# Clinical Data Review Tool

## Documentation for package ‘clinDataReview’ version 1.2.2

- 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.
addReferenceLinesClinDataPlot | Add reference (horizontal/vertical/diagonal) lines to a clinical data plot
annotateData | Annotate a SDTM dataset.
barplotClinData | Barplot interactive plot.
boxplotClinData | Boxplot interactive plot.
checkAvailabilityMetadata | Check availability of arguments in list
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
convertMdToHtml | Convert clinical data Markdown files to HTML
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
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 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.
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
getFacetVars | Get facetting variables from facet parameters.
getFctTypeReferenceLines | Get the names of the 'ggplot' function to use for the reference lines
getHeightLab | Get height of labels: title, subtitle or caption
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 'Markdown' 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
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
processData | Run specified data processing steps.
renamePathDateInfoMetadata | Rename variable names of metadata info
renderInNewSession | Render a rmarkdown doc in a new session, with the possibility to save output in a log file, and saving also session information.
render_clinDataReviewReport | Render a clinical data 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.
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