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patientProfilesVis (version 2.0.8)

Visualization of Patient Profiles

Description

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).

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install.packages('patientProfilesVis')

Monthly Downloads

688

Version

2.0.8

License

MIT + file LICENSE

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Maintainer

Laure Cougnaud

Last Published

June 13th, 2024

Functions in patientProfilesVis (2.0.8)

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
getSplitVectorByInt

Split/combine a vector of size(s) to have a fixed combined size
isSubjectProfileTimeVariant

Check if the all profile(s) is/are 'time-variant', so not a subject profile 'text' module or empty plot
interactionWithMissing

Get interaction variable between different variables.
getPageVar

Get variable with page of the plot, used for automatic paging of a plot
formatParamVarTextPlot

Format text variables for the subject profile text plotting function.
getOptimalColWidth

Get optimal column widths, based on the minimum word size and median number of characters in each column.
getTimeTrans

Get useful transformation for the time variable in patient profiles.
getWidthPlot

Get width for a plot for a certain page layout
getTimeLimSubjectProfilePlots

Get the limits to set for the subject profile plots, depending on the alignment policy set.
getPathTemplate

Get path of the report template in the patientProfilesVis package
getShapePalettePatientProfile

Get a shape palette for patient profile visualizations.
subjectProfileExport

Create report
subjectProfileCombine

Combine subject profile plots.
subjectProfileEventPlot

Visualize events in subject profiles, so event with a single time.
subjectProfileIntervalPlot

Visualize time interval in subject profiles, so event with a start and end time.
prepareSubjectProfile

prepare list of subject profile (s) to be combined with the combineVerticallyGGplot
sortSubjects

Sort subjects based on a specified dataset/variable.
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
patientProfilesVis-common-args

Arguments used across the functions of the patientProfilesVis package.
patientProfilesVis-palette

Parameters for all patient profiles visualization palette functions.
addReferenceLinesProfilePlot

Add reference lines to a profile plot
combineVerticallyGGplot

checkTimeExpand

Check if some of the modules are time expanded, and extract maximum time expand for each module.
convertAesVar

Convert aesthetic variable for patient profile visualization.
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.
formatTimeLim

Format specified timeLim.
formatTimeInterval

Set missing start/end time variable in the data.
getNLinesSubjectProfile

Get approximately the number of 'lines' in the vertical direction of a subject profile.
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)
filterMissingInVar

Filter missing records in data in the time and y variables, with informative message.
getColorPalettePatientProfile

Get a color palette for patient profile visualizations.
filterData

Filter a dataset for records of interest, for use in the patient profiles.
defineIndex

Define LaTeX index based on specified variable(s) of the dataset
getAesScaleManual

Get custom 'scale_[type]_manual' function
createSubjectProfileReport

Create subject profile report.
countNLines

Count number of lines ('\n' character) per character in a vector