toxTables {ProAE}

Create toxicity tables for individual and composite PRO-CTCAE survey items.

Description

Data format should be in 'long' format, where each PRO-CTCAE item is a variable/column.

Usage

toxTables(
  dsn,
  id_var,
  cycle_var,
  baseline_val,
  type = "bl_adjusted",
  test = "c",
  riskdiff = FALSE,
  risk_ci = "wald",
  risk_ci_alpha = 0.05,
  arm_var = NA,
  cycle_limit = NA
)

Arguments

dsn

A data.frame object with PRO-CTCAE data.

id_var

A character string. Name of ID variable differentiating each PRO-CTCAE survey/participant entered as a quoted string.

cycle_var

A character string. Name of variable differentiating one longitudinal/repeated. PRO-CTCAE survey from another, within an individual ID.

baseline_val

A number indicating the expected baseline cycle/time point.

type

A character string. Type of summary measure to be be used. Options include: "max_post_bl" = Use subjects' maximum score post-baseline visit. "bl_adjusted" = Use subjects' baseline adjusted score over the study period. "max" = Use subjects' maximum score over the study period. The baseline adjusted score is derived by the following: If the maximum score post-baseline is more severe than the baseline score, then the use maximum score post-baseline is used as the adjusted score. Otherwise, if the maximum score post-baseline is the same or less serve than the baseline score, then zero (0) is used as the adjusted score. Defaults to "bl_adjusted".

test

A character string. Specify the statistical test to apply where comparing rates among arms. Options include: "c" = chi square, "f" = fisher's exact. Defaults to "c".

riskdiff

Logical. Calculates risk differences between two arms. Valid if there are only two arms in the data.frame specified. This option will countermand options called with the test parameter. Defaults to FALSE.

risk_ci

A character string. Specify the confidence interval type to be constructed for risk differences. Options include: "wald", and "agresti-caffo". Defaults to "wald".

risk_ci_alpha

A number between 0 and 1. Specify the alpha level of the risk difference confidence intervals. Defaults to 0.05.

arm_var

A character string. Name of arm variable differentiating treatment groups. Must be character or factor class. Overall frequencies will be reported if no arm/grouping variable is provided. Defaults to NA.

cycle_limit

A number. Limit the data to be analyzed up to and including a given cycle number or time point. Defaults to NA.

Value

A list object with data.frame elements for individual items and composite grades.

Examples

toxTables(dsn=ProAE::tox_acute, id_var="id", cycle_var="Cycle", baseline_val=1)