In shannonpileggi/gtreg: Regulatory Tables for Clinical Research

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

gtreg

Installation

You can install {gtreg} with the following code.

install.packages("gtreg")

You can install the development version of {gtreg} from GitHub with:

# install.packages("devtools")
devtools::install_github("shannonpileggi/gtreg")

Overview

The {gtreg} package creates tabular data summaries appropriate for regulatory submissions. The package builds the tables using {gtsummary}.

Here are slides and a recorded talk (17 min) from "Introducing {gtreg}: an R package to produce regulatory tables for clinical research" presented at the 2022 R in Medicine conference.

Screenshot of YouTube recording on title slide {width=70%}

Functions for adverse event (AE) reporting

Summarize Raw Adverse Counts

tbl_ae_count() provides counts of all AEs, and omits percentage statistics as multiple AEs can occur per subject.

library(gtreg)
tbl_ae_count <- 
  df_adverse_events |> 
  tbl_ae_count(
    ae = adverse_event,
    soc = system_organ_class, 
    by = drug_attribution
  ) |>
  add_overall(across = "by") |>
  modify_spanning_header(all_ae_cols() ~ "**Drug Attribution**") |>
  bold_labels()

# Had to manually save images in temp file, not sure if better way.
gt::gtsave(as_gt(tbl_ae_count), file = file.path(tempdir(), "temp2.png"))

# Have to do this workaround since the README needs markdown format for GitHub page but a different format for the website.
if (identical(Sys.getenv("IN_PKGDOWN"), "true")) {
  as_gt(tbl)
} else {
  knitr::include_graphics("man/figures/README-example-tbl_ae_count-1.png")
}

Summarize Adverse Events by Grade

tbl_ae() counts one AE per subject by maximum grade; percentage statistics are provided by default with the denominators reflecting the number of patients in the study.

library(gtreg)
gtsummary::theme_gtsummary_compact()

tbl_ae <- 
  df_adverse_events |>
  tbl_ae(
    id_df = df_patient_characteristics,
    id = patient_id,
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade, 
    strata = trt
  ) |>
  modify_header(all_ae_cols() ~ "**Grade {by}**") |> 
  bold_labels()

# Had to manually save images in temp file, not sure if better way.
gt::gtsave(as_gt(tbl_ae), file = file.path(tempdir(), "temp.png"))

# Have to do this workaround since the README needs markdown format for GitHub page but a different format for the website.
if (identical(Sys.getenv("IN_PKGDOWN"), "true")) {
  as_gt(tbl)
} else {
  knitr::include_graphics("man/figures/README-example-tbl_ae-1.png")
}

Focus on rates of high grade complications

tbl_ae_focus() also counts one AE per subject by maximum grade, and is a convenience to summarize dichotomous AE attributes.

tbl_ae_focus <- 
  df_adverse_events |>
  tbl_ae_focus(
    id_df = df_patient_characteristics,
    id = patient_id,
    ae = adverse_event,
    include = c(any_complication, grade3_complication)
  )

# Had to manually save images in temp file, not sure if better way.
gt::gtsave(as_gt(tbl_ae_focus), file = file.path(tempdir(), "temp3.png"))

# Have to do this workaround since the README needs markdown format for GitHub page but a different format for the website.
if (identical(Sys.getenv("IN_PKGDOWN"), "true")) {
  as_gt(tbl)
} else {
  knitr::include_graphics("man/figures/README-example-tbl_ae_focus-1.png")
}

Other Functions for Clinical Reporting

Regulatory summary

tbl_reg_summary() creates a data summary table often seen in regulatory submissions.

tbl_reg_summary <-
  df_patient_characteristics |>
  tbl_reg_summary(by = trt, include = c(marker, status))

# Had to manually save images in temp file, not sure if better way.
gt::gtsave(as_gt(tbl_reg_summary), file = file.path(tempdir(), "temp4.png"))

# Have to do this workaround since the README needs markdown format for GitHub page but a different format for the website.
if (identical(Sys.getenv("IN_PKGDOWN"), "true")) {
  as_gt(tbl)
} else {
  knitr::include_graphics("man/figures/README-example-tbl_reg_summary-1.png")
}

Print an AE listing

tbl_listing() creates a gtsummary-class listing of data to enable grouped printing.

tbl_listing <-
  head(df_adverse_events, n = 10) |>
  select(system_organ_class, adverse_event, grade, drug_attribution, patient_id) |>
  dplyr::arrange(adverse_event, desc(grade)) |>
  tbl_listing(group_by = system_organ_class) |>
  bold_labels()

# Had to manually save images in temp file, not sure if better way.
gt::gtsave(as_gt(tbl_listing), file = file.path(tempdir(), "temp5.png"))

# Have to do this workaround since the README needs markdown format for GitHub page but a different format for the website.
if (identical(Sys.getenv("IN_PKGDOWN"), "true")) {
  as_gt(tbl)
} else {
  knitr::include_graphics("man/figures/README-example-tbl_listing-1.png")
}