Introducing {gtreg}

Shannon Pileggi & Daniel D. Sjoberg

Introduction

  • Introduction

  • About adverse events

  • First adverse event tables

  • Modified adverse event tables

  • Other convenience functions

  • Exporting options

Licensing



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

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


R installed? Pretty recent?

I am on version 4.2.0

RStudio installed? Pretty recent?

I am on version 2022.07.1+554

Have these packages?

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

gtreg

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

  {gtreg} is built on

     {gtsummary} is built on

       {gt}

{gtreg} overview

About adverse events

  • Introduction

  • About adverse events

  • First adverse event tables

  • Modified adverse event tables

  • Other convenience functions

  • Exporting options

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

  • Introduction

  • About adverse events

  • First adverse event tables

  • Modified adverse event tables

  • Other convenience functions

  • Exporting options

Data

df_adverse_events

  • 100 unique subjects

  • 1 row 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

  • 10 unique subjects

  • multiple rows 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_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

Modified adverse event tables

  • Introduction

  • About adverse events

  • First adverse event tables

  • Modified adverse event tables

  • Other convenience functions

  • Exporting options

Modified adverse event tables

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() 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')
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

tbl_ae() with other aesthetics

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') |> 
  modify_header(
    all_ae_cols() ~ "**Grade {by}**"
    ) %>%
  modify_spanning_header(
     all_ae_cols(TRUE, TRUE) ~ "**{strata}**  \nN = {n}"
    ) |> 
  bold_labels()
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

Other convenience functions

  • Introduction

  • About adverse events

  • First adverse event tables

  • Modified adverse event tables

  • Other convenience functions

  • Exporting options

Other convenience 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

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

Exporting options

  • Introduction

  • About adverse events

  • First adverse event tables

  • Modified adverse event tables

  • Other convenience functions

  • Exporting options

Exporting options

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"
  )
```

Thank you!

{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}