inst/HelpExamples/ToxPlot_byToxicity_example.R

In csmoxford/robustToxicities: Toxicity tables

# 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)

##########################################################
ToxPlot_byToxicity(rt)

##########################################################
# Subset to a range. Usefull for plotting over a number of figures if there
# are lots of adverse events
ToxPlot_byToxicity(rt, rowID_range = c(1,7))

##########################################################
# subset to a specific set of adverse events
rt@toxData$ass_TRUE = rt@toxData$Treatment == "Placebo"
ToxPlot_byToxicity(rt)

###########################################################
# Add causality data
rt@toxData$ass_TRUE = TRUE

# With causality
# Not provided so generate some for illustrative purposes
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","B"),
  width = c(1.5,1.5),
  cex = 1.2)

ToxPlot_byToxicity(rt,
                   causality = causality)

#########################################################
# Add event data

event_EOT = ToxPlot_eventInfo(
  columns = c("end_of_treatment_date"),
  label = c("End Of Treatment"),
  lwd = 4,
  col = c("blue")
)

event_EOA = ToxPlot_eventInfo(
  columns = c("end_of_assessment_date"),
  label = c("End Of Assessment"),
  lwd = 4,
  col = c("green")
)

ToxPlot_byToxicity(rt,
                   causality = causality,
                   xlim = c(-7, 100),
                   events = list(event_EOT, event_EOA))

########################################################
# Change offset

event_SOT = ToxPlot_eventInfo(
  columns = c("Registration_date"),
  label = c("Registration Date"),
  lwd = 4,
  col = c("orange")
)

ToxPlot_byToxicity(rt,
                   causality = causality,
                   xlim = c(-67, 40),
                   xlab = "Days from end of treatment",
                   events = list(event_SOT, event_EOT, event_EOA),
                   offsetEvent = "end_of_treatment_date")