This is core object of this package. This object stores the original dataset as well as the automatically cleaned dataset and a list of notes and queries generated when cleaning the dataset. A list of options is also provided to store plot and tabulation options and provide additional metadata. Finally treatment and cycle labels are also required.
toxData
The toxicitydataset
patientData
Patient level data
patidCol
Column name for the participant identifier
treatmentCol
Column name for the treatment
toxCategoryCol
Column name for aderse event category
toxNameCol
Column name for adverse event name
toxGradeCol
Column name for the adverse event grade
dateOfStartTox
Column name for date of adverse event start or change in grade
dateOfEndTox
Column name for date of adverse event end or change in grade
dateOfStartOfToxWindow
Column name for date of study entry (eg registration)
dateOfEndOfToxWindow
Column name for the end of the time window for the particitant to be observed for toxicities
periodDividerCols
Column names for date dividing times into periods or cycles (optional)
periodDividerLabels
Display names for data periodDividerCols
treatmentCodes
Codes which match the values in treatmentCol
treatmentLabels
Labels to used instea of the treatment codes
queries
A data.frame containing all the queries and note generated when loading the data
options
An s4 object of class toxicityOptions-class
containing options and metadata for the files.
wasQueried
Logical detailing if queries were run on this object.
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