NEWS

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patientProfilesVis 2.0.9 (2024-06-18)

• fix ggplot2 >= 3.5.0: include all palette elements in legend if specified
• fix links in Rd files

patientProfilesVis 2.0.8 (2024-06-13)

• fixes for ggplot2 updates: - no use of aes_string - geom_line: use of linewidth instead of size
• subjectProfileIntervalPlot: new caption parameter

patientProfilesVis 2.0.7 (2024-03-09)

• tests: - add explicit package name for non exported functions
• combine vertically ggplot: fix for extraction margin widths (ggplot >= 3.5.0)

patientProfilesVis 2.0.6 (2023-12-12)

• tests - time transformation: fix for scales 1.3.0
• doc: remove description-like items in itemize (R-devel 11/10/2023)
• add Cairo to system requirements (for creation of pdf report)

patientProfilesVis 2.0.5 (2022-11-18)

• reference lines - updates for ggplot2 >= 3.4.0: - unit test for 'custom subject variable' more generic - geom line: switch from size -> linewidth

patientProfilesVis 2.0.4

• subject profile line plot: fix unit test random generation of subject IDs

patientProfilesVis 2.0.3

• add tests for getNLinesSubjectProfile

patientProfilesVis 2.0.2 (2021-09-28)

• fix issue empty page start report
• fix issue figure overflows page for parameter var with multiple lines
• interval plot: fix issue small height for non specified time start/end shape var
• get shape palette patient profiles: fix for asText set to FALSE
• time profile interval plot: remove deprecated param timeLabel (replaced by timeLab)
• subject profile combine: remove spec of timeAlign as a logical (deprecated, replaced by timeAlign = 'all'/'none')
• unit tests: updates based on independent review

patientProfilesVis 2.0.1 (2021-07-13)

• vignette: shorten path exported figures (CRAN requirement for Windows)

patientProfilesVis 2.0.0 (2021-06-14)

• change default color palette to generic: get[Color|Shape|Linetype]PalettePatientProfile
• fix in case bookmarkVar is a factor
• new options to set color/shape palette globally
• figure dir not created if exportFigures is FALSE on Windows
• no export of getPathTemplate

patientProfilesVis 1.5.0

• add unit tests
• no export of subjectProfileTheme
• subjectProfileTextPlot: - fix ordering in case paramNameVar is a factor - param value lab is used even if not table - table output: - records sorted based on value var (especially for factor) - fix in case only one param value var is specified
• subjectProfileEventPlot/subjectProfileLinePlot/subjectProfileIntervalPlot: - records sorted based on levels of param var if factor - missing values in paramVar or paramNameVar are not filtered - extract number of lines legend from plot instead of data for simplicity
• subjectProfileEventPlot: - fix when paramVarLab not specified for all vars - x lab set to time lab by default
• subjectProfileEvent/subjectProfileLinePlot: - shape lab set to color lab if color but not shape var specified - fix in case shape and color vars are the same
• subjectProfileLinePlot: - remove warning if ref var are missing
• subjectProfileIntervalPlot - correct typo: 'data-by-subject' -> 'data-based' - remove rangeSimilarStartEnd parameter (not used) - add info on imputation in the caption
• subjectProfileCombine: + attribute nLinesPlot -> metaData$nLines for consistency with subject plot fct
• getPageVar: - fix when only one var is specified
• fct renaming: - getNLinesYGgplot -> getNLinesSubjectProfile - getXLimSubjectProfilePlots -> getTimeLimSubjectProfilePlots

patientProfilesVis 1.4.3

• change default palette for Windows support: u25C0 -> u25C4, u25B6 -> u25BA, u271A -> +, u2605 (star) -> u2666 (diamond), u25EF -> u25CB

patientProfilesVis 1.4.2

• subjectProfile[Interval|Event|Line]Plot: fix extraction size legend, add space between legend lines

patientProfilesVis 1.4.1

• fix unit tests

patientProfilesVis 1.4.0

• add unit tests figures
• filterData/subjectProfile[X]Plot/createSubjectProfileReport: new subsetSample parameter

patientProfilesVis 1.3.0

• change imports of color palette
• createSubjectProfileReport: test if input list is empty

patientProfilesVis 1.2.0

• add vignette with standard patient profiles for SDTM data
• prepareSubjectProfile: fix in case trans and all missing values for interval plot
• subjectProfileLinePlot: fix for orientation of paramNameVar labels in ggplot2 >= 3.0.0
• fix bug when Rmd created after createSubjectProfileReport
• get[]ShapePalettePatientProfile: fix mix Unicode and ggplot2 palettes (asText = TRUE)

patientProfilesVis 1.1.0

• formatParamVar -> formatVarForPlotLabel/formatLongLabel: moved to utility pkg

patientProfilesVis 1.0.0

• change default time imputation in subjectProfileIntervalPlot (see 'timeImpType' parameter)
• getXLimSubjectProfilePlots: fixes for empty interval plot

patientProfilesVis 0.12.1

• formatParamVar: fix message issue grouping
• subjectProfileTextPlot: fix panel grid ggplot2 >= 3.3.0

patientProfilesVis 0.12.0

• checkTimeTrans: fix in case all cont module have the same transf
• subjectProfileLinePlot: shapeSize, paramNameVar can be multiple
• createSubjectProfileReport: exportBatchSize, subjectSort[] used also for order export of patient profiles, subjectSortDecreasing

patientProfilesVis 0.11.0

• subjectProfileLinePlot: yLimFrom new parameter

patientProfilesVis 0.10.0

• legend: fix when number of levels in aes var higher that represented levels
• subjectProfile[Interval|Line|Event]Plot: alpha parameter
• createSubjectProfileReport: suppress warnings Sweave
• prepareSubjectProfile: remove message: 'scale already present'
• vignette: more extensive example timeAlign/timeAlignPerSubject

patientProfilesVis 0.9.2

• createSubjectProfileReport: set knitr environment (to be used within rmd doc)
• export convertAesVar

patientProfilesVis 0.9.1

• createSubjectProfileReport: margin set by patient if reportPerSubject

patientProfilesVis 0.9.0

• subjectProfileCombine: fix extraction time limits in case no plot
• remove panel border for empty plot
• timeExpand

patientProfilesVis 0.8.0

• subjectProfileTextPlot: fix in case paramValueVar is empty
• subjectProfileIntervalPlot: use vertical segment if start and end dates are equal

patientProfilesVis 0.7.0

• timeAlign, timeAlignPerSubject: specification per or across modules
• subjectProfileIntervalPlot: fix when timeTrans and same start/end values

patientProfilesVis 0.6.0

• subjectProfileTextPlot: table format
• custom 'trans', getTimeTrans

patientProfilesVis 0.5.0

• createSubjectProfileReport: reportPerSubject and extend outputFile for different directory

patientProfilesVis 0.4.0

• createSubjectProfileReport/subjectProfileIntervalPlot: timeAlign
• defineIndex: fix index specification
• report: support unicode font (use cairo_pdf instead of pdf)

patientProfilesVis 0.3.0

• subjectProfileIntervalPlot: new parameters: timeStartShapeVar/timeEndShapeVar
• fix issue tibble: convert input data as data.frame

patientProfilesVis 0.2.0

• save nLines at module plot creation instead of extracting them when combining plots
• when combining plots across modules, close graphic device only at the end
• formatParamVar: fix warning when multiple 'paramGroupVar'
• get[]ShapePalettePatientProfile
• getPageVar: fix for plot with multiple lines
• fix to remove warning: 'Coordinate system already present.'
• subjectProfileLinePlot: fix to remove warning: 'geom_path: Each group consists of only one observation'
• additional messages for verbose
• enable parallelized computations with 'nCores'
• createSubjectProfileReport: subjectSubset fix
• 'paging' parameter: enable export into one page
• subsetData parameter available in each plot function

patientProfilesVis 0.1.0

• example datasets moved to the utility pkg
• get[]ColorPalettePatientProfile/get[]LinetypePalettePatientProfile

patientProfilesVis 0.0.16

• subjectProfileTextPlot: concatenate multiple value variable with ', '
• subjectProfileIntervalPlot: timeLabel
• subjectProfile[Interval|Event|Line]Plot: use standard color palette if no color variable is specified

patientProfilesVis 0.0.15

• changes for []UtilityFct version 0.0.3
• subjectProfile[Event|Interval]Plot: paramVarSep, by default ' - ' instead of ' '
• getNLinesYGgplot: add space for subject profile event and interval
• formatParamVar: fix when empty string in paramVar

patientProfilesVis 0.0.14

• createSubjectProfileReport: add subjectSubset[Data|Var|Value] parameters
• child document: remove space and file separator for file name of exported image, include shiny progress message for each patient
• formatParamVar: fix in case similar levels with space difference

patientProfilesVis 0.0.13

• remove knitPrintListPlotsKnitr function
• include tests for each subjectProfile[*]Plot function with vdiffr package

patientProfilesVis 0.0.12

• include directly plots in report
• getPageVar/countNLines: fix when variable contains missing value
• subjectProfileTextPlot: wrap text in panel across multiple lines (formatParamVarTextPlot new function)
• getNLinesYGgplot: fix for text plot + increase size for text
• report: fix for margins and landscape layout

patientProfilesVis 0.0.11

• subjectProfileTextPlot: fix in case subjectVar same as paramNameVar/paramValueVar

patientProfilesVis 0.0.10

• externalise the functions getPatient[Color|Shape]Palette, and data function in utility pkg

patientProfilesVis 0.0.9

• getNLinesGgplot: check/extract number of lines in legend (getNLinesLegend new function)
• formatTimeInterval: fix issue extraction limits
• filterData/formatParamVar: warning in case variable not in data

patientProfilesVis 0.0.8

• subjectProfileCombine/prepareSubjectProfile/combineVerticallyGGplot: changes to align plots across pages
• subjectProfileTextPlot: possibility to have multiple paramValueVar if paramNameVar specified
• subjectProfileLinePlot: shapeVar/colorVar for point only
• formatParamVar/subjectProfileReportFormat: set maximum length y-variable: yLabelWidth

patientProfilesVis 0.0.7

• subjectProfileCombine: adapt progress message
• use egg package to combine plots across modules
• automatic split within module: subjectProfileReportFormat, getPageVar functions and formatReport parameter
• getNLinesYGgplot: fix for interval plot
• combineVerticallyGGplot: close plotting window in case the egg package is used
• subjectProfileCombineOnce: fix automatic split of figures into multiple pages (new function: getSplitVectorByInt)
• bookmark: fixes for multiple plots per subject in knitPrintListPlotsKnitr and double backslash in defineIndex, only one column

patientProfilesVis 0.0.6

• subjectProfileLinePlot: include colorPalette
• subjectProfileIntervalPlot: don't delete records without start date, different arrows for missing start/end dates
• subjectProfileIntervalPlot: consider min/max time per subject in case of missing date, include timeLimData/timeLimVar
• addReferenceLinesProfilePlot: fix issue for panel plot (e.g. line plot) and use geom_text to get labels reference lines

patientProfilesVis 0.0.5

• add concomitant medications in vignette
• getNLinesYGgplot: extend to multiple panels
• subjectProfileLinePlot: add paramValueRangeVar
• subsetVar and subsetValue

patientProfilesVis 0.0.4

• subjectProfileIntervalPlot: re-label [start|end]Var -> time[Start|end]Var and use arrow for non-ending interval
• use viridisLite instead of viridis paclage
• createSubjectProfileReport: automatic split of modules across pages in report
• subjectProfileTextPlot: concatenate information if duplicated info
• subjectProfileLinePlot
• getXLimSubjectProfilePlots: fix extraction limits for interval plot
• add sessionInfo, shiny parameter
• rename loadDataADaM by loadDataADaMSDTM
• defineIndex: fix when only one variable is used
• createSubjectProfileReport: possibility to sort subjects based on a variable

patientProfilesVis 0.0.3

• subjectProfileTextPlot: possibility to have multiple paramValueVar in same line, fix ordering
• subjectProfileTextPlot: paramValueVar can be a function
• subjectProfile[Interval|Event]Plot: colorPalette and getPatientColorPalette
• subjectProfileEventPlot: shapePalette and getPatientShapePalette
• add label attributes reported in case plot is empty
• add grouping variable
• subjectProfileTheme
• loadDataADAM: include support for date/time format
• createSubjectProfileReport/subjectProfileCombine: add refLines parameter
• new addReferenceLinesProfilePlot function
• add bookmark functionality
• include missing values in palette

patientProfilesVis 0.0.2

• remove utility pkg from the dependencies

patientProfilesVis 0.0.1

• initial commit