createSubjectProfileReport {patientProfilesVis}

Create subject profile report.

Description

By default all subjects available in at least one module of listPlots are considered. If only a set of subjects are of interest, these are specified either:

• directly with the subject IDs of interest via subjectSubset

• by extracting subjects with a specific value (subjectSubsetValue) in a variable (subjectSubsetVar) in a specific dataset subjectSubsetData

Usage

createSubjectProfileReport(
  listPlots,
  timeLim = NULL,
  timeAlign = "all",
  timeAlignPerSubject = "none",
  refLines = NULL,
  refLinesData = NULL,
  refLinesTimeVar = NULL,
  refLinesLabelVar = NULL,
  bookmarkData = NULL,
  bookmarkVar = NULL,
  subjectSortData = bookmarkData,
  subjectSortVar = bookmarkVar,
  subjectSortDecreasing = FALSE,
  subjectVar = "USUBJID",
  subjectSubset = NULL,
  subjectSubsetData = NULL,
  subjectSubsetVar = NULL,
  subjectSubsetValue = NULL,
  subjectSample = NULL,
  seed = 123,
  subset = NULL,
  outputFile = "subjectProfile.pdf",
  exportFigures = FALSE,
  reportPerSubject = FALSE,
  exportBatchSize = NULL,
  labelVars = NULL,
  maxNLines = NULL,
  shiny = FALSE,
  formatReport = subjectProfileReportFormat(),
  verbose = FALSE,
  nCores = 1
)

Arguments

listPlots

nested list of plots, as returned by the subjectProfileTextPlot, subjectProfileEventPlot, subjectProfileIntervalPlot or subjectProfileLinePlot functions.

timeLim

Time limits, as a numeric vector of length 2, or a list with time limits for each module, or nested list with time limits for each module and subject. If not specified, these are set to the time limits specified when creating each module (stored in attributes(x)$metaData$timeLim) otherwise to the range defined by timeAlign and timeAlignPerSubject. Note that this doesn't modify the geoms of the plots, it only extends the axis range. So for interval module(s) if the specified timeLim is smaller than the time limits in the input plot, no arrows are created in case than the time goes above/below specified timeLim (the segment is cut).

timeAlign

Character vector with time alignment across modules/subjects, either:

• 'all' (by default): all plots have the same time limits

• 'none': each of the plot (module*subject) has its own time limits

• character vector with names of the modules which should have the same time limits (should correspond to the names of listPlots)

timeAlignPerSubject

Character vector, specifying if the plots should be aligned (or not) across subjects

• 'none' (by default): all modules to align have the same time limit across subjects

• 'all': all modules to align have different time limits per subject

• character vector with subset of the modules to align per subject (should correspond to the names of listPlots)

Only the modules already specified in timeAlign can be aligned by subject.

refLines

(optional) nested list with details for reference line(s). Each sublist contains:

• (required) 'label': string with label for the reference line

• (required) 'time': unique time (x) coordinate for the reference line

• (optional) 'color': color for the reference line, 'black' by default

• (optional) 'linetype': linetype for the reference line, 'dotted' by default

refLinesData

data.frame with data from which the reference line(s) should be extracted

refLinesTimeVar

string, variable of refLinesData with time for reference line(s)

refLinesLabelVar

string, variable of refLinesData with label for reference line(s)

bookmarkData, bookmarkVar

Data.frame with data containing information for the index, and character vector with corresponding variable(s) of interest. An index will be created at the end of the subject profile report.
The index contains a section per variable, referencing the pages of the report containing subject profiles for each category/variable.

subjectSortData

Data.frame with data containing information on how the subjects should be sorted (by default same as bookmarkData):

• in the report, in case one single report is created for all subjects

• for the export, in case reportPerSubject is TRUE

This data should contain subjectSortVar and subjectVar.

subjectSortVar

Character vector, variable(s) of subjectSortData indicating the order for the subjects in the report, (by default same as bookmarkVar).

subjectSortDecreasing

Logical, if TRUE (FALSE by default) subjects are sorted based on decreasing order of subjectSortVar.

subjectVar

String, variable of data with subject ID

subjectSubset

subjectSubset (optional) Character vector with subjects of interest (available in subjectVar), NULL by default.

subjectSubsetData

Data.frame used to select subset of subjects of interest.

subjectSubsetVar

String with variable of subjectSubsetData that should be considered to filter subjects. If not specified, all subjects available in subjectSubsetData are considered.

subjectSubsetValue

Character vector with value(s) of subjectSubsetVar of interest to filter subjects on.

subjectSample

(optional) Integer of length 1 with number of random subject(s) that should be considered in the specified subset dataset. By default, all specified subjects are considered (set to NULL).

seed

(optional) Integer of length 1 with seed used to select random subjects if subjectSample is specified (123 by default).

subset

Character vector with subjects of interest (among names of each list in listPlots).

outputFile

string, path to the output report

exportFigures

Logical, if TRUE (FALSE by default) the subject profile figures are also exported in pdf format in a 'figures' folder.
Figures are named as [subjectID]-[page].pdf

reportPerSubject

Logical, if TRUE (FALSE by default) export a subject profile report by subject.

exportBatchSize

(optional) Integer, if specified, the patient-profile reports are created by batch of this number of subjects. This might speed up the export for a high number of subjects. Only available if report is created by subject (reportPerSubject is TRUE) and modules are not aligned across subjects (timeAlignPerSubject is: 'all').

labelVars

Named character vector with variable labels (names are the variable code)

maxNLines

Maximum number of lines for a combined plot, to fit in the page height.
When the different visualizations are combined for each subject, they will be allocated to different pages if the number of lines of the combined visualization is higher than this number.

shiny

logical, set to TRUE (FALSE by default) if the report is generated from a Shiny application. Messages during report creation will be included in the Shiny interface, and it will be mentioned at the end of the report. In this case, the shiny package should be available.

formatReport

list with parameters used to specify the format of the report, e.g. output of the subjectProfileReportFormat function

verbose

logical, if TRUE print messages during execution

nCores

Integer containing the number of cores used for the computation (1 by default). If more than 1, computation is parallelized, in this case the package parallel is required.

Value

The path(s) of the report(s) is returned invisibly, and the report is created at the location specified by outputFile.
If the report is created by subject, the name of the exported subject profile is built as: [filename]-[subjectID].pdf, with [filename] extracted from outputFile. Space and platform-specific file separator are replaced by a dash in the filename.
If no patient profiles are available in the input, nothing is returned and a warning is triggered.

Author(s)

Laure Cougnaud