | 2.1.1 |
| Maintainer: | Jeremy Wildfire <jwildfire@gmail.com> |
| Description: | A framework for evaluation of clinical trial safety. Users can interactively explore their data using the included 'Shiny' application. |
| URL: | https://github.com/SafetyGraphics/safetyGraphics |
| BugReports: | https://github.com/SafetyGraphics/safetyGraphics/issues |
| Depends: | R (≥ 4.0) |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.1 |
| Suggests: | ggplot2 (≥ 3.3.0), knitr (≥ 1.34), rmarkdown (≥ 2.10), shinydashboard (≥ 0.7.1), shinytest (≥ 1.5.0), testthat (≥ 3.0.4), usethis (≥ 2.0.1), listviewer (≥ 3.0.0), shinybusy (≥ 0.2.2), shinyWidgets (≥ 0.6.1) |
| Imports: | dplyr (≥ 1.0.0), DT (≥ 0.19), datamods (≥ 1.1.5), htmlwidgets (≥ 1.5.0), jsonlite (≥ 1.7.0), magrittr (≥ 2.0.0), purrr (≥ 0.3.0), rclipboard (≥ 0.1.3), rlang (≥ 0.4.11), safetyData (≥ 1.0.0), safetyCharts (≥ 0.3), shiny (≥ 1.6.0), shinyjs (≥ 2.0.0), sortable (≥ 0.4.4), stringr (≥ 1.4.0), tidyr (≥ 1.2.0), yaml (≥ 2.2.1) |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2022-12-14 21:34:13 UTC; jwildfire |
| Author: | Jeremy Wildfire [cre, aut], Becca Krouse [aut], Preston Burns [aut], Xiao Ni [aut], James Buchanan [aut], Susan Duke [aut] |
| Repository: | CRAN |
| Date/Publication: | 2022-12-14 22:00:02 UTC |
Pipe operator
Description
See magrittr::%>% for details.
Usage
lhs %>% rhs
safetyGraphics package
Description
Create Interactive Graphics Related to Clinical Trial Safety
Details
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
)
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 |
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 |
filterDomain |
domain used for the data/filter tab. Demographics (" |
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. |
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
Adds a navbar tab that initializes the Chart Module UI
Description
Adds a navbar tab that initializes the Chart Module UI
Usage
chartsNav(chart, ns)
Arguments
chart |
chart metadata |
ns |
namespace |
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)
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). |
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)
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)
Arguments
data |
A data frame in which to detect the data standard - required. |
domain |
the domain to evaluate - should match a value of |
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" )
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)
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 |
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"
)
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
)
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)
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)
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)
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 |
Check whether a column is found in a data set
Description
Checks whether a specified column is found in a specified data set
Usage
hasColumn(columnName, data)
Arguments
columnName |
The column to look for. |
data |
the data.frame to search. |
Value
logical scalar. TRUE if the column is found. FALSE otherwise
Examples
safetyGraphics:::hasColumn(columnName="PARAM",data=safetyData::adam_adlbc) #TRUE
safetyGraphics:::hasColumn(columnName="Not_a_column",data=safetyData::adam_adlbc) #FALSE
Check whether a specified field value is found in a data set
Description
This checks whether a specific value is found in a specified column in a specified data set
Usage
hasField(fieldValue, columnName, data)
Arguments
fieldValue |
A value to check for. |
columnName |
The column to check. |
data |
the data.frame to search. |
Value
logical scalar. TRUE if field_value is found. FALSE otherwise
Examples
#TRUE
safetyGraphics:::hasField(
fieldValue="Bilirubin (umol/L)",
columnName="PARAM",
data=safetyData::adam_adlbc
)
#FALSE
safetyGraphics:::hasField(
fieldValue="Not_a_real_value",
columnName="",
data=safetyData::adam_adlbc
)
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)
Arguments
input |
mod input |
output |
mod output |
session |
mod session |
UI for the home module
Description
UI for the home module
Usage
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())
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())
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)
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)
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
)
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 |
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
packagefield of the YAML config. Function names must include either thenameorworkflowfields of the YAML config.
Make Chart Export
Description
Creates R code that allows chart to be exported
Usage
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)
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, showLinks = TRUE, class = "chart-header")
Arguments
chart |
list containing chart specifications |
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)
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 |
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)
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)
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)
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)
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)
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)
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)
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)
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)
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 |
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)
Arguments
chart |
chart object like the one generated by makeChartConfig(). |
Value
returns the chart object with a new functions object added.
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,
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 |
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 |
filterDomain |
domain used for the data/filter tab. Demographics (" |
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. |
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
)
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
)
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 (" |
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, domainData, mapping, standards)
Arguments
id |
module ID |
meta |
data frame containing the metadata for use in the app. |
domainData |
named list of data.frames to be loaded in to 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 |
standards |
a list of information regarding data standards. Each list item should use the format returned by safetyGraphics::detectStandard. |
Set the value for a given named parameter
Description
Sets the value for a named parameter (key) to given value in a list (settings)
Usage
setMappingListValue(key, value, settings, forceCreate = FALSE)
Arguments
key |
a list defining the position of parameter in the settings object. |
value |
the value to set |
settings |
The settings list used to generate a chart like |
forceCreate |
Specifies whether the function should create a new list() when none exisits. This most commonly occurs when deeply nested objects. |
Value
the updated settings object
Examples
testSet<-list(a=list(b="myValue"))
safetyGraphics:::setMappingListValue(key=list("a","b"), value="notMyValue", settings=testSet)
#returns list(a=list(b="notMyValue")))
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)
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)
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)
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)
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)
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)
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)
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)
Arguments
id |
module id |
Server for the setting page
Description
Server for the setting page
Usage
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)
Arguments
id |
module ID |
Helper function to convert keys from text to nested lists
Description
Convert settings keys from text vectors (using the "–" delimiter) to a list of lists
Usage
textKeysToList(textKeys)
Arguments
textKeys |
a list (or vector) of character keys using the "–" delimiter to indicate hierarchy |
Value
A list of unnamed lists, with position in the nested list indicating hierarchy
Examples
safetyGraphics:::textKeysToList("id_col")
#list(list("id_col"))
#list(list("id_col"),list("measure_col","label"))
safetyGraphics:::textKeysToList(c("id_col","measure_col--label"))