Arguments used across the functions of the patientProfilesVis package.
No return value, used for the documentation of the functions of the package.
Data.frame with data.
String, variable of data with color.
String, label for colorVar.
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)
String, variable of data for shape of the points.
By default, same as colorVar.
String, label for shapeVar.
Set by default to colorLab if colorVar
but not shapeVar is not specified.
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.
(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.
String, label for the x-axis.
String, label for the y-axis.
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.'
String, title for the plot.
String, variable of data with time,
displayed in the x axis.
Records with missing time are not displayed in the plot.
String, label for timeVar.
This is used in the message
indicating missing values for timeVar,
and for the default label of the x-axis.
Character vector with variable(s) of data
with parameters. Variable content is displayed in the y-axis.
Named character vector,
with label for the parameter variable(s) (paramVar).
This is used to set the default title.
(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.
transformation for the time variable,
(see trans parameter in scale_x_continuous, and
trans_new).
For example, produced by the getTimeTrans function.
Vector of range expansion constants for the time axis
(see expand parameter in scale_x_continuous).
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
Numeric with transparency, 1 by default.
Named character vector with variable labels (names are the variable code)
String, variable of data with subject ID
list with parameters used to specify the format of the report,
e.g. output of the subjectProfileReportFormat function
string with character(s) used to concatenate multiple
paramVar, ' - ' by default.