Set missing start/end time variable in the data.
formatTimeInterval(
data,
timeStartVar,
timeStartLab = getLabelVar(timeStartVar, labelVars = labelVars),
timeEndVar,
timeEndLab = getLabelVar(timeEndVar, labelVars = labelVars),
timeStartShapeVar = NULL,
timeEndShapeVar = NULL,
subjectVar = "USUBJID",
timeLim = NULL,
timeLimData = NULL,
timeLimStartVar = NULL,
timeLimStartLab = getLabelVar(timeLimStartVar, labelVars = labelVars),
timeLimEndVar = NULL,
timeLimEndLab = getLabelVar(timeLimEndVar, labelVars = labelVars),
timeImpType = c("minimal", "data-based", "none"),
labelVars = NULL
)list with:
'data': Data with:
imputed timeStartVar and timeEndVar
new column 'timeStartStatus':
character vector containing status of timeStartVar variable:
'Complete' or 'Missing start' or NA
new column 'timeEndStatus':
character vector containing status of timeEndVar variable:
'Complete' or 'Missing end' or NA
'timeLim': vector of length 2 with minimum/maximum time limits across subjects.
'timeLimSpecified': vector of length 2 with time limits as specified
by the user, either extracted from timeLim or from timeLimData.
If missing value within timeLim, the corresponding minimum/maximum
value in the (updated) data is used.
'timeShapePalette': Named character vector with symbols for the different time status
'caption': String with extra explanation concerning imputation that could be included in plot caption.
Data.frame with data.
String, variable of data
with start of time interval.
String, label for timeStartVar,
displayed in a message and in the plot caption.
String, variable of data
with end of time interval.
String, label for timeEndVar,
displayed in a message and in the plot caption.
(optional) String, variable of data
used for the shape of the symbol displayed
at the start of the time interval.
If not specified, default shape palette is used,
see section 'Time interval representation'.
String, variable of data
used for the shape of the symbol
displayed at the end of the time interval.
If not specified, default shape palette is used,
see section 'Time interval representation'.
String, variable of data with subject ID
(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.
Data.frame with data used to impute time
in case some time records are missing in data,
see section: 'Time interval representation'.
String, variable of timeLimData with
start of the time interval.
String, label for timeLimeStartVar,
displayed in a message and in the plot caption.
String, variable of timeLimData with
end of the time interval.
String, label for timeLimEndVar,
displayed in a message and in the plot caption.
String with imputation type: 'minimal' (default),
'data-based' or 'none', see section: 'Time interval representation'.
This imputation type is not used if a dataset used to impute time is
specified.
Named character vector with variable labels (names are the variable code)
In case the start or the end of the time interval contain missing values:
if a dataset (timeLimData), start (timeLimStartVar)
and end (timeLimEndVar) variables are specified:
for each subject:
the minimum and maximum time values across these specified time variables are extracted
missing start values are replaced by the minimum time
missing start values are replaced by the maximum time
if all values are missing for this subject, they are taken across subjects
otherwise, depending on the imputation type (timeImpType):
'minimal' (by default):
if the start and the end of the interval are missing: no imputation is done, only the label is displayed
if the start time is missing and the end time is not missing: start time is imputed with end time, and status is set to 'Missing start'
if the end time is missing and the start time is not missing: end time is imputed with start time, and status is set to 'Missing end'
'data-based' (default in version < 1.0.0): minimum/maximum values in the start/end time variables in the data are considered for the specific subject (if available). If there are missing for a specific subject, they are taken across subjects. If all time are missings, the range is set to 0 and Inf
'none': no imputation is done
The symbols displayed at the start and end of the interval are:
by default:
a filled square labelled 'Complete' if the time is not missing
a filled left-directed arrow in case of missing start time
a filled right-directed arrow in case of missing end time
if the variable(s) used for the shape of the start or end
of the interval are specified (via
timeStartShapeVar/timeEndShapeVar):
labels are based on these variables, and a standard shape palette is used
The time limits are the same across subjects, and set to:
timeLim if specified
maximum time range in timeLimStartVar and
timeLimEndVar in timeLimData
if specified
the maximum range on the data obtained after imputation of missing values
Laure Cougnaud