patientProfilesVis-common-args {patientProfilesVis}

Arguments used across the functions of the patientProfilesVis package.

Description

Arguments used across the functions of the patientProfilesVis package.

Arguments

data

Data.frame with data.

colorVar

String, variable of data with color.

colorLab

String, label for colorVar.

colorPalette

Named vector with color palette. The variable should be named with the corresponding element in colorVar.
Colors can also be defined for the entire session, by setting options(patientProfilesVis.colors = X) with X either:

• a vector with colors

• a function returning a vector of colors for a specified number of elements (viridis by default)

shapeVar

String, variable of data for shape of the points. By default, same as colorVar.

shapeLab

String, label for shapeVar. Set by default to colorLab if colorVar but not shapeVar is not specified.

shapePalette

Named character vector with shape palette for shapeVar. The variable should be named with the corresponding element in shapeVar.
Shapes can also be defined for the entire session, by setting options(patientProfilesVis.shapes = X) with X either:

• a vector with shapes

• a function returning a vector of shapes for a specified number of elements

Note it is advised to specify the shapes as character, e.g. 'cross' instead of 4, in case Unicode symbols should also be used.

paramGroupVar

(optional) Character vector with variable(s) of data based on which the data will be grouped and sorted (in the y-axis) in the plot.

xLab

String, label for the x-axis.

yLab

String, label for the y-axis.

label

String, label for the visualization. This label is stored as attributes of the output from the subjectProfile[]Plot function.
This label is displayed in the final profile report, in case no data is available for for a specific patient, as: 'No [label] available.'

title

String, title for the plot.

timeVar

String, variable of data with time, displayed in the x axis.
Records with missing time are not displayed in the plot.

timeLab

String, label for timeVar. This is used in the message indicating missing values for timeVar, and for the default label of the x-axis.

paramVar

Character vector with variable(s) of data with parameters. Variable content is displayed in the y-axis.

paramLab

Named character vector, with label for the parameter variable(s) (paramVar).
This is used to set the default title.

timeLim

(optional) Vector of length 2 with time limits (x-axis). If not specified, these are extracted from the minimum timeStartVar and maximum timeEndVar per subject.
The time limits are stored as attributes of the plots, used to align the plots in the final report.

timeTrans

transformation for the time variable, (see trans parameter in scale_x_continuous, and trans_new). For example, produced by the getTimeTrans function.

timeExpand

Vector of range expansion constants for the time axis (see expand parameter in scale_x_continuous).

listPlots

Named list of subject profiles. Each sublist contains subject profiles as returned by the subjectProfile[X]Plot function, so nested by subject and page. The names of the list should be unique, and are used

alpha

Numeric with transparency, 1 by default.

labelVars

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

subjectVar

String, variable of data with subject ID

formatReport

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

paramVarSep

string with character(s) used to concatenate multiple paramVar, ' - ' by default.

Value

No return value, used for the documentation of the functions of the package.