Man pages for clinDataReview
Clinical Data Review Tool

addDateOfReportRunAdd date of report running
addFacetPanelAdd facet-panel to single plotly plot.
addLayerToScatterPlotHelper function to add layer to scatter plot
addReferenceLinesClinDataPlotAdd reference (horizontal/vertical/diagonal) lines to a...
addSelectBtnAdd selection box(es) to a plotly plot.
addWatermarkAdd a watermark to a 'plotly' object.
annotateDataAnnotate a dataset.
barplotClinDataBarplot visualization of clinical data.
boxplotClinDataBoxplot interactive plot.
buildBookBuild the book
checkAvailabilityMetadataCheck availability of arguments in list
checkChapterParallelCheck if a chapter is run internally in parallel or not.
checkConfigFileCheck a configuration file (in _YAML_ format) based on a...
checkReportTitlesCheck report titles
checkTemplatesNameChecks of config files template.
checkValueTypeCheck if the specified 'valueType' parameter can be passed to...
clinDataReview-common-argsCommon arguments for the functions of the clinDataReview...
clinDataReview-common-args-reportCommon parameters for the clinical data reporting function
clinDataReview-common-args-summaryStatsVisCommon arguments for the plotting functions summary...
clinDataReview-templatesRmarkdown templates for clinical data
collapseHtmlContentFunction to create collapsible HTML content
combineButtonsAndPlotCombine select box(es) and the plot
convertMdToHtmlConvert the Md file for a specific chapter to html
convertReportToAspxConvert report format from .html to .aspx
countNLinesCount number of lines in a vector
createClinDataReviewReportSkeletonCreate the skeleton of a report
createExampleMetadataCreate an example metadata file
createMainConfigSkeletonCreate the config file for the skeleton
createOutputYamlCreate a output YAML file
createPatientProfileVarCreate link to patient profile
createRedirectPageCreate a redirect page
createTemplateDocCreate documentation for clinical data template reports...
errorbarClinDataInteractive plot of confidence interval/error interval of...
exportSessionInfoToMdCombine all session informations across all clinical data...
filterDataFilter a dataset based on specified filters.
filterDataSingleFilter data for a single filter
forceParamsForce the evaluation of the parameters from config file.
formatDataForPlotClinDataFormat data for interactive plot for clinical data
formatHoverTextFormat hover text for use in plotly interactive plots. The...
formatPathDateInfoMetadataFormat the info on paths from metadata
formatPlotlyClinDataFormat interactive plot, with possibility to download patient...
formatToHierarchicalDataFormat data to a hierarchical data, in the format as required...
getAxisLabGet axis label
getAxisLabsSet different variables for the x-axis labels
getAxisLimPlotGet axis limits for a 'ggplot' plot from the input dataset.
getDataReferenceLinesExtract data for the reference lines
getDimGgplotGet plot dimensions
getExtraDirsGet extra directory(ies) required for the clinical data...
getFacetVarsGet facetting variables from facet parameters.
getFctCodeGet function code
getFctTypeReferenceLinesGet the names of the 'ggplot' function to use for the...
getHeightLabGet height of labels: title, subtitle or caption
getHTMLTocGet HTML toc
getIndexHTMLTitleGet index of the line containing the HTML title in a vector...
getInterimResFileGet interim res file
getJitterVarAdd jitter to the variable of the plot, based on the...
getJsDepClinDataReviewGet Javascript custom scripts required for specific clinical...
getMdFromConfigGet path of the 'HTML' file corresponding to a specific...
getMdHeaderGet Markdown header, for creation in Rmarkdown.
getMetadataRead metadata file
getParamsFromConfigGet parameters from a config file
getParFctReferenceLinesGet parameter of function used for reference lines
getPathHyperlinkGet path ('href') property from hyperlink(s).
getPathTemplateGet path of template clinical data report
getPlotTableVarsExtract variables displayed in the attached table, for each...
getPositionAndMarginsGet margins and positions of specific elements for a clinical...
getSizePlotGet dimensions for a clinical data plot
getTocNumberingGet TOC numbering
getWatermarkGet a watermark, to be included in a clinical visualization
gitbook_clinDataReview_reportClinical data format for bookdown report.
html_clinDataReview_reportClinical data format for rmarkdown report.
JSONSchToRdGet R Documentation from a JSON schema.
knit_print.clinDataReviewPrint 'clinDataReviewTable' object in a knitted document...
knitPrintClinDataReviewInclude output from clinical data, or list of such outputs in...
knit_print.clinDataReviewMetadataPrint metadata file in the clinical data report
layoutClinDataSet layout for a clinical data plot.
merge.sessionInfoMerge multiple session information
moveSkeletonFilesMove skeleton files from the package to a directory
moveXptMove data sets from clinUtils
plotCountClinDataInteractive plot of 'count' data
postProcessReportConvert clinical data Markdown files to HTML
print.clinDataReviewPrint a 'clinDataReview' object in the console
processDataProcess a dataset.
renamePathDateInfoMetadataRename variable names of metadata info
renderChapterRender one chapter of a clinical report, based on a...
render_clinDataReviewReportRender a clinical data review report.
renderFileRender a rmarkdown file, possibly in a new R session
scatterplotClinDataScatterplot of variables of interest for clinical data...
setFacetLayoutWrapSet facetting layout for 'wrap' facetting.
setPaletteStaticScatterplotClinDataGet standard palette for the 'staticScatterplotClinData'...
splitChapterSplit a chapter based on the 'split_by' parameter.
staticScatterplotClinDataScatterplot of variables of interest for clinical data...
sunburstClinDataSunburst interactive plot.
tableClinDataCreate a 'clinical data table', associated to a plot.
timeProfileIntervalPlotVisualize time intervals across subjects/parameters.
transformDataTransform data.
treemapClinDataTreemap interactive plot.
varToFmGet formula for a specific variable, to be used in aesthetic...
zipClinDataReviewZip the clinical data report
clinDataReview documentation built on June 22, 2024, 10:03 a.m.