Clinical Data Review Tool

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Documentation for package ‘clinDataReview’ version 1.6.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

addDateOfReportRun	Add date of report running
addFacetPanel	Add facet-panel to single plotly plot.
addLayerToScatterPlot	Helper function to add layer to scatter plot
addReferenceLinesClinDataPlot	Add reference (horizontal/vertical/diagonal) lines to a clinical data plot
addSelectBtn	Add selection box(es) to a plotly plot.
addWatermark	Add a watermark to a 'plotly' object.
annotateData	Annotate a dataset.
barplotClinData	Barplot visualization of clinical data.
boxplotClinData	Boxplot interactive plot.
buildBook	Build the book
checkAvailabilityMetadata	Check availability of arguments in list
checkChapterParallel	Check if a chapter is run internally in parallel or not.
checkConfigFile	Check a configuration file (in _YAML_ format) based on a requirement file in JSON Schema format.
checkReportTitles	Check report titles
checkTemplatesName	Checks of config files template.
checkValueType	Check if the specified 'valueType' parameter can be passed to the 'branchvalues' of the 'plot_ly' treemap/sunburst visualizations.
clinDataReview-common-args	Common arguments for the functions of the clinDataReview package
clinDataReview-common-args-report	Common parameters for the clinical data reporting function
clinDataReview-common-args-summaryStatsVis	Common arguments for the plotting functions summary statistics of the clinDataReview package
clinDataReview-templates	Rmarkdown templates for clinical data
collapseHtmlContent	Function to create collapsible HTML content
combineButtonsAndPlot	Combine select box(es) and the plot
convertMdToHtml	Convert the Md file for a specific chapter to html
convertReportToAspx	Convert report format from .html to .aspx
countNLines	Count number of lines in a vector
createClinDataReviewReportSkeleton	Create the skeleton of a report
createExampleMetadata	Create an example metadata file
createMainConfigSkeleton	Create the config file for the skeleton
createOutputYaml	Create a output YAML file
createPatientProfileVar	Create link to patient profile
createRedirectPage	Create a redirect page
createTemplateDoc	Create documentation for clinical data template reports available in the 'template' folder of the package.
errorbarClinData	Interactive plot of confidence interval/error interval of clinical data.
exportSessionInfoToMd	Combine all session informations across all clinical data reports and export them into a dedicated Markdown document
filterData	Filter a dataset based on specified filters.
filterDataSingle	Filter data for a single filter
forceParams	Force the evaluation of the parameters from config file.
formatDataForPlotClinData	Format data for interactive plot for clinical data
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.
formatPathDateInfoMetadata	Format the info on paths from metadata
formatPlotlyClinData	Format interactive plot, with possibility to download patient profiles on a click event.
formatToHierarchicalData	Format data to a hierarchical data, in the format as required by the plotly sunburst and treemap.
getAxisLab	Get axis label
getAxisLabs	Set different variables for the x-axis labels
getAxisLimPlot	Get axis limits for a 'ggplot' plot from the input dataset.
getDataReferenceLines	Extract data for the reference lines
getDimGgplot	Get plot dimensions
getExtraDirs	Get extra directory(ies) required for the clinical data review report
getFacetVars	Get facetting variables from facet parameters.
getFctCode	Get function code
getFctTypeReferenceLines	Get the names of the 'ggplot' function to use for the reference lines
getHeightLab	Get height of labels: title, subtitle or caption
getHTMLToc	Get HTML toc
getIndexHTMLTitle	Get index of the line containing the HTML title in a vector of HTML strings
getInterimResFile	Get interim res file
getJitterVar	Add jitter to the variable of the plot, based on the different groups of a grouping variable
getJsDepClinDataReview	Get Javascript custom scripts required for specific clinical data functionalities.
getMdFromConfig	Get path of the 'HTML' file corresponding to a specific config file.
getMdHeader	Get Markdown header, for creation in Rmarkdown.
getMetadata	Read metadata file
getParamsFromConfig	Get parameters from a config file
getParFctReferenceLines	Get parameter of function used for reference lines
getPathHyperlink	Get path ('href') property from hyperlink(s).
getPathTemplate	Get path of template clinical data report
getPlotTableVars	Extract variables displayed in the attached table, for each available plotting function of the clinDataReview package.
getPositionAndMargins	Get margins and positions of specific elements for a clinical data plot
getSizePlot	Get dimensions for a clinical data plot
getTocNumbering	Get TOC numbering
getWatermark	Get a watermark, to be included in a clinical visualization
gitbook_clinDataReview_report	Clinical data format for bookdown report.
html_clinDataReview_report	Clinical data format for rmarkdown report.
JSONSchToRd	Get R Documentation from a JSON schema.
knitPrintClinDataReview	Include output from clinical data, or list of such outputs in a Rmarkdown report, with an appropriate title.
knit_print.clinDataReview	Print 'clinDataReviewTable' object in a knitted document (e.g. Rmarkdown document).
knit_print.clinDataReviewMetadata	Print metadata file in the clinical data report
layoutClinData	Set layout for a clinical data plot.
merge.sessionInfo	Merge multiple session information
moveSkeletonFiles	Move skeleton files from the package to a directory
moveXpt	Move data sets from clinUtils
plotCountClinData	Interactive plot of 'count' data
postProcessReport	Convert clinical data Markdown files to HTML
print.clinDataReview	Print a 'clinDataReview' object in the console
processData	Process a dataset.
renamePathDateInfoMetadata	Rename variable names of metadata info
renderChapter	Render one chapter of a clinical report, based on a configuration file
renderFile	Render a rmarkdown file, possibly in a new R session
render_clinDataReviewReport	Render a clinical data review report.
scatterplotClinData	Scatterplot of variables of interest for clinical data visualization.
setFacetLayoutWrap	Set facetting layout for 'wrap' facetting.
setPaletteStaticScatterplotClinData	Get standard palette for the 'staticScatterplotClinData' function.
splitChapter	Split a chapter based on the 'split_by' parameter.
staticScatterplotClinData	Scatterplot of variables of interest for clinical data visualization
sunburstClinData	Sunburst interactive plot.
tableClinData	Create a 'clinical data table', associated to a plot.
timeProfileIntervalPlot	Visualize time intervals across subjects/parameters.
transformData	Transform data.
treemapClinData	Treemap interactive plot.
varToFm	Get formula for a specific variable, to be used in aesthetic specification in 'plot_ly'.
zipClinDataReview	Zip the clinical data report