Introducing {gtreg}: an R package to produce regulatory tables for clinical research

Shannon Pileggi & Daniel Sjoberg

Introduction

Licensing


This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA4.0).

Instructors

Shannon Pileggi

pipinghotdata.com

@PipingHotData

github.com/shannonpileggi

linkedin.com/in/shannon-m-pileggi/

Daniel Sjoberg

danieldsjoberg.com

@statistishdan

github.com/ddsjoberg

linkedin.com/in/ddsjoberg/

Checklist


Install recent R release

Current version 4.2.1

Install RStudio

I am on version 2022.07.1+554

Install packages

install.packages(c("gtreg", "gtsummary", "tidyverse", "labelled", "usethis"))

Ensure you can knit Rmarkdown files

Schedule

Time Activity
09:00 - 09:50 Section 1
09:50 - 10:00 Break
10:00 - 10:50 Section 2
10:50 - 11:00 Break
11:00 - 12:00 Section 3


Please add any questions to the public Zoom chat. These may be answered in the moment or addressed at the end depending on context.

Overview

gtreg

https://shannonpileggi.github.io/gtreg/

  {gtreg} is built on

     {gtsummary} is built on

       {gt}

{gtreg} overview

About adverse events

Adverse events

patient_id trt system_organ_class adverse_event grade drug_attribution
ID 1 Drug B Blood and lymphatic system disorders Anaemia 4 Unrelated
ID 1 Drug B Blood and lymphatic system disorders Increased tendency to bruise 5 Unrelated
ID 1 Drug B Blood and lymphatic system disorders Increased tendency to bruise 4 Unlikely
ID 1 Drug B Blood and lymphatic system disorders Thrombocytopenia 1 Probably
ID 1 Drug B Blood and lymphatic system disorders Thrombocytopenia 3 Definite

  • An adverse event (AE) is a medical issue that occurs during the course of treatment or observation.

  • AEs are classified according to a hierarchy, and we typically report lower level terms within a system organ class.

  • AEs also record severity / grade and likelihood of attribution to treatment.

Summary table challenges

patient_id trt system_organ_class adverse_event grade drug_attribution
ID 1 Drug B Blood and lymphatic system disorders Anaemia 4 Unrelated
ID 1 Drug B Blood and lymphatic system disorders Increased tendency to bruise 5 Unrelated
ID 1 Drug B Blood and lymphatic system disorders Increased tendency to bruise 4 Unlikely
ID 1 Drug B Blood and lymphatic system disorders Thrombocytopenia 1 Probably
ID 1 Drug B Blood and lymphatic system disorders Thrombocytopenia 3 Definite

  • Subjects experience multiple adverse events.

  • Not all enrolled subjects experience an adverse event.

  • The percent of subjects experiencing specific AEs is of interest; typically AEs are counted by maximum grade per event per subject.

  • Multiple AE tables are often required (treatment emergent AEs, AEs on specific treatment cycles, serious AEs, etc.).

Counting by maximum grade


patient_id system_organ_class adverse_event grade
ID 1 Blood and lymphatic system disorders Anaemia 4
ID 1 Blood and lymphatic system disorders Increased tendency to bruise 5
ID 1 Blood and lymphatic system disorders Increased tendency to bruise 4
ID 1 Blood and lymphatic system disorders Thrombocytopenia 1
ID 1 Blood and lymphatic system disorders Thrombocytopenia 3

Counting by maximum grade


Patient ID System Organ Class Adverse Event Grade
Term 1
    ID 1 Blood and lymphatic system disorders Anaemia 4
Term 2
    ID 1 Blood and lymphatic system disorders Increased tendency to bruise 5
    ID 1 Blood and lymphatic system disorders Increased tendency to bruise 4
Term 3
    ID 1 Blood and lymphatic system disorders Thrombocytopenia 1
    ID 1 Blood and lymphatic system disorders Thrombocytopenia 3

Counting by maximum grade


Patient ID System Organ Class Adverse Event Grade
Term 1
    ID 1 Blood and lymphatic system disorders Anaemia 4
Term 2
    ID 1 Blood and lymphatic system disorders Increased tendency to bruise 5
    ID 1 Blood and lymphatic system disorders Increased tendency to bruise 4
Term 3
    ID 1 Blood and lymphatic system disorders Thrombocytopenia 1
    ID 1 Blood and lymphatic system disorders Thrombocytopenia 3


Similar logic applies when counting by severity (e.g. mild, moderate, severe) - if stored as a factor, the highest factor level is retained (severe).

First adverse event tables

Data

df_adverse_events

  • 10 unique subjects

  • multiple rows per subject

patient_id trt system_organ_class adverse_event grade drug_attribution any_complication grade3_complication
ID 1 Drug B Blood and lymphatic system disorders Anaemia 4 Unrelated TRUE TRUE
ID 1 Drug B Blood and lymphatic system disorders Increased tendency to bruise 5 Unrelated TRUE TRUE
ID 1 Drug B Blood and lymphatic system disorders Increased tendency to bruise 4 Unlikely TRUE TRUE
ID 1 Drug B Blood and lymphatic system disorders Thrombocytopenia 1 Probably TRUE FALSE
ID 1 Drug B Blood and lymphatic system disorders Thrombocytopenia 3 Definite TRUE TRUE
ID 1 Drug B Gastrointestinal disorders Intestinal dilatation 2 Definite TRUE FALSE

df_patient_characteristics

  • 100 unique subjects

  • 1 row per subject

patient_id trt age marker status discontinued off_trt_ae
ID 1 Drug B 28 4.807148 Adverse Event Yes Intestinal dilatation
ID 2 Drug B 47 7.714544 Completed Study No NA
ID 3 Drug B 39 6.449793 Completed Study No NA
ID 4 Drug B 45 6.319944 Subject Withdrew Yes NA
ID 5 Drug B 58 5.785283 Physician Decision Yes NA
ID 6 Drug A 42 5.630501 Completed Study No NA

Variable labels

  • A variable label is an attribute of a variable in a data frame.

  • Where applicable, variable labels (not variable names) are printed in {gtsummary} and {gtreg} tables.

  • The example data in {gtreg} comes with variable labels; you can also create your own via labelled::set_variable_labels().

str(df_patient_characteristics)

View(df_patient_characteristics)

First adverse event tables

tbl_ae_count()

  • Count all AEs (not by maximum grade).
df_adverse_events |> 
  tbl_ae_count(
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade
  )
Adverse Event 1 2 3 4 5
Blood and lymphatic system disorders 8 6 11 12 13
    Anaemia 1 — 3 3 3
    Increased tendency to bruise — — 2 5 2
    Iron deficiency anaemia 4 3 — 3 3
    Thrombocytopenia 3 3 6 1 5
Gastrointestinal disorders 14 9 7 11 9
    Difficult digestion 1 — — 3 1
    Intestinal dilatation 3 1 — — 1
    Myochosis 1 4 3 2 3
    Non-erosive reflux disease 5 — — 4 3
    Pancreatic enzyme abnormality 4 4 4 2 1
adverse_event system_organ_class grade
Anaemia Blood and lymphatic system disorders 4
Increased tendency to bruise Blood and lymphatic system disorders 5
Increased tendency to bruise Blood and lymphatic system disorders 4
Thrombocytopenia Blood and lymphatic system disorders 1
Thrombocytopenia Blood and lymphatic system disorders 3
Intestinal dilatation Gastrointestinal disorders 2
Intestinal dilatation Gastrointestinal disorders 1
Myochosis Gastrointestinal disorders 3
Myochosis Gastrointestinal disorders 5
Non-erosive reflux disease Gastrointestinal disorders 5

tbl_ae()

  • Count AEs per subject by maximum grade.
df_adverse_events |> 
  tbl_ae(
    id = patient_id,
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade
  )
Adverse Event N = 10
1 2 3 4 5
Blood and lymphatic system disorders — 1 (10) — 2 (20) 7 (70)
    Anaemia — — 2 (20) 2 (20) 3 (30)
    Increased tendency to bruise — — — 4 (40) 2 (20)
    Iron deficiency anaemia 1 (10) 2 (20) — 2 (20) 2 (20)
    Thrombocytopenia — 1 (10) 3 (30) 1 (10) 4 (40)
Gastrointestinal disorders — — — 4 (40) 6 (60)
    Difficult digestion 1 (10) — — 3 (30) 1 (10)
    Intestinal dilatation 2 (20) 1 (10) — — 1 (10)
    Myochosis — 3 (30) 1 (10) 1 (10) 3 (30)
    Non-erosive reflux disease 4 (40) — — 3 (30) 3 (30)
    Pancreatic enzyme abnormality 2 (20) 1 (10) 2 (20) 2 (20) 1 (10)
patient_id adverse_event system_organ_class grade
ID 1 Anaemia Blood and lymphatic system disorders 4
ID 1 Increased tendency to bruise Blood and lymphatic system disorders 5
ID 1 Increased tendency to bruise Blood and lymphatic system disorders 4
ID 1 Thrombocytopenia Blood and lymphatic system disorders 1
ID 1 Thrombocytopenia Blood and lymphatic system disorders 3
ID 1 Intestinal dilatation Gastrointestinal disorders 2
ID 1 Intestinal dilatation Gastrointestinal disorders 1
ID 1 Myochosis Gastrointestinal disorders 3
ID 1 Myochosis Gastrointestinal disorders 5
ID 1 Non-erosive reflux disease Gastrointestinal disorders 5

tbl_ae()

  • Count AEs per subject by maximum grade.

  • Supply id_df to achieve subject denominator.

df_adverse_events |> 
  tbl_ae(
    id = patient_id,
    id_df = df_patient_characteristics,
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade
  )
Adverse Event N = 100
1 2 3 4 5
Blood and lymphatic system disorders — 1 (1.0) — 2 (2.0) 7 (7.0)
    Anaemia — — 2 (2.0) 2 (2.0) 3 (3.0)
    Increased tendency to bruise — — — 4 (4.0) 2 (2.0)
    Iron deficiency anaemia 1 (1.0) 2 (2.0) — 2 (2.0) 2 (2.0)
    Thrombocytopenia — 1 (1.0) 3 (3.0) 1 (1.0) 4 (4.0)
Gastrointestinal disorders — — — 4 (4.0) 6 (6.0)
    Difficult digestion 1 (1.0) — — 3 (3.0) 1 (1.0)
    Intestinal dilatation 2 (2.0) 1 (1.0) — — 1 (1.0)
    Myochosis — 3 (3.0) 1 (1.0) 1 (1.0) 3 (3.0)
    Non-erosive reflux disease 4 (4.0) — — 3 (3.0) 3 (3.0)
    Pancreatic enzyme abnormality 2 (2.0) 1 (1.0) 2 (2.0) 2 (2.0) 1 (1.0)

df_adverse_events

patient_id adverse_event system_organ_class grade
ID 1 Anaemia Blood and lymphatic system disorders 4
ID 1 Increased tendency to bruise Blood and lymphatic system disorders 5
ID 1 Increased tendency to bruise Blood and lymphatic system disorders 4
ID 1 Thrombocytopenia Blood and lymphatic system disorders 1
ID 1 Thrombocytopenia Blood and lymphatic system disorders 3

df_patient_characteristics

patient_id trt
ID 1 Drug B
ID 2 Drug B
ID 3 Drug B
ID 4 Drug B
ID 5 Drug B

tbl_ae() with strata

df_adverse_events |> 
  tbl_ae(
    id = patient_id,
    id_df = df_patient_characteristics,
    strata = trt,
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade
  )
Adverse Event Drug A, N = 44 Drug B, N = 56
1 2 3 4 5 1 2 3 4 5
Blood and lymphatic system disorders — 1 (2.3) — 1 (2.3) 1 (2.3) — — — 1 (1.8) 6 (11)
    Anaemia — — 1 (2.3) 1 (2.3) — — — 1 (1.8) 1 (1.8) 3 (5.4)
    Increased tendency to bruise — — — 1 (2.3) — — — — 3 (5.4) 2 (3.6)
    Iron deficiency anaemia — — — 1 (2.3) 1 (2.3) 1 (1.8) 2 (3.6) — 1 (1.8) 1 (1.8)
    Thrombocytopenia — 1 (2.3) — 1 (2.3) — — — 3 (5.4) — 4 (7.1)
Gastrointestinal disorders — — — 2 (4.5) 1 (2.3) — — — 2 (3.6) 5 (8.9)
    Difficult digestion — — — 3 (6.8) — 1 (1.8) — — — 1 (1.8)
    Intestinal dilatation 1 (2.3) — — — — 1 (1.8) 1 (1.8) — — 1 (1.8)
    Myochosis — 2 (4.5) 1 (2.3) — — — 1 (1.8) — 1 (1.8) 3 (5.4)
    Non-erosive reflux disease 3 (6.8) — — — — 1 (1.8) — — 3 (5.4) 3 (5.4)
    Pancreatic enzyme abnormality — — 1 (2.3) 1 (2.3) 1 (2.3) 2 (3.6) 1 (1.8) 1 (1.8) 1 (1.8) —

df_adverse_events

patient_id trt adverse_event system_organ_class grade
ID 1 Drug B Anaemia Blood and lymphatic system disorders 4
ID 1 Drug B Increased tendency to bruise Blood and lymphatic system disorders 5
ID 1 Drug B Increased tendency to bruise Blood and lymphatic system disorders 4
ID 1 Drug B Thrombocytopenia Blood and lymphatic system disorders 1
ID 1 Drug B Thrombocytopenia Blood and lymphatic system disorders 3

df_patient_characteristics

patient_id trt
ID 1 Drug B
ID 2 Drug B
ID 3 Drug B
ID 4 Drug B
ID 5 Drug B

tbl_ae_focus()

  • Count dichotomous AE attributes via include.

  • Supply id_df to achieve subject denominator.

df_adverse_events |> 
  tbl_ae_focus(
    id = patient_id,
    id_df = df_patient_characteristics,
    ae = adverse_event,
    soc = system_organ_class, 
    include = c(any_complication, grade3_complication)
  )
Adverse Event N = 100
Any Grade Complication Grade 3+ Complication
Blood and lymphatic system disorders 10 (10) 9 (9.0)
    Anaemia 7 (7.0) 7 (7.0)
    Increased tendency to bruise 6 (6.0) 6 (6.0)
    Iron deficiency anaemia 7 (7.0) 4 (4.0)
    Thrombocytopenia 9 (9.0) 8 (8.0)
Gastrointestinal disorders 10 (10) 10 (10)
    Difficult digestion 5 (5.0) 4 (4.0)
    Intestinal dilatation 4 (4.0) 1 (1.0)
    Myochosis 8 (8.0) 5 (5.0)
    Non-erosive reflux disease 10 (10) 6 (6.0)
    Pancreatic enzyme abnormality 8 (8.0) 5 (5.0)

df_adverse_events

patient_id adverse_event system_organ_class any_complication grade3_complication
ID 1 Anaemia Blood and lymphatic system disorders TRUE TRUE
ID 1 Increased tendency to bruise Blood and lymphatic system disorders TRUE TRUE
ID 1 Increased tendency to bruise Blood and lymphatic system disorders TRUE TRUE
ID 1 Thrombocytopenia Blood and lymphatic system disorders TRUE FALSE
ID 1 Thrombocytopenia Blood and lymphatic system disorders TRUE TRUE

df_patient_characteristics

patient_id trt
ID 1 Drug B
ID 2 Drug B
ID 3 Drug B
ID 4 Drug B
ID 5 Drug B

Exercise 1


Recommended: Enter the dedicated RStudio Cloud work space (with packages pre-installed) to complete Exercise 1. It may still be helpful to peek at the exercises web page to verify that your tables match the desired output.

Click here to enter R in Pharma RStudio Cloud work space for {gtreg}


Otherwise: Use your personal computer and follow along the exercises on the website. Challenge yourself not to peek at the code solutions until you have completed the exercise.

15:00

Modified adverse event tables

Modified adverse event tables

tbl_ae() with add_overall()

See documentation for more add_overall() functionality.

df_adverse_events |> 
  tbl_ae(
    id = patient_id,
    id_df = df_patient_characteristics,
    strata = trt,
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade
  ) |> 
  add_overall(across = 'by') |>
  bold_labels()
Adverse Event Drug A, N = 44 Drug B, N = 56
1 2 3 4 5 Overall 1 2 3 4 5 Overall
Blood and lymphatic system disorders — 1 (2.3) — 1 (2.3) 1 (2.3) 3 (6.8) — — — 1 (1.8) 6 (11) 7 (12)
    Anaemia — — 1 (2.3) 1 (2.3) — 2 (4.5) — — 1 (1.8) 1 (1.8) 3 (5.4) 5 (8.9)
    Increased tendency to bruise — — — 1 (2.3) — 1 (2.3) — — — 3 (5.4) 2 (3.6) 5 (8.9)
    Iron deficiency anaemia — — — 1 (2.3) 1 (2.3) 2 (4.5) 1 (1.8) 2 (3.6) — 1 (1.8) 1 (1.8) 5 (8.9)
    Thrombocytopenia — 1 (2.3) — 1 (2.3) — 2 (4.5) — — 3 (5.4) — 4 (7.1) 7 (12)
Gastrointestinal disorders — — — 2 (4.5) 1 (2.3) 3 (6.8) — — — 2 (3.6) 5 (8.9) 7 (12)
    Difficult digestion — — — 3 (6.8) — 3 (6.8) 1 (1.8) — — — 1 (1.8) 2 (3.6)
    Intestinal dilatation 1 (2.3) — — — — 1 (2.3) 1 (1.8) 1 (1.8) — — 1 (1.8) 3 (5.4)
    Myochosis — 2 (4.5) 1 (2.3) — — 3 (6.8) — 1 (1.8) — 1 (1.8) 3 (5.4) 5 (8.9)
    Non-erosive reflux disease 3 (6.8) — — — — 3 (6.8) 1 (1.8) — — 3 (5.4) 3 (5.4) 7 (12)
    Pancreatic enzyme abnormality — — 1 (2.3) 1 (2.3) 1 (2.3) 3 (6.8) 2 (3.6) 1 (1.8) 1 (1.8) 1 (1.8) — 5 (8.9)

df_adverse_events

patient_id trt adverse_event system_organ_class grade
ID 1 Drug B Anaemia Blood and lymphatic system disorders 4
ID 1 Drug B Increased tendency to bruise Blood and lymphatic system disorders 5
ID 1 Drug B Increased tendency to bruise Blood and lymphatic system disorders 4
ID 1 Drug B Thrombocytopenia Blood and lymphatic system disorders 1
ID 1 Drug B Thrombocytopenia Blood and lymphatic system disorders 3

df_patient_characteristics

patient_id trt
ID 1 Drug B
ID 2 Drug B
ID 3 Drug B
ID 4 Drug B
ID 5 Drug B

Modifying headers

https://shannonpileggi.github.io/gtreg/articles/table-modifications.html

Use modify_header() and modify_spanning_header() with all_ column selectors.

tbl_ae() with modified headers

df_adverse_events |> 
  tbl_ae(
    id = patient_id,
    id_df = df_patient_characteristics,
    strata = trt,
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade
  ) |> 
 add_overall(across = 'by') |> 
 bold_labels() |> 
 modify_header(
    all_ae_cols() ~ "**Grade {by}**"
    ) %>%
  modify_spanning_header(
     all_ae_cols(TRUE, TRUE) ~ "**{strata}**  \nN = {n}"
    )
Adverse Event Drug A
N = 44 		Drug B
N = 56
Grade 1 Grade 2 Grade 3 Grade 4 Grade 5 Overall Grade 1 Grade 2 Grade 3 Grade 4 Grade 5 Overall
Blood and lymphatic system disorders — 1 (2.3) — 1 (2.3) 1 (2.3) 3 (6.8) — — — 1 (1.8) 6 (11) 7 (12)
    Anaemia — — 1 (2.3) 1 (2.3) — 2 (4.5) — — 1 (1.8) 1 (1.8) 3 (5.4) 5 (8.9)
    Increased tendency to bruise — — — 1 (2.3) — 1 (2.3) — — — 3 (5.4) 2 (3.6) 5 (8.9)
    Iron deficiency anaemia — — — 1 (2.3) 1 (2.3) 2 (4.5) 1 (1.8) 2 (3.6) — 1 (1.8) 1 (1.8) 5 (8.9)
    Thrombocytopenia — 1 (2.3) — 1 (2.3) — 2 (4.5) — — 3 (5.4) — 4 (7.1) 7 (12)
Gastrointestinal disorders — — — 2 (4.5) 1 (2.3) 3 (6.8) — — — 2 (3.6) 5 (8.9) 7 (12)
    Difficult digestion — — — 3 (6.8) — 3 (6.8) 1 (1.8) — — — 1 (1.8) 2 (3.6)
    Intestinal dilatation 1 (2.3) — — — — 1 (2.3) 1 (1.8) 1 (1.8) — — 1 (1.8) 3 (5.4)
    Myochosis — 2 (4.5) 1 (2.3) — — 3 (6.8) — 1 (1.8) — 1 (1.8) 3 (5.4) 5 (8.9)
    Non-erosive reflux disease 3 (6.8) — — — — 3 (6.8) 1 (1.8) — — 3 (5.4) 3 (5.4) 7 (12)
    Pancreatic enzyme abnormality — — 1 (2.3) 1 (2.3) 1 (2.3) 3 (6.8) 2 (3.6) 1 (1.8) 1 (1.8) 1 (1.8) — 5 (8.9)

df_adverse_events

patient_id trt adverse_event system_organ_class grade
ID 1 Drug B Anaemia Blood and lymphatic system disorders 4
ID 1 Drug B Increased tendency to bruise Blood and lymphatic system disorders 5
ID 1 Drug B Increased tendency to bruise Blood and lymphatic system disorders 4
ID 1 Drug B Thrombocytopenia Blood and lymphatic system disorders 1
ID 1 Drug B Thrombocytopenia Blood and lymphatic system disorders 3

df_patient_characteristics

patient_id trt
ID 1 Drug B
ID 2 Drug B
ID 3 Drug B
ID 4 Drug B
ID 5 Drug B

Exercise 2


Recommended: Enter the dedicated RStudio Cloud work space (with packages pre-installed) to complete Exercise 1. It may still be helpful to peek at the exercises web page to verify that your tables match the desired output.

Click here to enter R in Pharma RStudio Cloud work space for {gtreg}


Otherwise: Use your personal computer and follow along the exercises on the website. Challenge yourself not to peek at the code solutions until you have completed the exercise.

15:00

Other tabling functions

Other tabling functions

tbl_reg_summary()

Create summary tables with standard regulatory formatting.

 df_patient_characteristics |> 
  tbl_reg_summary(
    by = trt, 
    include = c(marker, status)
    ) |> 
  bold_labels()
Characteristic Drug A, N = 441 Drug B, N = 561
Biological Marker
    N 44 56
    Mean (SD) 5.47 (0.97) 5.46 (1.04)
    Median (IQR) 5.27 (4.98, 5.91) 5.43 (4.67, 6.10)
    Range 3.53, 8.42 3.66, 8.00
    N missing 0 0
Study Status
    Completed Study 20 (45%) 29 (52%)
    Adverse Event 4 (9.1%) 10 (18%)
    Progressive Disease 4 (9.1%) 4 (7.1%)
    Physician Decision 5 (11%) 3 (5.4%)
    Subject Withdrew 4 (9.1%) 6 (11%)
    Active 7 (16%) 4 (7.1%)
1 n (%)

df_patient_characteristics

patient_id trt marker status
ID 1 Drug B 4.807148 Adverse Event
ID 2 Drug B 7.714544 Completed Study
ID 3 Drug B 6.449793 Completed Study
ID 4 Drug B 6.319944 Subject Withdrew
ID 5 Drug B 5.785283 Physician Decision

Exercise 3


Recommended: Enter the dedicated RStudio Cloud work space (with packages pre-installed) to complete Exercise 1. It may still be helpful to peek at the exercises web page to verify that your tables match the desired output.

Click here to enter R in Pharma RStudio Cloud work space for {gtreg}


Otherwise: Use your personal computer and follow along the exercises on the website. Challenge yourself not to peek at the code solutions until you have completed the exercise.

10:00

tbl_listing()

A fancy 💅 way to print grouped data.

df_adverse_events |> 
  head(n = 10) |> 
  select(system_organ_class, adverse_event, grade, drug_attribution, patient_id) |> 
  arrange(adverse_event, desc(grade)) |> 
  tbl_listing(
    group_by = system_organ_class
    ) |> 
  bold_labels()
Adverse Event Grade Drug Attribution Patient ID
Blood and lymphatic system disorders
    Anaemia 4 Unrelated ID 1
    Increased tendency to bruise 5 Unrelated ID 1
    Increased tendency to bruise 4 Unlikely ID 1
    Thrombocytopenia 3 Definite ID 1
    Thrombocytopenia 1 Probably ID 1
Gastrointestinal disorders
    Intestinal dilatation 2 Definite ID 1
    Intestinal dilatation 1 Definite ID 1
    Myochosis 5 Probably ID 1
    Myochosis 3 Unlikely ID 1
    Non-erosive reflux disease 5 Unrelated ID 1

df_adverse_events

system_organ_class adverse_event grade drug_attribution patient_id
Blood and lymphatic system disorders Anaemia 4 Unrelated ID 1
Blood and lymphatic system disorders Increased tendency to bruise 5 Unrelated ID 1
Blood and lymphatic system disorders Increased tendency to bruise 4 Unlikely ID 1
Gastrointestinal disorders Intestinal dilatation 2 Definite ID 1
Gastrointestinal disorders Intestinal dilatation 1 Definite ID 1
Gastrointestinal disorders Myochosis 5 Probably ID 1
Gastrointestinal disorders Myochosis 3 Unlikely ID 1
Gastrointestinal disorders Non-erosive reflux disease 5 Unrelated ID 1
Blood and lymphatic system disorders Thrombocytopenia 3 Definite ID 1
Blood and lymphatic system disorders Thrombocytopenia 1 Probably ID 1

tbl_listing() extensions

Remember this table?

Patient ID System Organ Class Adverse Event Grade
Term 1
    ID 1 Blood and lymphatic system disorders Anaemia 4
Term 2
    ID 1 Blood and lymphatic system disorders Increased tendency to bruise 5
    ID 1 Blood and lymphatic system disorders Increased tendency to bruise 4
Term 3
    ID 1 Blood and lymphatic system disorders Thrombocytopenia 1
    ID 1 Blood and lymphatic system disorders Thrombocytopenia 3 
dat |>
  tbl_listing(
    group_by = ae_label
  ) |> 
  bold_labels() |> 
  as_gt() |> 
  gt::tab_style(
    style = list(
      cell_fill(color = "#FFFBC8")
      ),
    locations = cells_body(rows = c(2, 4, 8))
  )
patient_id system_organ_class adverse_event grade ae_label
ID 1 Blood and lymphatic system disorders Anaemia 4 Term 1
ID 1 Blood and lymphatic system disorders Increased tendency to bruise 5 Term 2
ID 1 Blood and lymphatic system disorders Increased tendency to bruise 4 Term 2
ID 1 Blood and lymphatic system disorders Thrombocytopenia 1 Term 3
ID 1 Blood and lymphatic system disorders Thrombocytopenia 3 Term 3

Exercise 4


Recommended: Enter the dedicated RStudio Cloud work space (with packages pre-installed) to complete Exercise 1. It may still be helpful to peek at the exercises web page to verify that your tables match the desired output.

Click here to enter R in Pharma RStudio Cloud work space for {gtreg}


Otherwise: Use your personal computer and follow along the exercises on the website. Challenge yourself not to peek at the code solutions until you have completed the exercise.

10:00

Table shells

Table shells

Strategy

https://shannonpileggi.github.io/gtreg/articles/table-shells.html

Table shells can be generated for any tbl_ae() and tbl_reg_summary() by:

  1. Create dummy data or use your own data.

  2. Pass the data to your function of choice.

  3. Overwrite the statistic(s) shown to a fixed character string by implementing the style_xxx() function in the digits argument.

style_xxx(8:11)

[1] “xx” “xx” “xx” “xx”

style_xxx(8:11, width = 4, digits = 1)

[1] “xx.x” “xx.x” “xx.x” “xx.x”

Uniform shell for tbl_ae()

df_adverse_events |> 
  tbl_ae(
    id = patient_id,
    id_df = df_patient_characteristics,
    strata = trt,
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade, 
    digits = style_xxx,
    zero_symbol = NULL
  ) |> 
 bold_labels() |> 
 modify_header(all_ae_cols() ~ "**Grade {by}**") %>%
 modify_spanning_header(all_ae_cols(TRUE, TRUE) ~ "**{strata}**  \nN = xx")
Adverse Event Drug A
N = xx 		Drug B
N = xx
Grade 1 Grade 2 Grade 3 Grade 4 Grade 5 Grade 1 Grade 2 Grade 3 Grade 4 Grade 5
Blood and lymphatic system disorders xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)
    Anaemia xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)
    Increased tendency to bruise xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)
    Iron deficiency anaemia xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)
    Thrombocytopenia xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)
Gastrointestinal disorders xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)
    Difficult digestion xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)
    Intestinal dilatation xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)
    Myochosis xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)
    Non-erosive reflux disease xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)
    Pancreatic enzyme abnormality xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx) xx (xx)

df_adverse_events

patient_id trt adverse_event system_organ_class grade
ID 1 Drug B Anaemia Blood and lymphatic system disorders 4
ID 1 Drug B Increased tendency to bruise Blood and lymphatic system disorders 5
ID 1 Drug B Increased tendency to bruise Blood and lymphatic system disorders 4
ID 1 Drug B Thrombocytopenia Blood and lymphatic system disorders 1
ID 1 Drug B Thrombocytopenia Blood and lymphatic system disorders 3

df_patient_characteristics

patient_id trt
ID 1 Drug B
ID 2 Drug B
ID 3 Drug B
ID 4 Drug B
ID 5 Drug B

Custom shell for tbl_ae()

df_adverse_events |> 
  tbl_ae(
    id = patient_id,
    id_df = df_patient_characteristics,
    strata = trt,
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade, 
    digits = list(
      style_xxx, # style for n
      function(x) style_xxx(x, width = 4, digits = 1) # style for %
    ),
    zero_symbol = NULL
  ) |> 
 bold_labels() |> 
 modify_header(all_ae_cols() ~ "**Grade {by}**") %>%
 modify_spanning_header(all_ae_cols(TRUE, TRUE) ~ "**{strata}**  \nN = xx")
Adverse Event Drug A
N = xx 		Drug B
N = xx
Grade 1 Grade 2 Grade 3 Grade 4 Grade 5 Grade 1 Grade 2 Grade 3 Grade 4 Grade 5
Blood and lymphatic system disorders xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)
    Anaemia xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)
    Increased tendency to bruise xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)
    Iron deficiency anaemia xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)
    Thrombocytopenia xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)
Gastrointestinal disorders xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)
    Difficult digestion xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)
    Intestinal dilatation xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)
    Myochosis xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)
    Non-erosive reflux disease xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)
    Pancreatic enzyme abnormality xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x) xx (xx.x)

df_adverse_events

patient_id trt adverse_event system_organ_class grade
ID 1 Drug B Anaemia Blood and lymphatic system disorders 4
ID 1 Drug B Increased tendency to bruise Blood and lymphatic system disorders 5
ID 1 Drug B Increased tendency to bruise Blood and lymphatic system disorders 4
ID 1 Drug B Thrombocytopenia Blood and lymphatic system disorders 1
ID 1 Drug B Thrombocytopenia Blood and lymphatic system disorders 3

df_patient_characteristics

patient_id trt
ID 1 Drug B
ID 2 Drug B
ID 3 Drug B
ID 4 Drug B
ID 5 Drug B

Exercise 5


Recommended: Enter the dedicated RStudio Cloud work space (with packages pre-installed) to complete Exercise 1. It may still be helpful to peek at the exercises web page to verify that your tables match the desired output.

Click here to enter R in Pharma RStudio Cloud work space for {gtreg}


Otherwise: Use your personal computer and follow along the exercises on the website. Challenge yourself not to peek at the code solutions until you have completed the exercise.

10:00

Exporting options

Exporting options

https://shannonpileggi.github.io/gtreg/articles/output-gtreg.html

Exporting options

table1 <- df_adverse_events |> 
  tbl_ae(
    id = patient_id,
    id_df = df_patient_characteristics,
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade
  ) |> 
  modify_header(
    all_ae_cols() ~ "**Grade {by}**"
    ) %>%
  bold_labels()
table1
Adverse Event N = 100
Grade 1 Grade 2 Grade 3 Grade 4 Grade 5
Blood and lymphatic system disorders — 1 (1.0) — 2 (2.0) 7 (7.0)
    Anaemia — — 2 (2.0) 2 (2.0) 3 (3.0)
    Increased tendency to bruise — — — 4 (4.0) 2 (2.0)
    Iron deficiency anaemia 1 (1.0) 2 (2.0) — 2 (2.0) 2 (2.0)
    Thrombocytopenia — 1 (1.0) 3 (3.0) 1 (1.0) 4 (4.0)
Gastrointestinal disorders — — — 4 (4.0) 6 (6.0)
    Difficult digestion 1 (1.0) — — 3 (3.0) 1 (1.0)
    Intestinal dilatation 2 (2.0) 1 (1.0) — — 1 (1.0)
    Myochosis — 3 (3.0) 1 (1.0) 1 (1.0) 3 (3.0)
    Non-erosive reflux disease 4 (4.0) — — 3 (3.0) 3 (3.0)
    Pancreatic enzyme abnormality 2 (2.0) 1 (1.0) 2 (2.0) 2 (2.0) 1 (1.0) 
table1 |>  
  as_flex_table() |> 
  flextable::save_as_docx(
    path = here::here("ae_table.docx")
    )

table1 |>  
 as_hux_xlsx(
   file = here::here("ae_table.xlsx")
   )

---
output: pdf_document
---
<stuff>  
  
```{r}
table1 |> 
  as_kable_extra(
    booktabs = TRUE
  ) |> 
  kableExtra::kable_styling(
    latex_options = "striped",
    stripe_color = "gray!15"
  )
```

Exercise 6


Recommended: Enter the dedicated RStudio Cloud work space (with packages pre-installed) to complete Exercise 1. It may still be helpful to peek at the exercises web page to verify that your tables match the desired output.

Click here to enter R in Pharma RStudio Cloud work space for {gtreg}


Otherwise: Use your personal computer and follow along the exercises on the website. Challenge yourself not to peek at the code solutions until you have completed the exercise.

05:00

Thank you!

🙏 Click here to submit workshop feedback

{gtreg} website

    https://shannonpileggi.github.io/gtreg/

{gtreg} installation

# install from CRAN
install.packages("gtreg") 
# or install development version from github
devtools::install_github("shannonpileggi/gtreg")

{gtreg} issues

    https://github.com/shannonpileggi/gtreg/issues

{gtreg} feature requests or questions: ask on https://github.com/shannonpileggi/gtreg/discussions

Introducing {gtreg}