# Clinical Data Review Tool

## Documentation for package ‘clinDataReview’ version 1.4.0

- 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.
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.
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
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