Treatment Toxicity Profile

Treatment Toxicity Profile

Usage

toxicityprofile(
  data,
  patientID,
  adverseEvent,
  grade,
  treatment,
  systemOrganClass,
  timeToEvent,
  plotType = "stacked_bar",
  sortBy = "frequency",
  showHighGradeOnly = FALSE,
  minIncidence = 5,
  gradeColors = "ctcae",
  showPercentages = TRUE,
  showConfidenceIntervals = FALSE,
  groupComparison = FALSE,
  cumulativeIncidence = FALSE,
  confidenceLevel = "0.95"
)

Arguments

data

The data as a data frame.

patientID

Variable containing patient identifiers.

adverseEvent

Variable containing adverse event names or categories.

grade

CTCAE grade or severity level (1-5 or equivalent scale).

treatment

Treatment or study arm for comparison (optional).

systemOrganClass

System organ class (SOC) for grouping adverse events.

timeToEvent

Time from treatment start to adverse event occurrence.

plotType

Primary visualization method for toxicity profile.

sortBy

Method for ordering adverse events in the plot.

showHighGradeOnly

Display only grade 3+ adverse events.

minIncidence

Minimum incidence percentage for events to be displayed.

gradeColors

Color scheme for toxicity grades.

showPercentages

Display percentages on the plot.

showConfidenceIntervals

Display confidence intervals for incidence rates.

groupComparison

Perform statistical comparison between treatment groups.

cumulativeIncidence

Display cumulative incidence over time (requires time variable).

confidenceLevel

Confidence level for intervals and tests.

Value

A results object containing:

results$todo					a html
results$plot					an image
results$summary					a table
results$gradeDistribution					a table
results$groupComparison					a table
results$socSummary					a table

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$summary$asDF

as.data.frame(results$summary)