Package: patientProfilesVis 2.0.9

Laure Cougnaud

patientProfilesVis: Visualization of Patient Profiles

Creation of patient profile visualizations for exploration, diagnostic or monitoring purposes during a clinical trial. These static visualizations display a patient-specific overview of the evolution during the trial time frame of parameters of interest (as laboratory, ECG, vital signs), presence of adverse events, exposure to a treatment; associated with metadata patient information, as demography, concomitant medication. The visualizations can be tailored for specific domain(s) or endpoint(s) of interest. Visualizations are exported into patient profile report(s) or can be embedded in custom report(s).

Authors:Laure Cougnaud [aut, cre], Margaux Faes [rev], Open Analytics [cph]

patientProfilesVis_2.0.9.tar.gz
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patientProfilesVis.pdf |patientProfilesVis.html✨
patientProfilesVis/json (API)
NEWS

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

Peer review:

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

On CRAN:

13 exports 7 stars 1.57 score 79 dependencies 8 scripts 952 downloads

Last updated 3 months agofrom:700cee397c. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 16 2024
R-4.5-winERRORSep 16 2024
R-4.5-linuxERRORSep 16 2024
R-4.4-winERRORSep 16 2024
R-4.4-macERRORSep 16 2024
R-4.3-winERRORSep 16 2024
R-4.3-macERRORSep 16 2024

Exports:convertAesVarcreateSubjectProfileReportfilterDatagetColorPalettePatientProfilegetNLinesSubjectProfilegetShapePalettePatientProfilegetTimeTranssubjectProfileCombinesubjectProfileEventPlotsubjectProfileIntervalPlotsubjectProfileLinePlotsubjectProfileReportFormatsubjectProfileTextPlot

Dependencies:base64encbitbit64bslibcachemcliclinUtilscliprcolorspacecowplotcpp11crayoncrosstalkdata.tabledigestDTevaluatefansifarverfastmapfontawesomeforcatsfsggplot2gluegridExtragtablehavenhighrhmshtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigplyrprettyunitsprogresspromisesR6rappdirsRColorBrewerRcppreadrreshape2rlangrmarkdownsassscalesstringistringrtibbletidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunyaml

Introduction to the patientProfilesVis package

Laure Cougnaud

Rendered frompatientProfilesVis-introduction.Rmdusingknitr::rmarkdownon Sep 16 2024.

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

Template to create patient profiles for SDTM datasets

Laure Cougnaud

Rendered frompatientProfiles-template-SDTM.Rmdusingknitr::rmarkdownon Sep 16 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Add reference lines to a profile plotaddReferenceLinesProfilePlot
Check if some of the modules are time expanded, and extract maximum time expand for each module.checkTimeExpand
Check if the subject profiles are time transformed, and if some of the plots to align (with specified 'timeLim') have compatible time transformation alignments.checkTimeTrans
Check if specified variable(s) are present in the data.checkVar
Combine vertically multiple 'ggplot'.combineVerticallyGGplot
Convert aesthetic variable for patient profile visualization.convertAesVar
Count number of lines ('\n' character) per character in a vectorcountNLines
Create subject profile report.createSubjectProfileReport
Define LaTeX index based on specified variable(s) of the datasetdefineIndex
Filter a dataset for records of interest, for use in the patient profiles.filterData
Filter missing records in data in the time and y variables, with informative message.filterMissingInVar
Format text variables for the subject profile text plotting function.formatParamVarTextPlot
Set missing start/end time variable in the data.formatTimeInterval
Format specified 'timeLim'.formatTimeLim
Get custom 'scale_[type]_manual' functiongetAesScaleManual
Get a color palette for patient profile visualizations.getColorPalettePatientProfile
Get maximum number of lines of a 'combined plot' for a specific documentgetMaxNLinesCombinePlot
Get number of lines for specific label either from a 'ggplot2' object via 'gg' or from the label via 'value'getNLinesLabel
Get number of lines in the legend, either from directly the 'ggplot2' object, or from the values of the legend ('legendValues') and title ('legendTitle')getNLinesLegend
Get approximately the number of 'lines' in the vertical direction of a subject profile.getNLinesSubjectProfile
Get optimal column widths, based on the minimum word size and median number of characters in each column.getOptimalColWidth
Get variable with page of the plot, used for automatic paging of a plotgetPageVar
Get path of the report template in the 'patientProfilesVis' packagegetPathTemplate
Get a shape palette for patient profile visualizations.getShapePalettePatientProfile
Split/combine a vector of size(s) to have a fixed combined sizegetSplitVectorByInt
Get the limits to set for the subject profile plots, depending on the alignment policy set.getTimeLimSubjectProfilePlots
Get useful transformation for the time variable in patient profiles.getTimeTrans
Get width for a plot for a certain page layoutgetWidthPlot
Get interaction variable between different variables.interactionWithMissing
Check if the all profile(s) is/are 'time-variant', so not a subject profile 'text' module or empty plotisSubjectProfileTimeVariant
Arguments used across the functions of the patientProfilesVis package.patientProfilesVis-common-args
Parameters for all patient profiles visualization palette functions.patientProfilesVis-palette
prepare list of subject profile (s) to be combined with the 'combineVerticallyGGplot'prepareSubjectProfile
Sort subjects based on a specified dataset/variable.sortSubjects
Combine subject profile plots.subjectProfileCombine
Visualize events in subject profiles, so event with a single time.subjectProfileEventPlot
Create reportsubjectProfileExport
Visualize time interval in subject profiles, so event with a start and end time.subjectProfileIntervalPlot
Visualize subject profiles of the evolution of continuous parameters versus time (spaghetti plot).subjectProfileLinePlot
Get list with format specification for subject profile report.subjectProfileReportFormat
Visualize text-information in subject profiles.subjectProfileTextPlot
Custom 'theme' for subject profile plot. Currently classic dark-on-light ggplot2 theme with alternated grey color for vertical grid linessubjectProfileTheme