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https://shannonpileggi.github.io/gtreg/
Regulatory Tables for Clinical Research
https://shannonpileggi.github.io/gtreg/
Last synced: 3 months ago
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Regulatory Tables for Clinical Research
- Host: GitHub
- URL: https://shannonpileggi.github.io/gtreg/
- Owner: shannonpileggi
- License: gpl-3.0
- Created: 2021-11-29T20:06:00.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-07-25T14:49:31.000Z (3 months ago)
- Last Synced: 2024-07-28T00:24:57.109Z (3 months ago)
- Language: R
- Homepage: https://shannonpileggi.github.io/gtreg/
- Size: 16.3 MB
- Stars: 36
- Watchers: 5
- Forks: 9
- Open Issues: 10
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Support: .github/SUPPORT.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# gtreg 
[](https://github.com/shannonpileggi/gtreg/actions)
[](https://app.codecov.io/gh/shannonpileggi/gtreg?branch=main)
[](https://CRAN.R-project.org/package=gtreg) [](https://lifecycle.r-lib.org/articles/stages.html#experimental)
## Installation
You can install {gtreg} with the following code.
``` r
install.packages("gtreg")
```
You can install the development version of {gtreg} from [GitHub](https://github.com/shannonpileggi/gtreg) with:
``` r
# 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](https://shannonpileggi.github.io/introducing-gtreg-rmed-2022/#/title-slide) and a [recorded talk (17 min)](https://youtu.be/DmslEfczYqM) from "Introducing {gtreg}: an R package to produce regulatory tables for clinical research" presented at the 2022 R in Medicine conference.
[{width=70%}](https://youtu.be/DmslEfczYqM)
## 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.
```{r example2}
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()
```
```{r example-tbl_ae_count, include = FALSE}
# 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"))
```
```{r out.width = "76%", echo = FALSE}
# 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.
```{r example}
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()
```
```{r example-tbl_ae, include = FALSE}
# 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"))
```
```{r out.width = "100%", echo = FALSE}
# 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.
```{r example3}
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)
)
```
```{r example-tbl_ae_focus, include = FALSE}
# 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"))
```
```{r out.width = "62%", echo = FALSE}
# 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.
```{r example4}
tbl_reg_summary <-
df_patient_characteristics |>
tbl_reg_summary(by = trt, include = c(marker, status))
```
```{r example-tbl_reg_summary, include = FALSE}
# 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"))
```
```{r out.width = "42%", echo = FALSE}
# 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.
```{r example5}
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()
```
```{r example-tbl_listing, include = FALSE}
# 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"))
```
```{r out.width = "62%", echo = FALSE}
# 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")
}
```
## Code of Conduct
Please note that the gtreg project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.