toxAUC {ProAE}

Create longitudinal mean score line plots for PRO-CTCAE data with modified Area Under the Curve (AUC) estimates showing descriptive symptomatic adverse event burden worsening and improvement from baseline.

Description

Data format should be in 'long' format, where each PRO-CTCAE item is a variable/column. AUC calculations will only include subjects with non- missing baseline values (within each PRO-CTCAE item).

Usage

toxAUC(
  dsn,
  id_var,
  cycle_var,
  baseline_val,
  arm_var = NA,
  auc = "above",
  cycle_limit = NA,
  y_limit = 4,
  tab_ymin = NA,
  tab_ymax = NA,
  round_dec = 2,
  permute_tests = FALSE,
  permute_n = 2000,
  bootstrap_ci = FALSE,
  bootstrap_ci_alpha = 0.05,
  bootstrap_n = 2000,
  arm_colors = NA,
  x_label = NA,
  add_item_title = FALSE,
  cycle_label = FALSE,
  cycle_vals = NA,
  cycle_labs = NA
)

Arguments

dsn

A data.frame object with PRO-CTCAE data

id_var

A character string. Name of ID variable differentiating each unique patient.

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.

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.

auc

A character string. Specifies the partitioning of area shown. options include: "above" = accumulated area above the baseline horizontal can be interpreted as worsening severity from baseline. "below" = accumulated area below the baseline horizontal can be interpreted the as the amount of decreased severity from baseline. "both" = accumulated area above and below the baseline horizontal are shown. Defaults to "above".

cycle_limit

A number. Limit the number of cycles to be use to calculate the AUC metrics up to and including a given cycle number. All available cycle time points are used if no cycle number is provided. Defaults to NA.

y_limit

A number. Y axis limit for plots. Defaults to 4.

tab_ymin

A number. Y axis coordinate for adjusting the vertical placement of the AUC table within the figure. Defaults to NA.

tab_ymax

A number. Y axis coordinate for adjusting the vertical placement of the AUC table within the figure. Defaults to NA.

round_dec

A number. Number of decimal places to be shown within the AUC table. Defaults to 2.

permute_tests

Logical. Calls to calculate p values comparing the difference in AUC between two arms using a permutation test. Typical two- sided null hypothesis for a permutation test is applied. That is, assigning subjects to groups is interchangeable when calculating AUC. Computation time may be extensive depending on data size, number of PRO-CTCAE items, and number of permutations called. Consider staring out an open window or crafting a haiku during this time. Defaults to FALSE.

permute_n

A number. The number of permutations to be used for permutation tests. Defaults to 2000.

bootstrap_ci

Logical. Calls to construct alpha-level confidence intervals for the difference in AUC between arms. Similar considerations for computation time as permute_tests are recommended here. Defaults to FALSE.

bootstrap_ci_alpha

A number. Specifies the alpha level for bootstrap confidence intervals. Must be between 0 and 1. Defaults to 0.05.

bootstrap_n

A number. The number of bootstrap iterations to be used for bootstrap confidence intervals. Defaults to 2000.

arm_colors

A column vector of valid colors. Allows the user to define the colors of arms shown in the returned figure. Column vector must have length greater than or equal to the number of arms. Default colors provided.

x_label

A character string. Label for the x axis of the plot. Defaults to NA resulting in x axis labeled with cycle_var variable name.

add_item_title

Logical. Adds the item short label to the title of each figure. Defaults to FALSE.

cycle_label

Logical. Assign custom labels to cycles/time point. If TRUE, the cycle_vals and cycle_labs must also be specified.

cycle_vals

Numeric column vector. Vector of values seen within the cycle_var variable. Must be same length of cycle_labs. Defaults to NA.

cycle_labs

Character column vector. Vector of labels to be mapped to the associated cycle_vals. Must be same length of cycle_vals. Defaults to NA.

Examples

## Not run: 
AUC=toxAUC(dsn = ProAE::tox_acute,
id_var = "id",
cycle_var = "Cycle",
baseline_val = 1)
AUC[[1]]

## End(Not run)