NEWS

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clinDataReview 1.6.1 (2024-06-18)

• fix when reference line is numeric and x-variable a factor/character

clinDataReview 1.6.0 (2024-06-13)

• summary plot template: support 'r-lazy' parameters in 'plotParams'
• boxplot, barplot, scatterplot, error bar: new parameters xLabVar and yLabVar
• remove trailing space in default title
• support watermark in all plots
• fixes for ggplot2 updates: - fix tests for new warnings - no use of aes_string - geom_line: use of linewidth instead of size

clinDataReview 1.5.2 (2024-05-17)

• default palettes: use .onLoad instead of .onAttach
• tests: - extra test for default color palette - add grDevices to Suggests

clinDataReview 1.5.1 (2024-04-24)

• add extra config files: - discontinuation: summary table and listing - summary barplot of visits - laboratory: error bar and shift plots - efficacy: error bar
• skeleton: - fix: absolute path for logo (if nCores > 1)
• tests: - render report in parallel: fix with upper-case 'class.output' (knitr 1.46) - moveXpt: update for extra datasets (clinUtils 0.1.5)

clinDataReview 1.5.0 (2023-12-11)

• scatterplot: - support non character axis transformation - support 'colour' (UK English spelling) - new highlight box for id variable (idHighlightBox)
• doc: remove description-like items in itemize (R-devel 11/10/2023)
• tests - selection variable: fix for crosstalk 1.2.1

clinDataReview 1.4.0 (2023-02-24)

• option to convert reports to .aspx reports to facilitate deployment on sharepoint
• timeProfileInterval fix no error when duplicate columns are included

clinDataReview 1.3.1 (2022-10-10)

• fix for CRAN suggests packages: - remove pander, reshape2 dependency - use inTextSummaryTable conditionally in examples

clinDataReview 1.3.0

• render clinical data review report: - new implementation to support: parallelization ('nCores' and 'parallel'), and 'split_by' by config file - internal functions: convertMdToHTML and checkReportTitles - a warning is returned when report fails and inputDir is different than working dir - Rmd -> Md output is printed during chapter run, not at the end - new 'verbose' parameter
• merge session infos: fix when session infos have different elements
• skeleton report: update tutorial section and screenshots
• template reports: - support multiple dataFileName - plot template: no failure if data is empty and tableParams is specified
• config file: - check: use 'ajv' engine to fix note meta schema version - check: add configDir parameter for consistency with other fcts - get parameters: warning instead of message when parameters in general and specific config
• filter data: - post-processing function (postFct) - grouping variable: - remove rownames with groups & improve message - one single warning instead of one warning per group - fix issue in case of multiple filters and a grouping variable
• filter and annotate data: - valueFct: support primitive function for verbose message
• process data: add examples in doc
• plots: - scatterplot: - include smoothing layer - include passing additional parameters via pointPars, linePars and smoothPars - time profile, scatterplot, barplot and errorbar plots: selection button - time profile plot: add colorVar to default hoverVars

clinDataReview 1.2.3

• clean exports: no exports of: - addReferenceLinesClinDataPlot - countNLines - formatDataForPlotClinData - getFctTypeReferenceLines
• checkConfigFile: update test

clinDataReview 1.2.2 (2022-02-23)

• remove space before start chunk sessionInfo.Rmd
• 'data visualization' vignette: include patient profiles only in interactive mode
• run less examples (to reduce time R CMD check)

clinDataReview 1.2.1 (2021-10-02)

• fix unit tests R < 4.0.0

clinDataReview 1.2.0 (2021-10-01)

• annotate data: - fix when filters specified for current dataset - remove var by in check of variables already in data - fix functional groups annotation when code variable is a factor
• transform data: fix extraction labels for multiple transformations
• plot: add caption & subtitle
• plot dimensions: - consistent size policy across visualizations - reduce default height to fit in screen window - width not adjusted if height is specified - automatic margins adjustments
• new error bar plot
• scatterplot: - variables for labels for x-axis & plot template: table params - track warning 'Ignoring unknown aesthetics: text' for hover
• time profile plot: include color lab
• barplot: fix position legend
• summary table template: - new type of comparison: 'table-combine' - fix for extraction total data from old batch - tableParams/stats: support !r-lazy & by loop var - patient profiles after specified stats (when stats var not specified)
• listing, plot & summary table templates: fix processData from dataset & old batch
• template listing, summary plot/table: fix looping var with '.'
• report rendering: - copy extra directories only if they exist - quiet now remove any pandoc output
• conversion Md to HTML: parameters can be passed to rmarkdown::render
• skeleton: - fix issue creation comparisonData folder in Windows - listing: button show/hide colums & export landscape pdf
• vignette: fix for Pandoc (CRAN Solaris) - interactive vis
• unit tests: updates based on independent review

clinDataReview 1.1.0 (2021-07-14)

• new boxplotClinData functionality
• barplotClinData: textVar
• support non syntactical variable name
• plotCountClinData: display counts for parents & grand total
• listing template: export to docx with listingDocx
• summary table template: comparison type 'newData-diff' available
• count template: remove bar variable by default in table
• unit tests/doc: fix for Pandoc (CRAN Solaris) + SystemRequirements

clinDataReview 1.0.0 (2021-06-30)

• new 'startup' config param for all visualizations template
• remove color specification for collapsible button
• new 'reportSkeleton' functionality
• change name to "clinDataReview"
• patient profiles template: support '!r' spec for colorPalette/shapePalette
• render report: new parameter inputDir
• remove visual tests + write_svg_plotly

clinDataReview 0.9.2

• fix for highlight_key -> crosstalk::SharedData
• barplotMonitoring: fix link legend <-> x-axis in case color/x variables are nested

clinDataReview 0.9.1

• listing template: format columns as factor for table comparison interactive

clinDataReview 0.9.0

• get metadata functionality
• unit tests
• add 'zipMedicalMonitoring' function
• getPlotTableVars: - fix issues vars label scatterplot, time profile interval plot - extract lab from tableLab + labelVars if tableVars is specified - extra doc, tests
• Js FileSaver library: remove reference to FileSaver.min.js.map
• help page 'medicalMonitoring-templates' properly created in pkg built + tests
• fix issue DT header not aligned upon first click on shared plot
• include metadata MeMo ADs in report
• scatterplotMonitoring: scale params
• config params import extension: - standard evaluation with '!r' - lazy evaluation with '!r-lazy' + use for 'plotParams' in plot/patient profile template

clinDataReview 0.8.0

• fix extraction of labels for 'getPlotTableVars' when 'valueVar' not in 'tableVars'
• remove 'settings' argument in 'getMdHeader'
• filterData: fix for returnAll <-> varNew
• scrapeHtml: minor changes in extracting the path
• countsVisualizationTemplate: fix when colorVar not specified for all parent vars
• patient profiles template: Windows shape palette: u25C0 -> u25C4, u25B6 -> u25BA, u271A -> +, u2605 (star) -> u2666 (diamond)
• patient profiles template: shape palette for aesthetic: u25AA -> u25A0, u25CF -> u25CB
• unit tests
• comparison table functionality based on data.table

clinDataReview 0.7.0

• fix MOMP -> report in vignette
• fix createTemplateDoc
• add space in 'getParamsFromConfig' in two error messages
• fix in 'render_medicalMonitoringReport' when calling 'checkReportTitles': add configDir as argument
• add unit tests
• formatToHierarchicalData: fix for more than two vars (multiple parentVars)
• timeProfileIntervalPlot: fix overlap x-axis title and legend when few y elements
• timeProfileIntervalPlot: fix overlap top plot and modebar (no hover issue)
• barplotMonitoring: fix link legend <-> x-axis selection, legend on top
• minify/update JS dep: FileSaver, JSZip, JSZipUtils
• updates for compareTable data.table implementation
• getPlotTableVars: fixes
• scatterplotMonitoring: fix in case x/y/aesVar are not standard R names (e.g. contain space)

clinDataReview 0.6.0

• checkReportTitles: write error when config file does not exist
• listingTemplate: add labelVars in sapply call to extract the labelVars even when no dataProcessing exists
• countsVisualizationTemplate/plotCountMonitoring: fix in case no parent variable
• annotateData: export filter dataset in xpt format
• tableMonitoring: pathVar/idVar optional + warning
• countsVisualization json: allow multiple typePlot
• scatterplotMonitoring(Static): fix to extract labels for aes var
• checkTemplateNames/checkReportTitles/render_medicalMonitoringReport: include warning if import failed
• patientProfilesTemplate: extend to xpt
• countsVisualizationTemplate JSON sch: fix for typePlot of length 1
• plotTemplate/summaryTableTemplate/summaryPlotTemplate: use labels in comparison table
• render_medicalMonitoringReport: copy extraDirs before report rendering

clinDataReview 0.5.0

• knitPrintListMedicalMonitoring: fix inclusion list with empty element
• tableMonitoring: keep order idVar in tableVars if specified
• listingTemplate: fix when loopingVar and comparisonType are specified, comparison type as first col table
• if comparisonTableType and no previous dataset available: warning + no comparison
• barplotMonitoring: colorPalette and barmode
• move spec of tableVars for all plot fct in getPlotTableVars, plotTemplate: comparisonTableType
• patient profile template: fix to use labels in columns table

clinDataReview 0.4.0

• render_medicalMonitoringReport: logFile, runFctInNewSession, export combined sessionInfo
• scrape html files
• include template reports in the package
• document templates with JSON schema + utility functions to convert to Rd

clinDataReview 0.3.0

• collapseHtmlContent: custom 'hideshow' button
• alertData function
• render med mon: modular approach (convertMdToHtml, getParamsFromConfig), render in new R session
• timeProfileIntervalPlot: fix height plot + fix in case start and end value are the same
• filterData: filter of missing values only, valueFct can be string
• scatterplotMonitoring: pathExpand, lineInclude
• processData: group all data processing step in one param

clinDataReview 0.2.0

• formatToHierarchicalData: fix in case same values in different vars
• annotateData: varFct
• new 'transformData' function
• staticScatterplotMonitoring: [x/y]LimExpandData
• includeInButton -> collapseHtmlContent, remove bootstrap/jquery dep
• plotCountMonitoring: colorVar
• getPathHyperlink: works for input factor
• annotateData: function can be specified as string via varFct
• timeProfileIntervalPlot
• patientProfiles.js: fix for one selected ID
• render_medicalMonitoringReport

clinDataReview 0.1.0

• initial commit