Package: clinDataReview 1.6.1

Laure Cougnaud

clinDataReview: Clinical Data Review Tool

Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.

Authors:Laure Cougnaud [aut, cre], Michela Pasetto [aut], Lennart Tuijnder [aut], Adriaan Blommaert [aut], Arne De Roeck [ctb, rev], Open Analytics [cph]

clinDataReview_1.6.1.tar.gz
clinDataReview_1.6.1.zip(r-4.7)clinDataReview_1.6.1.zip(r-4.6)clinDataReview_1.6.1.zip(r-4.5)
clinDataReview_1.6.1.tgz(r-4.6-any)clinDataReview_1.6.1.tgz(r-4.5-any)
clinDataReview_1.6.1.tar.gz(r-4.7-any)clinDataReview_1.6.1.tar.gz(r-4.6-any)
clinDataReview_1.6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
clinDataReview/json (API)

# Install 'clinDataReview' in R:
install.packages('clinDataReview', repos = c('https://openanalytics.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/openanalytics/clindatareview/issues

On CRAN:

Conda:

6.44 score 12 stars 51 scripts 410 downloads 39 exports 83 dependencies

Last updated from:51f8c48866. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR208
source / vignettesOK215
linux-release-x86_64ERROR197
macos-release-arm64ERROR169
macos-oldrel-arm64ERROR142
windows-develERROR158
windows-releaseERROR144
windows-oldrelERROR187
wasm-releaseOK151

Exports:addWatermarkannotateDatabarplotClinDataboxplotClinDatacheckConfigFilecollapseHtmlContentconvertReportToAspxcreateClinDataReviewReportSkeletoncreatePatientProfileVarcreateRedirectPageerrorbarClinDatafilterDataforceParamsformatHoverTextformatPlotlyClinDatagetExtraDirsgetJsDepClinDataReviewgetMdHeadergetMetadatagetParamsFromConfiggetPathHyperlinkgetPathTemplategetPlotTableVarsgetWatermarkgitbook_clinDataReview_reporthtml_clinDataReview_reportknitPrintClinDataReviewplotCountClinDatapostProcessReportprocessDatarender_clinDataReviewReportscatterplotClinDatasunburstClinDatatableClinDatatimeProfileIntervalPlottransformDatatreemapClinDatavarToFmzipClinDataReview

Dependencies:askpassbase64encbitbit64bookdownbslibcachemcliclinUtilscliprcpp11crayoncrosstalkcurldata.tabledigestdplyrDTevaluatefarverfastmapfontawesomeforcatsfsgenericsggplot2gluegtablehavenhighrhmshtmltoolshtmlwidgetshttrisobandjquerylibjsonlitejsonvalidateknitrlabelinglaterlazyevallifecyclemagrittrmemoisemimeopensslotelpillarpkgconfigplotlyplyrprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrrlangrmarkdownS7sassscalesstringistringrsystibbletidyrtidyselecttinytextzdbutf8V8vctrsviridisLitevroomwithrxfunxml2yaml

Visualization of clinical data
Patient profiles | Data visualization | Visualization of individual profiles | Explore the visualization data | Link with patient profiles | Spaghetti plot of time profile | Scatterplot | eDish plot | Visualization of time-intervals | Visualization of summary statistics | Categorical variables | Compute count statistics | Sunburst | Treemap | Barplot | Continuous variable | Compute summary statistics | Plot error bars/confidence intervals | Boxplot | Multiple visualizations in a loop | Watermark | Palettes | Set palette for the entire session | Appendix | Session info
Rendered fromclinDataReview-dataVisualization.Rmdusingknitr::rmarkdown

Last update: 2024-06-11
Started: 2022-02-01

Creation of a clinical data review report
Create an example report | File structure | Input | Output | Template reports | Render a clinical data review report | Production | Create a report for production | Create redirect page | Convert to .aspx format | Zip and send the report to collaborators | Add metadata | Development | Modular framework | (Re-)run part(s) of the report | Create the final clinical data report from the Markdown reports | Debug a sub-report | Optimization for big clinical trial data | Optimize the report creation | Optimize the report loading time | Optimize the report structure | Appendix | Session info
Rendered fromclinDataReview-reporting.Rmdusingknitr::rmarkdown

Last update: 2023-02-14
Started: 2022-02-01

Pre-processing of clinical data for clinical data review report
Data format | Annotate data | Filter data | Transform data | Process data | Appendix | Session info
Rendered fromclinDataReview-dataPreprocessing.Rmdusingknitr::rmarkdown

Last update: 2022-10-12
Started: 2022-02-01

Readme and manuals

Help Manual

Help pageTopics
Add date of report runningaddDateOfReportRun
Add facet-panel to single plotly plot.addFacetPanel
Helper function to add layer to scatter plotaddLayerToScatterPlot
Add reference (horizontal/vertical/diagonal) lines to a clinical data plotaddReferenceLinesClinDataPlot
Add selection box(es) to a plotly plot.addSelectBtn
Add a watermark to a 'plotly' object.addWatermark
Annotate a dataset.annotateData
Barplot visualization of clinical data.barplotClinData
Boxplot interactive plot.boxplotClinData
Build the bookbuildBook
Check availability of arguments in listcheckAvailabilityMetadata
Check if a chapter is run internally in parallel or not.checkChapterParallel
Check a configuration file (in _YAML_ format) based on a requirement file in JSON Schema format.checkConfigFile
Check report titlescheckReportTitles
Checks of config files template.checkTemplatesName
Check if the specified 'valueType' parameter can be passed to the 'branchvalues' of the 'plot_ly' treemap/sunburst visualizations.checkValueType
Common arguments for the functions of the clinDataReview packageclinDataReview-common-args
Common parameters for the clinical data reporting functionclinDataReview-common-args-report
Common arguments for the plotting functions summary statistics of the clinDataReview packageclinDataReview-common-args-summaryStatsVis
Rmarkdown templates for clinical dataclinDataReview-templates
Function to create collapsible HTML contentcollapseHtmlContent
Combine select box(es) and the plotcombineButtonsAndPlot
Convert the Md file for a specific chapter to htmlconvertMdToHtml
Convert report format from .html to .aspxconvertReportToAspx
Count number of lines in a vectorcountNLines
Create the skeleton of a reportcreateClinDataReviewReportSkeleton
Create an example metadata filecreateExampleMetadata
Create the config file for the skeletoncreateMainConfigSkeleton
Create a output YAML filecreateOutputYaml
Create link to patient profilecreatePatientProfileVar
Create a redirect pagecreateRedirectPage
Create documentation for clinical data template reports available in the 'template' folder of the package.createTemplateDoc
Interactive plot of confidence interval/error interval of clinical data.errorbarClinData
Combine all session informations across all clinical data reports and export them into a dedicated Markdown documentexportSessionInfoToMd
Filter a dataset based on specified filters.filterData
Filter data for a single filterfilterDataSingle
Force the evaluation of the parameters from config file.forceParams
Format data for interactive plot for clinical dataformatDataForPlotClinData
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.formatHoverText
Format the info on paths from metadataformatPathDateInfoMetadata
Format interactive plot, with possibility to download patient profiles on a click event.formatPlotlyClinData
Format data to a hierarchical data, in the format as required by the plotly sunburst and treemap.formatToHierarchicalData
Get axis labelgetAxisLab
Set different variables for the x-axis labelsgetAxisLabs
Get axis limits for a 'ggplot' plot from the input dataset.getAxisLimPlot
Extract data for the reference linesgetDataReferenceLines
Get plot dimensionsgetDimGgplot
Get extra directory(ies) required for the clinical data review reportgetExtraDirs
Get facetting variables from facet parameters.getFacetVars
Get function codegetFctCode
Get the names of the 'ggplot' function to use for the reference linesgetFctTypeReferenceLines
Get height of labels: title, subtitle or captiongetHeightLab
Get HTML tocgetHTMLToc
Get index of the line containing the HTML title in a vector of HTML stringsgetIndexHTMLTitle
Get interim res filegetInterimResFile
Add jitter to the variable of the plot, based on the different groups of a grouping variablegetJitterVar
Get Javascript custom scripts required for specific clinical data functionalities.getJsDepClinDataReview
Get path of the 'HTML' file corresponding to a specific config file.getMdFromConfig
Get Markdown header, for creation in Rmarkdown.getMdHeader
Read metadata filegetMetadata
Get parameters from a config filegetParamsFromConfig
Get parameter of function used for reference linesgetParFctReferenceLines
Get path ('href') property from hyperlink(s).getPathHyperlink
Get path of template clinical data reportgetPathTemplate
Extract variables displayed in the attached table, for each available plotting function of the clinDataReview package.getPlotTableVars
Get margins and positions of specific elements for a clinical data plotgetPositionAndMargins
Get dimensions for a clinical data plotgetSizePlot
Get TOC numberinggetTocNumbering
Get a watermark, to be included in a clinical visualizationgetWatermark
Clinical data format for bookdown report.gitbook_clinDataReview_report
Clinical data format for rmarkdown report.html_clinDataReview_report
Get R Documentation from a JSON schema.JSONSchToRd
Print 'clinDataReviewTable' object in a knitted document (e.g. Rmarkdown document).knit_print.clinDataReview
Print metadata file in the clinical data reportknit_print.clinDataReviewMetadata
Include output from clinical data, or list of such outputs in a Rmarkdown report, with an appropriate title.knitPrintClinDataReview
Set layout for a clinical data plot.layoutClinData
Merge multiple session informationmerge.sessionInfo
Move skeleton files from the package to a directorymoveSkeletonFiles
Move data sets from clinUtilsmoveXpt
Interactive plot of 'count' dataplotCountClinData
Convert clinical data Markdown files to HTMLpostProcessReport
Print a 'clinDataReview' object in the consoleprint.clinDataReview
Process a dataset.processData
Rename variable names of metadata inforenamePathDateInfoMetadata
Render a clinical data review report.render_clinDataReviewReport
Render one chapter of a clinical report, based on a configuration filerenderChapter
Render a rmarkdown file, possibly in a new R sessionrenderFile
Scatterplot of variables of interest for clinical data visualization.scatterplotClinData
Set facetting layout for 'wrap' facetting.setFacetLayoutWrap
Get standard palette for the 'staticScatterplotClinData' function.setPaletteStaticScatterplotClinData
Split a chapter based on the 'split_by' parameter.splitChapter
Scatterplot of variables of interest for clinical data visualizationstaticScatterplotClinData
Sunburst interactive plot.sunburstClinData
Create a 'clinical data table', associated to a plot.tableClinData
Visualize time intervals across subjects/parameters.timeProfileIntervalPlot
Transform data.transformData
Treemap interactive plot.treemapClinData
Get formula for a specific variable, to be used in aesthetic specification in 'plot_ly'.varToFm
Zip the clinical data reportzipClinDataReview