R: Visualization of Patient Profiles

# Visualization of Patient Profiles

## Documentation for package ‘patientProfilesVis’ version 2.0.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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