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clinDataReview (version 1.6.2)

Clinical Data Review Tool

Description

Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.

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Install

install.packages('clinDataReview')

Monthly Downloads

477

Version

1.6.2

License

MIT + file LICENSE

Issues

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Repository

https://github.com/openanalytics/clinDataReview

Maintainer

Laure Cougnaud

Last Published

April 11th, 2025

Functions in clinDataReview (1.6.2)

checkChapterParallel

Check if a chapter is run internally in parallel or not.

checkReportTitles

Check report titles

clinDataReview-common-args-summaryStatsVis

Common arguments for the plotting functions summary statistics of the clinDataReview package

checkConfigFile

Check a configuration file (in _YAML_ format) based on a requirement file in JSON Schema format.

Check if the specified valueType parameter can be passed to the branchvalues of the plot_ly treemap/sunburst visualizations.

clinDataReview-common-args-report

Common parameters for the clinical data reporting function

clinDataReview-common-args

Common arguments for the functions of the clinDataReview package

checkTemplatesName

Checks of config files template.

checkAvailabilityMetadata

Check availability of arguments in list

createClinDataReviewReportSkeleton

Create the skeleton of a report

createMainConfigSkeleton

Create the config file for the skeleton

createOutputYaml

Create a output YAML file

clinDataReview-templates

Rmarkdown templates for clinical data

Count number of lines in a vector

collapseHtmlContent

Function to create collapsible HTML content

convertReportToAspx

Convert report format from .html to .aspx

createExampleMetadata

Create an example metadata file

combineButtonsAndPlot

Combine select box(es) and the plot

convertMdToHtml

Convert the Md file for a specific chapter to html

Force the evaluation of the parameters from config file.

filterDataSingle

Filter data for a single filter

Filter a dataset based on specified filters.

exportSessionInfoToMd

Combine all session informations across all clinical data reports and export them into a dedicated Markdown document

createRedirectPage

Create a redirect page

createTemplateDoc

Create documentation for clinical data template reports available in the 'template' folder of the package.

formatDataForPlotClinData

Format data for interactive plot for clinical data

createPatientProfileVar

Create link to patient profile

errorbarClinData

Interactive plot of confidence interval/error interval of clinical data.

Set different variables for the x-axis labels

Get extra directory(ies) required for the clinical data review report

formatPathDateInfoMetadata

Format the info on paths from metadata

getDataReferenceLines

Extract data for the reference lines

formatHoverText

Format hover text for use in plotly interactive plots. The labels are wrapped to multiple lines if exceed the width of the plotly hover box, e.g. in case labels for points with same x/y coordinates overlap, and corresponding labels are truncated.

Get plot dimensions

Get facetting variables from facet parameters.

formatPlotlyClinData

Format interactive plot, with possibility to download patient profiles on a click event.

getIndexHTMLTitle

Get index of the line containing the HTML title in a vector of HTML strings

getFctTypeReferenceLines

Get the names of the ggplot function to use for the reference lines

Get function code

formatToHierarchicalData

Format data to a hierarchical data, in the format as required by the plotly sunburst and treemap.

Get height of labels: title, subtitle or caption

Get axis limits for a ggplot plot from the input dataset.

getPathHyperlink

Get path ('href') property from hyperlink(s).

getParamsFromConfig

Get parameters from a config file

getMdFromConfig

Get path of the HTML file corresponding to a specific config file.

getPlotTableVars

Extract variables displayed in the attached table, for each available plotting function of the clinDataReview package.

getPathTemplate

Get path of template clinical data report

Get Markdown header, for creation in Rmarkdown.

getTocNumbering

Get TOC numbering

html_clinDataReview_report

Clinical data format for rmarkdown report.

Add jitter to the variable of the plot, based on the different groups of a grouping variable

getParFctReferenceLines

Get parameter of function used for reference lines

Read metadata file

getJsDepClinDataReview

Get Javascript custom scripts required for specific clinical data functionalities.

gitbook_clinDataReview_report

Clinical data format for bookdown report.

knit_print.clinDataReviewMetadata

Print metadata file in the clinical data report

Get a watermark, to be included in a clinical visualization

Set layout for a clinical data plot.

knit_print.clinDataReview

Print clinDataReviewTable object in a knitted document (e.g. Rmarkdown document).

knitPrintClinDataReview

Include output from clinical data, or list of such outputs in a Rmarkdown report, with an appropriate title.

merge.sessionInfo

Merge multiple session information

moveSkeletonFiles

Move skeleton files from the package to a directory

setPaletteStaticScatterplotClinData

Get standard palette for the staticScatterplotClinData function.

setFacetLayoutWrap

Set facetting layout for 'wrap' facetting.

render_clinDataReviewReport

Render a clinical data review report.

scatterplotClinData

Scatterplot of variables of interest for clinical data visualization.

Move data sets from clinUtils

Get dimensions for a clinical data plot

getInterimResFile

Get interim res file

plotCountClinData

Interactive plot of 'count' data

renamePathDateInfoMetadata

Rename variable names of metadata info

getPositionAndMargins

Get margins and positions of specific elements for a clinical data plot

Process a dataset.

Render a rmarkdown file, possibly in a new R session

Render one chapter of a clinical report, based on a configuration file

postProcessReport

Convert clinical data Markdown files to HTML

print.clinDataReview

Print a clinDataReview object in the console

Split a chapter based on the 'split_by' parameter.

sunburstClinData

Sunburst interactive plot.

Create a 'clinical data table', associated to a plot.

treemapClinData

Treemap interactive plot.

Get formula for a specific variable, to be used in aesthetic specification in plot_ly.

zipClinDataReview

Zip the clinical data report

staticScatterplotClinData

Scatterplot of variables of interest for clinical data visualization

Transform data.

timeProfileIntervalPlot

Visualize time intervals across subjects/parameters.

Add selection box(es) to a plotly plot.

boxplotClinData

Boxplot interactive plot.

Get R Documentation from a JSON schema.

addDateOfReportRun

Add date of report running

Add facet-panel to single plotly plot.

addLayerToScatterPlot

Helper function to add layer to scatter plot

Add a watermark to a plotly object.

addReferenceLinesClinDataPlot

Add reference (horizontal/vertical/diagonal) lines to a clinical data plot

Annotate a dataset.

barplotClinData

Barplot visualization of clinical data.