SetupRobustToxicities: robustToxicitiesClass generator
In csmoxford/robustToxicities: Toxicity tables

Description Usage Arguments Details Value Examples

The robustToxicities package aims to make creating publication ready table and graphs from time based toxicity data easy. The package also performs some built in data cleaning actions.

SetupRobustToxicities(toxData, patientData, patidCol, treatmentCol = NULL,
  toxCategoryCol, toxNameCol, toxGradeCol, dateOfStartOfToxWindow,
  dateOfStartTox, dateOfEndTox, dateOfEndOfToxWindow,
  periodDividerCols = character(0), periodDividerLabels = character(0),
  treatmentCodes = NULL, treatmentLabels = NULL, options = NULL)

`toxData`	The toxicity level data set
`patientData`	The patient level data
`patidCol`	Column name for the participant identifier
`treatmentCol`	Column name for the treatment. Will be created if not provided
`toxCategoryCol`	Column name for aderse event category
`toxNameCol`	Column name for adverse event name
`toxGradeCol`	Column name for the adverse event grade
`dateOfStartOfToxWindow`	Column name for date of study entry (eg registration)
`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
`dateOfEndOfToxWindow`	Column name for the end of the time window for the particitant to be observed for toxicities (optional)
`periodDividerCols`	Column names for date dividing times into periods or cycles (optional)
`periodDividerLabels`	Display names for data periodDividerCols param treatmentLabels A vector of treatment labels
`treatmentCodes`	Levels of treatment in the treatmentCol
`treatmentLabels`	What to name each treatment in output tables
`options`	Optional. An object of class toxicityOptions. The easiest place to start is with `DefaultToxicityOptions()`. See `DefaultToxicityOptions` for more details on options.

Run this to create an object of class robustToxicitiesClass. Then run it through QueryRobustToxicities to check for errors before creating tables and graphs of the data.

This function takes two linked data.frames. A one row per patient, patient level data.frame (patientData) and a one row per toxicity data.frame of toxicities (toxData). The remaining parameters tell the package where the columns which are required to create the plots and graphs are. There is also an options class (toxicityOptions-class) which can be edited from the default later. Since the robustToxicitiesClass object is an s4 class slots are accessed using the @ symbol.

An object of class robustToxicitiesClass

# Patient Level Data
data("rt_patientData")
# Toxicity Level Data
data("rt_toxicityData")


# Run the setup command passing in all the column names.
rt = SetupRobustToxicities(
  toxData = rt_toxicityData,
  patientData = rt_patientData,
  patidCol = "patientNo", treatmentCol = "Treatment",
  toxCategoryCol = "category", toxNameCol = "toxicity",
  toxGradeCol = "grade", dateOfStartOfToxWindow = "Registration_date",
  dateOfStartTox = "ae_onset_date", dateOfEndTox = "ae_resolve_date",
  dateOfEndOfToxWindow = "end_of_assessment_date",
  periodDividerCols = c("Registration_date", "Cycle_1_date","Cycle_2_date",
                        "Cycle_3_date", "Cycle_4_date", "Cycle_5_date", "Cycle_6_date"),
  periodDividerLabels = c("Pre treatment", "Cycle 1","Cycle 2",
                          "Cycle 3","Cycle 4","Cycle 5", "Cycle 6"),
  treatmentCodes = NULL, treatmentLabels = NULL, options = NULL)

# Look for queries. Note: must be called before running any
# of the functions on this class.
rt = QueryRobustToxicities(rt)

###########################################################
# Table Examples.
###########################################################
# Summary, worst grade by cycle
ToxTable_summary(rt)

# ReporteRs flextable version
ft = FT_ToxTable_summary(rt)
ft$GetTable()


# Worst grade by patient for each toxicity type
ToxTable_cycle(rt)

# ReporteRs flextable version
ft = FT_ToxTable_cycle(rt)
ft$GetTable()

# Worst grade by category
ToxTable_category(rt)

# ReporteRs flextable version
ft = FT_ToxTable_category(rt)
ft$GetTable()

# Alternative style for worst grade by category
ToxTable_categories(rt)

###########################################################
# Plot Examples
###########################################################
ToxPlot_byToxicity(rt)

# With causality
# Not provided so generate some
rt@toxData$causality1 = sample(1:5,28, replace = TRUE)
rt@toxData$causality2 = sample(1:5,28, replace = TRUE)

causality = ToxPlot_causalityInfo(
  columns = c("causality1","causality2"),
  names = c("A","BA"),
  width = 1.5,
  pch = c(NA,NA,4,8,16),
  cex = 1.2)


ToxPlot_byToxicity(rt,
                   causality = causality)




ToxPlot_byPatient(rt)

ToxPlot_byCycle(rt)

###########################################################
# Alternative specification to cycles
###########################################################
# wrapper for toxPlot_byCycle adding alternative boundaries
timeBoundaries = c(0,21,42,63,84,105,126)
rt2 = CreateTimeDividers(rt, timeBoundaries)
ToxTable_summary(rt2)


ToxPlot_byTime(rt, timeBoundaries = timeBoundaries)