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Note: No additional development is currently planned on this package, but the safetyGraphics package has replaced it (with improvements!) for most purposes and is under active development.

Overview

safetyexploreR is an R package built using the HTML Widgets framework. safetyexploreR serves as an interface for Rho's safety explorer suite, a set of tools facilitating the exploration of adverse events, lab and vital sign data. The underlying tools are built using Webcharts, a JavaScript library based on d3.js.

Installation

safetyexploreR is still in development. The development version of this package can be installed using the following R code:

devtools::install_github('RhoInc/safetyexploreR', build_vignettes=TRUE)

Data specifications

Data requirements for Adverse Events Explorer and Timeline

The adverse events widgets require a data.frame that has a structure of 1 record per adverse event per subject. Required and optional variables are below. In parentheses are the required names for default settings.

Required variables include:

Unique participant ID ("USUBJID")
Adverse event major category ("AEBODSYS")
Adverse event minor category ("AEDCOD")
Adverse event reported term ("AETERM")
Group variable ("ARM")
Sequence number ("AESEQ")
Adverse event start date ("ASTDY")
Adverse event end date ("AENDY")

Optional variables include:

Adverse event seriousness ("AESER")
Adverse event severity ("AESEV")
Adverse event relationship ("AEREL")
Adverse event outcome ("AEOUT")
variables to be used in grouping, filtering, or listing such as: treatment arm, site ID, sex, race, query flag

Requirements for Safety Histogram, Outlier Explorer, Results Over Time, and Shift Plot

The other 4 safety widgets require a data.frame that has a structure of 1 record per value per visit per subject. Required and optional variables are below. In parentheses are the required names for default settings.

Required variables include:

Unique participant ID ("USUBJID")
Measure ("TEST")
Value ("STRESN")
Unit ("STRESU")
Normal range - lower limit ("STNRLO")
Normal range - upper limit ("STNRHI")
Timing of collection ("DY", "VISITN", "VISIT")

Optional variables include:

Age, sex, and race ("AGE", "SEX", "RACE")
variables to be used in grouping, filtering, or listing such as: treatment arm, site ID, query flag

Examples

There are two built-in example datasets, ADAE and ADBDS. Default charts can be rendered with the following code:

aeExplorer(data=ADAE)

aeTimelines(data=ADAE)

safetyHistogram(data=ADBDS)

safetyOutlierExplorer(data=ADBDS)

safetyResultsOverTime(data=ADBDS)

safetyShiftPlot(data=ADBDS)

Use

SafetyexploreR widgets can be rendered directly within your RStudio desktop application. You can embed widgets within an R Markdown report or a Shiny web application.