{ "_id": "6a1ea717b25058d4daad8cba", "Package": "clinDataReview", "Type": "Package", "Title": "Clinical Data Review Tool", "Version": "1.6.1", "Date": "2024-06-17", "Authors@R": "c(\nperson(given = \"Laure\", family = \"Cougnaud\", role = c(\"aut\", \"cre\"),\nemail = \"laure.cougnaud@openanalytics.eu\"),\nperson(given = \"Michela\", family = \"Pasetto\", role = \"aut\",\nemail = \"michela.pasetto@openanalytics.eu\"),\nperson(given = \"Lennart\", family = \"Tuijnder\", role = \"aut\"),\nperson(given = \"Adriaan\", family = \"Blommaert\", role = \"aut\"),\nperson(given = \"Arne\", family = \"De Roeck\", role = c(\"ctb\", \"rev\"),\ncomment = \"rev: tests\"),\nperson(given = \"Open Analytics\", role = \"cph\")\n)", "Description": "Creation of interactive tables, listings and figures\n('TLFs') and associated report for exploratory analysis of data\nin a clinical trial, e.g. for clinical oversight activities.\nInteractive figures include sunburst, treemap, scatterplot,\nline plot and barplot of counts data. Interactive tables\ninclude table of summary statistics (as counts of adverse\nevents, enrollment table) and listings. Possibility to compare\ndata (summary table or listing) across two data batches/sets. A\nclinical data review report is created via study-specific\nconfiguration files and template 'R Markdown' reports contained\nin the package.", "SystemRequirements": "pandoc (to create a clinical data review report)", "URL": "https://github.com/openanalytics/clinDataReview", "BugReports": "https://github.com/openanalytics/clinDataReview/issues", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.1", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libxml2-dev\nlibssl-dev libnode-dev libx11-dev zlib1g-dev", "Repository": "https://openanalytics.r-universe.dev", "Date/Publication": "2024-06-17 12:34:08 UTC", "RemoteUrl": "https://github.com/openanalytics/clindatareview", "RemoteRef": "HEAD", "RemoteSha": "51f8c48866daf0371a0123a6b1911fdb1ac34cee", "RemoteSubdir": "clinDataReview", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 09:44:33 UTC", "User": "root" }, "Author": "Laure Cougnaud [aut, cre],\nMichela Pasetto [aut],\nLennart Tuijnder [aut],\nAdriaan Blommaert [aut],\nArne De Roeck [ctb, rev] (rev: tests),\nOpen Analytics [cph]", "Maintainer": "Laure Cougnaud ", "MD5sum": "93ac992b998e8d0f592e905ce7ebb7d7", "_user": "openanalytics", "_type": "src", "_file": "clinDataReview_1.6.1.tar.gz", "_fileid": "b4aa3a561d9d67cdd949444e75c436b720174b3e819d2c77248a5b36eb1f1a60", "_filesize": 1123104, "_sha256": "b4aa3a561d9d67cdd949444e75c436b720174b3e819d2c77248a5b36eb1f1a60", "_created": "2026-06-02T09:44:33.000Z", "_published": "2026-06-02T09:49:11.930Z", "_distro": "noble", "_jobs": [ { "job": 79043489680, "time": 228, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7354407378" }, { "job": 79043489765, "time": 173, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7354387755" }, { "job": 79043489716, "time": 106, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7354364270" }, { "job": 79043489720, "time": 139, "config": 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"date": "2021-10-02" }, { "version": "1.2.2", "date": "2022-02-23" }, { "version": "1.3.1", "date": "2022-10-10" }, { "version": "1.4.0", "date": "2023-02-24" }, { "version": "1.5.0", "date": "2023-12-11" }, { "version": "1.5.1", "date": "2024-04-24" }, { "version": "1.5.2", "date": "2024-05-17" }, { "version": "1.6.0", "date": "2024-06-14" }, { "version": "1.6.1", "date": "2024-06-18" }, { "version": "1.6.2", "date": "2025-04-11" } ], "_exports": [ "addWatermark", "annotateData", "barplotClinData", "boxplotClinData", "checkConfigFile", "collapseHtmlContent", "convertReportToAspx", "createClinDataReviewReportSkeleton", "createPatientProfileVar", "createRedirectPage", "errorbarClinData", "filterData", "forceParams", "formatHoverText", "formatPlotlyClinData", "getExtraDirs", "getJsDepClinDataReview", "getMdHeader", "getMetadata", "getParamsFromConfig", "getPathHyperlink", "getPathTemplate", "getPlotTableVars", "getWatermark", "gitbook_clinDataReview_report", "html_clinDataReview_report", "knitPrintClinDataReview", "plotCountClinData", "postProcessReport", "processData", "render_clinDataReviewReport", "scatterplotClinData", "sunburstClinData", "tableClinData", "timeProfileIntervalPlot", "transformData", "treemapClinData", "varToFm", "zipClinDataReview" ], "_help": [ { "page": "addDateOfReportRun", "title": "Add date of report running", "topics": [ "addDateOfReportRun" ] }, { "page": "addFacetPanel", "title": "Add facet-panel to single plotly plot.", "topics": [ "addFacetPanel" ] }, { "page": "addLayerToScatterPlot", "title": "Helper function to add layer to scatter plot", "topics": [ "addLayerToScatterPlot" ] }, { "page": "addReferenceLinesClinDataPlot", "title": "Add reference (horizontal/vertical/diagonal) lines to a clinical data plot", "topics": [ "addReferenceLinesClinDataPlot" ] }, { "page": "addSelectBtn", "title": "Add selection box(es) to a plotly plot.", "topics": [ "addSelectBtn" ] }, { "page": "addWatermark", "title": "Add a watermark to a 'plotly' object.", "concept": [ "watermark helpers" ], "topics": [ "addWatermark" ] }, { "page": "annotateData", "title": "Annotate a dataset.", "topics": [ "annotateData" ] }, { "page": "barplotClinData", "title": "Barplot visualization of clinical data.", "concept": [ "visualizations of summary statistics for clinical data" ], "topics": [ "barplotClinData" ] }, { "page": "boxplotClinData", "title": "Boxplot interactive plot.", "concept": [ "visualizations of summary statistics for clinical data" ], "topics": [ "boxplotClinData" ] }, { "page": "buildBook", "title": "Build the book", "topics": [ "buildBook" ] }, { "page": "checkAvailabilityMetadata", "title": "Check availability of arguments in list", "topics": [ "checkAvailabilityMetadata" ] }, { "page": "checkChapterParallel", "title": "Check if a chapter is run internally in parallel or not.", "topics": [ "checkChapterParallel" ] }, { "page": "checkConfigFile", "title": "Check a configuration file (in _YAML_ format) based on a requirement file in JSON Schema format.", "topics": [ "checkConfigFile" ] }, { "page": "checkReportTitles", "title": "Check report titles", "concept": [ "clinical data reporting" ], "topics": [ "checkReportTitles" ] }, { "page": "checkTemplatesName", "title": "Checks of config files template.", "topics": [ "checkTemplatesName" ] }, { "page": "checkValueType", "title": "Check if the specified 'valueType' parameter can be passed to the 'branchvalues' of the 'plot_ly' treemap/sunburst visualizations.", "topics": [ "checkValueType" ] }, { "page": "clinDataReview-common-args", "title": "Common arguments for the functions of the clinDataReview package", "topics": [ "clinDataReview-common-args" ] }, { "page": "clinDataReview-common-args-report", "title": "Common parameters for the clinical data reporting function", "topics": [ "clinDataReview-common-args-report" ] }, { "page": "clinDataReview-common-args-summaryStatsVis", "title": "Common arguments for the plotting functions summary statistics of the clinDataReview package", "topics": [ "clinDataReview-common-args-summaryStatsVis" ] }, { "page": "clinDataReview-templates", "title": "Rmarkdown templates for clinical data", "topics": [ "clinDataReview-templates" ] }, { "page": "collapseHtmlContent", "title": "Function to create collapsible HTML content", "topics": [ "collapseHtmlContent" ] }, { "page": "combineButtonsAndPlot", "title": "Combine select box(es) and the plot", "topics": [ "combineButtonsAndPlot" ] }, { "page": "convertMdToHtml", "title": "Convert the Md file for a specific chapter to html", "topics": [ "convertMdToHtml" ] }, { "page": "convertReportToAspx", "title": "Convert report format from .html to .aspx", "topics": [ "convertReportToAspx" ] }, { "page": "countNLines", "title": "Count number of lines in a vector", "topics": [ "countNLines" ] }, { "page": "createClinDataReviewReportSkeleton", "title": "Create the skeleton of a report", "topics": [ "createClinDataReviewReportSkeleton" ] }, { "page": "createExampleMetadata", "title": "Create an example metadata file", "topics": [ "createExampleMetadata" ] }, { "page": "createMainConfigSkeleton", "title": "Create the config file for the skeleton", "topics": [ "createMainConfigSkeleton" ] }, { "page": "createOutputYaml", "title": "Create a output YAML file", "topics": [ "createOutputYaml" ] }, { "page": "createPatientProfileVar", "title": "Create link to patient profile", "topics": [ "createPatientProfileVar" ] }, { "page": "createRedirectPage", "title": "Create a redirect page", "topics": [ "createRedirectPage" ] }, { "page": "createTemplateDoc", "title": "Create documentation for clinical data template reports available in the 'template' folder of the package.", "topics": [ "createTemplateDoc" ] }, { "page": "errorbarClinData", "title": "Interactive plot of confidence interval/error interval of clinical data.", "concept": [ "visualizations of summary statistics for clinical data" ], "topics": [ "errorbarClinData" ] }, { "page": "exportSessionInfoToMd", "title": "Combine all session informations across all clinical data reports and export them into a dedicated Markdown document", "topics": [ "exportSessionInfoToMd" ] }, { "page": "filterData", "title": "Filter a dataset based on specified filters.", "topics": [ "filterData" ] }, { "page": "filterDataSingle", "title": "Filter data for a single filter", "topics": [ "filterDataSingle" ] }, { "page": "forceParams", "title": "Force the evaluation of the parameters from config file.", "concept": [ "clinical data reporting" ], "topics": [ "forceParams" ] }, { "page": "formatDataForPlotClinData", "title": "Format data for interactive plot for clinical data", "topics": [ "formatDataForPlotClinData" ] }, { "page": "formatHoverText", "title": "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.", "topics": [ "formatHoverText" ] }, { "page": "formatPathDateInfoMetadata", "title": "Format the info on paths from metadata", "topics": [ "formatPathDateInfoMetadata" ] }, { "page": "formatPlotlyClinData", "title": "Format interactive plot, with possibility to download patient profiles on a click event.", "topics": [ "formatPlotlyClinData" ] }, { "page": "formatToHierarchicalData", "title": "Format data to a hierarchical data, in the format as required by the plotly sunburst and treemap.", "topics": [ "formatToHierarchicalData" ] }, { "page": "getAxisLab", "title": "Get axis label", "topics": [ "getAxisLab" ] }, { "page": "getAxisLabs", "title": "Set different variables for the x-axis labels", "topics": [ "getAxisLabs" ] }, { "page": "getAxisLimPlot", "title": "Get axis limits for a 'ggplot' plot from the input dataset.", "topics": [ "getAxisLimPlot" ] }, { "page": "getDataReferenceLines", "title": "Extract data for the reference lines", "topics": [ "getDataReferenceLines" ] }, { "page": "getDimGgplot", "title": "Get plot dimensions", "topics": [ "getDimGgplot" ] }, { "page": "getExtraDirs", "title": "Get extra directory(ies) required for the clinical data review report", "topics": [ "getExtraDirs" ] }, { "page": "getFacetVars", "title": "Get facetting variables from facet parameters.", "topics": [ "getFacetVars" ] }, { "page": "getFctCode", "title": "Get function code", "topics": [ "getFctCode" ] }, { "page": "getFctTypeReferenceLines", "title": "Get the names of the 'ggplot' function to use for the reference lines", "topics": [ "getFctTypeReferenceLines" ] }, { "page": "getHeightLab", "title": "Get height of labels: title, subtitle or caption", "topics": [ "getHeightLab" ] }, { "page": "getHTMLToc", "title": "Get HTML toc", "topics": [ "getHTMLToc" ] }, { "page": "getIndexHTMLTitle", "title": "Get index of the line containing the HTML title in a vector of HTML strings", "topics": [ "getIndexHTMLTitle" ] }, { "page": "getInterimResFile", "title": "Get interim res file", "topics": [ "getInterimResFile" ] }, { "page": "getJitterVar", "title": "Add jitter to the variable of the plot, based on the different groups of a grouping variable", "topics": [ "getJitterVar" ] }, { "page": "getJsDepClinDataReview", "title": "Get Javascript custom scripts required for specific clinical data functionalities.", "topics": [ "getJsDepClinDataReview" ] }, { "page": "getMdFromConfig", "title": "Get path of the 'HTML' file corresponding to a specific config file.", "topics": [ "getMdFromConfig" ] }, { "page": "getMdHeader", "title": "Get Markdown header, for creation in Rmarkdown.", "concept": [ "clinical data reporting" ], "topics": [ "getMdHeader" ] }, { "page": "getMetadata", "title": "Read metadata file", "topics": [ "getMetadata" ] }, { "page": "getParamsFromConfig", "title": "Get parameters from a config file", "concept": [ "clinical data reporting" ], "topics": [ "getParamsFromConfig" ] }, { "page": "getParFctReferenceLines", "title": "Get parameter of function used for reference lines", "topics": [ "getParFctReferenceLines" ] }, { "page": "getPathHyperlink", "title": "Get path ('href') property from hyperlink(s).", "topics": [ "getPathHyperlink" ] }, { "page": "getPathTemplate", "title": "Get path of template clinical data report", "topics": [ "getPathTemplate" ] }, { "page": "getPlotTableVars", "title": "Extract variables displayed in the attached table, for each available plotting function of the clinDataReview package.", "topics": [ "getPlotTableVars" ] }, { "page": "getPositionAndMargins", "title": "Get margins and positions of specific elements for a clinical data plot", "topics": [ "getPositionAndMargins" ] }, { "page": "getSizePlot", "title": "Get dimensions for a clinical data plot", "topics": [ "getSizePlot" ] }, { "page": "getTocNumbering", "title": "Get TOC numbering", "topics": [ "getTocNumbering" ] }, { "page": "getWatermark", "title": "Get a watermark, to be included in a clinical visualization", "concept": [ "watermark helpers" ], "topics": [ "getWatermark" ] }, { "page": "gitbook_clinDataReview_report", "title": "Clinical data format for bookdown report.", "concept": [ "clinical data reporting" ], "topics": [ "gitbook_clinDataReview_report" ] }, { "page": "html_clinDataReview_report", "title": "Clinical data format for rmarkdown report.", "concept": [ "clinical data reporting" ], "topics": [ "html_clinDataReview_report" ] }, { "page": "JSONSchToRd", "title": "Get R Documentation from a JSON schema.", "topics": [ "JSONSchToRd" ] }, { "page": "knit_print.clinDataReview", "title": "Print 'clinDataReviewTable' object in a knitted document (e.g. Rmarkdown document).", "topics": [ "knit_print.clinDataReview" ] }, { "page": "knit_print.clinDataReviewMetadata", "title": "Print metadata file in the clinical data report", "topics": [ "knit_print.clinDataReviewMetadata" ] }, { "page": "knitPrintClinDataReview", "title": "Include output from clinical data, or list of such outputs in a Rmarkdown report, with an appropriate title.", "concept": [ "clinical data reporting" ], "topics": [ "knitPrintClinDataReview" ] }, { "page": "layoutClinData", "title": "Set layout for a clinical data plot.", "topics": [ "layoutClinData" ] }, { "page": "merge.sessionInfo", "title": "Merge multiple session information", "topics": [ "merge.sessionInfo" ] }, { "page": "moveSkeletonFiles", "title": "Move skeleton files from the package to a directory", "topics": [ "moveSkeletonFiles" ] }, { "page": "moveXpt", "title": "Move data sets from clinUtils", "topics": [ "moveXpt" ] }, { "page": "plotCountClinData", "title": "Interactive plot of 'count' data", "concept": [ "visualizations of summary statistics for clinical data" ], "topics": [ "plotCountClinData" ] }, { "page": "postProcessReport", "title": "Convert clinical data Markdown files to HTML", "concept": [ "clinical data reporting" ], "topics": [ "postProcessReport" ] }, { "page": "print.clinDataReview", "title": "Print a 'clinDataReview' object in the console", "topics": [ "print.clinDataReview" ] }, { "page": "processData", "title": "Process a dataset.", "topics": [ "processData" ] }, { "page": "renamePathDateInfoMetadata", "title": "Rename variable names of metadata info", "topics": [ "renamePathDateInfoMetadata" ] }, { "page": "render_clinDataReviewReport", "title": "Render a clinical data review report.", "concept": [ "clinical data reporting" ], "topics": [ "render_clinDataReviewReport" ] }, { "page": "renderChapter", "title": "Render one chapter of a clinical report, based on a configuration file", "topics": [ "renderChapter" ] }, { "page": "renderFile", "title": "Render a rmarkdown file, possibly in a new R session", "topics": [ "renderFile" ] }, { "page": "scatterplotClinData", "title": "Scatterplot of variables of interest for clinical data visualization.", "concept": [ "Clinical data visualization of individual profiles." ], "topics": [ "scatterplotClinData" ] }, { "page": "setFacetLayoutWrap", "title": "Set facetting layout for 'wrap' facetting.", "topics": [ "setFacetLayoutWrap" ] }, { "page": "setPaletteStaticScatterplotClinData", "title": "Get standard palette for the 'staticScatterplotClinData' function.", "topics": [ "setPaletteStaticScatterplotClinData" ] }, { "page": "splitChapter", "title": "Split a chapter based on the 'split_by' parameter.", "topics": [ "splitChapter" ] }, { "page": "staticScatterplotClinData", "title": "Scatterplot of variables of interest for clinical data visualization", "topics": [ "staticScatterplotClinData" ] }, { "page": "sunburstClinData", "title": "Sunburst interactive plot.", "concept": [ "visualizations of summary statistics for clinical data" ], "topics": [ "sunburstClinData" ] }, { "page": "tableClinData", "title": "Create a 'clinical data table', associated to a plot.", "topics": [ "tableClinData" ] }, { "page": "timeProfileIntervalPlot", "title": "Visualize time intervals across subjects/parameters.", "concept": [ "Clinical data visualization of individual profiles." ], "topics": [ "timeProfileIntervalPlot" ] }, { "page": "transformData", "title": "Transform data.", "topics": [ "transformData" ] }, { "page": "treemapClinData", "title": "Treemap interactive plot.", "concept": [ "visualizations of summary statistics for clinical data" ], "topics": [ "treemapClinData" ] }, { "page": "varToFm", "title": "Get formula for a specific variable, to be used in aesthetic specification in 'plot_ly'.", "topics": [ "varToFm" ] }, { "page": "zipClinDataReview", "title": "Zip the clinical data report", "topics": [ "zipClinDataReview" ] } ], "_readme": "https://github.com/openanalytics/clindatareview/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bit", "bit64", "bookdown", "bslib", "cachem", "cli", "clinUtils", "clipr", "cpp11", 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