Package 'ProAE' reference manual

Title:	PRO-CTCAE Scoring, Analysis, and Graphical Tools
Description:	A collection of tools to facilitate standardized analysis and graphical procedures when using the National Cancer Institute’s Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE) and other PRO measurements.
Authors:	Blake Langlais [aut, cre], Brie Noble [ctb], Mia Truman [ctb], Molly Voss [ctb], Amylou Dueck [aut]
Maintainer:	Blake Langlais <[email protected]>
License:	GPL-3
Version:	1.0.3
Built:	2024-10-22 07:22:43 UTC
Source:	CRAN

ProAE.

Description

This package is a collection of tools for analyzing and plotting PRO-CTCAE data

PRO-CTCAE variable / label crosswalk

Description

A crosswalk / look-up table of expected variable names for associated PRO-CTCAE symptom items.

Format

A data frame with 124 rows and 2 variables

Details

name. Expected variable name - item number/letter corresponds to the NCI-PRO-CTCAE (English) Item Library Version 1.0
short_label. Item label including the item symptom group and frequency, severity, interference, or presence component

Author(s)

Blake Langlais

References

https://healthcaredelivery.cancer.gov/pro-ctcae/instrument-pro.html

PRO-CTCAE data reflecting acute drug toxicity

Description

Simulated example data where the drug group experiences acute toxicity followed by symptom abatement over the course of treatment.

Format

A data frame with 1400 rows and 5 variables

Details

id. Subject identifier
Cycle. Time variable denoting visits/cycles (1-10)
arm. Treatment groups include drug and placebo
PROCTCAE_9A_SCL. PRO-CTCAE frequency item for nausea
PROCTCAE_9B_SCL. PRO-CTCAE severity item for nausea
PROCTCAE_9_COMP. PRO-CTCAE composite score for nausea

Author(s)

Blake Langlais

PRO-CTCAE data reflecting chronic drug toxicity

Description

Simulated example data where the drug group experiences chronic toxicity over the course of treatment.

Format

A data frame with 1400 rows and 5 variables

Details

id. Subject identifier
Cycle. Time variable denoting visits/cycles (1-10)
arm. Treatment groups include drug and placebo
PROCTCAE_9A_SCL. PRO-CTCAE frequency item for nausea
PROCTCAE_9B_SCL. PRO-CTCAE severity item for nausea
PROCTCAE_9_COMP. PRO-CTCAE composite score for nausea

Author(s)

Blake Langlais

PRO-CTCAE data reflecting cumulative drug toxicity

Description

Simulated example data where drug toxicity is cumulative over the course of treatment.

Format

A data frame with 1400 rows and 5 variables

Details

id. Subject identifier
Cycle. Time variable denoting visits/cycles (1-10)
arm. Treatment groups include drug and placebo
PROCTCAE_9A_SCL. PRO-CTCAE frequency item for nausea
PROCTCAE_9B_SCL. PRO-CTCAE severity item for nausea
PROCTCAE_9_COMP. PRO-CTCAE composite score for nausea

Author(s)

Blake Langlais

PRO-CTCAE data reflecting cyclical drug toxicity

Description

Simulated example data where the drug group experiences cyclically toxicity post-treatment administration

Format

A data frame with 1400 rows and 5 variables

Details

id. Subject identifier
Cycle. Time variable denoting visits/cycles (1-10)
arm. Treatment groups include drug and placebo
PROCTCAE_9A_SCL. PRO-CTCAE frequency item for nausea
PROCTCAE_9B_SCL. PRO-CTCAE severity item for nausea
PROCTCAE_9_COMP. PRO-CTCAE composite score for nausea

Author(s)

Blake Langlais

PRO-CTCAE data reflecting late incipient drug toxicity

Description

Simulated example data where the drug group experiences late incipient toxicity towards the end of the treatment period.

Format

A data frame with 1400 rows and 5 variables

Details

id. Subject identifier
Cycle. Time variable denoting visits/cycles (1-10)
arm. Treatment groups include drug and placebo
PROCTCAE_9A_SCL. PRO-CTCAE frequency item for nausea
PROCTCAE_9B_SCL. PRO-CTCAE severity item for nausea
PROCTCAE_9_COMP. PRO-CTCAE composite score for nausea

Author(s)

Blake Langlais

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

## End(Not run)

Create PRO-CTCAE severity frequency distribution figures for individual survey items and composite scores

Description

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

Usage

toxFigures(
  dsn,
  id_var,
  cycle_var,
  baseline_val,
  arm_var = NA,
  plot_limit = NA,
  colors = 1,
  bar_label = 0,
  cycle_label = FALSE,
  cycle_vals = NA,
  cycle_labs = NA,
  summary_only = FALSE,
  summary_highlight = FALSE,
  cycles_only = TRUE,
  x_lab_angle = 0,
  x_lab_vjust = 1,
  x_lab_hjust = 0,
  x_label = "Randomized Treatment Assignment",
  y_label = "Percent of Total Frequency",
  footnote_break = FALSE,
  suppress_legend = FALSE,
  add_item_title = FALSE
)
toxFigures(
  dsn,
  id_var,
  cycle_var,
  baseline_val,
  arm_var = NA,
  plot_limit = NA,
  colors = 1,
  bar_label = 0,
  cycle_label = FALSE,
  cycle_vals = NA,
  cycle_labs = NA,
  summary_only = FALSE,
  summary_highlight = FALSE,
  cycles_only = TRUE,
  x_lab_angle = 0,
  x_lab_vjust = 1,
  x_lab_hjust = 0,
  x_label = "Randomized Treatment Assignment",
  y_label = "Percent of Total Frequency",
  footnote_break = FALSE,
  suppress_legend = FALSE,
  add_item_title = FALSE
)

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.
`arm_var`	A character string. Name of arm variable differentiating treatment groups. Must be character or factor class. Overall AUC will be reported if no arm/grouping variable is provided. Defaults to `NA`.
`plot_limit`	A number. Limit the number of cycles to be plotted up to and including a given cycle number. All available cycle time points are plotted if no cycle number is provided. Defaults to `NA`.
`colors`	A number. Specify the coloring scheme of symptom scores within frequency bars. Options include: 1 = Blue and red color shading, 2 = qualitative color shades (color blind friendly), 3 = black and white. Defaults to 1.
`bar_label`	A number. Label frequency bars with sample size (n) or percent shown on the y-axis. Label options include: `1` = sample size (n) within each cycle (symptom score 0 or higher), `2` = sample size (n) within each cycle with present symptoms (symptom score > 0), `3` = sample size (n) within each cycle with severe symptoms (symptom score >= 3), `4` = percent of subjects within each cycle with present symptoms (symptom score > 0), `5` = percent of subjects within each cycle with severe symptoms (symptom score >= 3). No labels will be applied if not specified. Defaults to `NA`.
`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`.
`summary_only`	Logical. Only display the summary measures in figures / Suppress the individual time points from plotting. Defaults to `FALSE`.
`summary_highlight`	Logical. Add black box around summary measure bar chart. Defaults to `FALSE`.
`cycles_only`	Logical. Only display the longitudinal time points in figures / Suppress the summary measures from plotting. Defaults to `TRUE`.
`x_lab_angle`	A integer between 0 and 360. Allows the user to rotate the x axis labels in order to fit long arm names (0 or 45 recommended). Defaults to `0`.
`x_lab_vjust`	A number. A ggplot2 object option. Allows the user to vertically adjusts the x axis labels in order to fit arm names. Defaults to `1`.
`x_lab_hjust`	A number. A ggplot2 object option. Allows the user to horizontally adjusts the x axis labels in order to fit arm names. Defaults to `0`.
`x_label`	A character string. Label for the x axis of the plot. Defaults to `"Randomized Treatment Assignment"` if `arm_var` is specified, defaults to `"Overall"` if not `arm_var` is specified.
`y_label`	A character string. Label for the y axis of the plot. Defaults to `"Percent of Total Frequency"`.
`footnote_break`	Logical. Add a line break to the footnote Defaults to `FALSE`.
`suppress_legend`	Logical. Suppress the legend from appearing in figure. Defaults to `FALSE`.
`add_item_title`	Logical. Add the symptom item name as a title to the figure. Defaults to `FALSE`.

Value

A list object. The returned object is a (k X 2) or (k x 3) nested list. Where k is the number of PRO-CTCAE item groups (e.g. pain, fatigue, nausea); list[[1 ... i ... k]]. For each list item there are 2 or 3 elements. The 1st element of each list item is the name of the PRO-CTCAE item group returned as a string. The 2nd element is the PRO-CTCAE figure as a ggplot object. These objects can be modified as such.

Examples

## Not run: 
fig_acute = toxFigures(dsn = ProAE::tox_acute,
 cycle_var = "Cycle",
 baseline_val = 1,
 arm_var = "arm",
 id_var = "id",
 x_lab_angle = -45,
 x_lab_vjust =  .3,
 x_lab_hjust = .2,
 colors = 2)
fig_acute[[1]]

## End(Not run)
## Not run: 
fig_acute = toxFigures(dsn = ProAE::tox_acute,
 cycle_var = "Cycle",
 baseline_val = 1,
 arm_var = "arm",
 id_var = "id",
 x_lab_angle = -45,
 x_lab_vjust =  .3,
 x_lab_hjust = .2,
 colors = 2)
fig_acute[[1]]

## End(Not run)

Re-code PRO-CTCAE text responses, apply a zero-imputation procedures, and construct PRO-CTCAE composite scores.

Description

This function takes in a data frame set with PRO-CTCAE survey text fields/responses and returns a data frame with appropriate numerical re-coding. This function will accept 1 or up to all 124 PRO-CTCAE survey fields. All PRO-CTCAE variable names MUST conform to a pre-specified naming structure. PRO-CTCAE variable names are made up of FOUR components: 1)'PROCTCAE', 2) number [1,2,3, ..., i, ..., 80], 3) 'A', 'B', or 'C' component of the i-th PRO-CTCAE field, 4) and 'SCL' (if severity, interference, or frequency) or 'IND' (if yes/no variable). Each component must be delimited by an underscore (_)

Usage

toxScores(
  dsn,
  reformat = FALSE,
  impute = FALSE,
  composites = FALSE,
  short_labels = FALSE
)
toxScores(
  dsn,
  reformat = FALSE,
  impute = FALSE,
  composites = FALSE,
  short_labels = FALSE
)

Arguments

`dsn`	A data.frame object with PRO-CTCAE data
`reformat`	Reformat PRO-CTCAE text responses to numeric scores. Defaults to `FALSE`.
`impute`	Apply zero-imputation where appropriate. Defaults to `FALSE`.
`composites`	Construct composite score using available PRO-CTCAE variables within `dsn`. Defaults to `FALSE`.
`short_labels`	Add PRO-CTCAE short labels to available PRO-CTCAE variables within returned object

Details

[EX1] Question 1 of PRO-CTCAE should be: PROCTCAE_1A_SCL
[EX2] Question 48 of PRO-CTCAE should be: PROCTCAE_48A_SCL, PROCTCAE_48B_SCL, PROCTCAE_48C_SCL
[EX3]Question 73 of PRO-CTCAE should be: PROCTCAE_73A_IND

This function also constructs PRO-CTCAE composite scores. Composite score variables for respective PRO-CTCAE item groups are created and named as PROCTCAE_##_COMP.

https://healthcaredelivery.cancer.gov/pro-ctcae/pro-ctcae_english.pdf
Ethan Basch, et al. Development of a Composite Scoring Algorithm for the National Cancer Institute's Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE). ISOQOL 2019
Basch E, et al. Composite Grading Algorithm for the National Cancer Institute’s Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE). Clinical Trials 2020.

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

Value

A data.frame object.

Examples

tox_acute_comp = toxScores(dsn = ProAE::tox_acute, composites = TRUE)
tox_acute_comp = toxScores(dsn = ProAE::tox_acute, composites = TRUE)

Create patient-level and group-level summary statistics.

Description

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

Usage

toxSummary(
  dsn,
  id_var,
  cycle_var,
  summary_measure,
  baseline_val = NA,
  arm_var = NA
)
toxSummary(
  dsn,
  id_var,
  cycle_var,
  summary_measure,
  baseline_val = NA,
  arm_var = 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.
`summary_measure`	A character string. Type of summary statistic to be used. Please consult current literature for appropriate interpretations of the summary measure selected and suitable analysis procedures for comparing groups. Options include: `"max"` = Use subjects' maximum score. `"max_post_bl"` = Use subjects' maximum score post-baseline visit. `"bl_adjusted"` = Use subjects' baseline adjusted 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. `"toxicity_index"` = Construct patient-level toxicity index. `"AUC_worsening"` = Calculate group-level AUC describing
`baseline_val`	A number indicating the expected baseline cycle/time point.
`arm_var`	A character string. Name of arm variable differentiating treatment arms or other grouping factor. Required for group-level summary measures.

Value

A data.frame with only the id and PRO-CTCAE variables being summarized. Each subject will now only have 1 observation (PRO-CTCAE variables are now the summary measure value).

Examples

toxSummary(dsn=ProAE::tox_acute,
id_var="id",
cycle_var="Cycle",
baseline_val=1,
summary_measure = "max")
toxSummary(dsn=ProAE::tox_acute,
id_var="id",
cycle_var="Cycle",
baseline_val=1,
summary_measure = "max")

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
)
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 scores.

Examples

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

Package 'ProAE'

Help Index

ProAE.

Description

PRO-CTCAE variable / label crosswalk

Description

Format

Details

Author(s)

References

PRO-CTCAE data reflecting acute drug toxicity

Description

Format

Details

Author(s)

PRO-CTCAE data reflecting chronic drug toxicity

Description

Format

Details

Author(s)

PRO-CTCAE data reflecting cumulative drug toxicity

Description

Format

Details

Author(s)

PRO-CTCAE data reflecting cyclical drug toxicity

Description

Format

Details

Author(s)

PRO-CTCAE data reflecting late incipient drug toxicity

Description

Format

Details

Author(s)

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

Usage

Arguments

Examples

Create PRO-CTCAE severity frequency distribution figures for individual survey items and composite scores

Description

Usage

Arguments

Value

Examples

Re-code PRO-CTCAE text responses, apply a zero-imputation procedures, and construct PRO-CTCAE composite scores.

Description

Usage

Arguments

Details

Value

Examples

Create patient-level and group-level summary statistics.

Description

Usage

Arguments

Value

Examples

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

Description

Usage

Arguments

Value

Examples