stats-html.Rmd

---
title: "gtsummary + R Markdown"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE)
```

```{r libraries, message=FALSE}
library(gtsummary)
library(tidyverse)
library(survival)
```

# NOTE

This RMarkdown is the built-in example from the `gtsummary` R package. You can get the same file by running the code below:

```{r, eval = FALSE}
library(gtsummary)
system.file(package = "gtsummary") %>%
  file.path("rmarkdown_example/gtsummary_rmarkdown_html.Rmd") %>%
  file.edit()
```


## gtsummary tables

Tables created with {gtsummary} can be integrated into R markdown documents.
The {gtsummary} package was written to be a companion to the [{gt} package](https://gt.rstudio.com/) from RStudio, and {gtsummary} tables are printed using {gt} when possible.
Currently, {gt} supports **HTML** output, with **LaTeX** and **RTF** planned for the future.

```{r example}
patient_characteristics <-
  trial %>%
  select(trt, age, grade, response) %>%
  tbl_summary(by = trt)  
patient_characteristics
```

With HTML output, you can include complex tables with footnotes, indentation, and spanning table headers.

```{r}
# Side-by-side Regression Models
# logistic regression model
t1 <-
  glm(response ~ trt + grade + age, trial, family = binomial) %>%
  tbl_regression(exponentiate = TRUE)
# time to death Cox model
t2 <-
  coxph(Surv(ttdeath, death) ~ trt + grade + age, trial) %>%
  tbl_regression(exponentiate = TRUE)

# printing merged table
tbl_merge(
  tbls = list(t1, t2),
  tab_spanner = c("**Tumor Response**", "**Time to Death**")
)
```

## inline reporting

Any number/statistic from a {gtsummary} table can be reported inline in a R markdown document using the `inline_text()` function.  See example below:

> Among patients who received Drug A, `r inline_text(patient_characteristics, variable = grade, level = "III", column = "Drug A")` had grade III tumors.

For detailed examples using functions from {gtsummary}, visit the [{gtsummary} website](http://www.danieldsjoberg.com/gtsummary/).