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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.

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()

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()
#> Setting theme "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()

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)
  )

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)) 
#> Setting theme "Compact"

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()

Code of Conduct

Please note that the gtreg project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.