---
title: "Tutorial: tbl_regression"
date: "Last Updated: September 13, 2020"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteEncoding{UTF-8}
  %\VignetteIndexEntry{Tutorial: tbl_regression}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  chunk_output_type: console
---


```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  warning = FALSE,
  comment = "#>"
)

gt_compact_fun <- function(x) {
  gt::tab_options(x, 
                  table.font.size = 'small',
                  data_row.padding = gt::px(1),
                  summary_row.padding = gt::px(1),
                  grand_summary_row.padding = gt::px(1),
                  footnotes.padding = gt::px(1),
                  source_notes.padding = gt::px(1),
                  row_group.padding = gt::px(1))
}

# exit if car package not installed (added to pass Cmd Checks on old R versions)
if (!requireNamespace("car")) knitr::knit_exit()
```

```{r, echo = FALSE, results = 'asis'}
# we do NOT want the vignette to build on CRAN...it's taking too long
if (!identical(Sys.getenv("IN_PKGDOWN"), "true") && 
    !tolower(as.list(Sys.info())$user) %in% c("sjobergd", "currym", "whitingk", "whiting")) {
  msg <- 
    paste("View this vignette on the",
          "[package website](https://www.danieldsjoberg.com/gtsummary/articles/tbl_regression.html).")
  cat(msg)
  knitr::knit_exit()
}
```

## Introduction

The [`tbl_regression()`](https://www.danieldsjoberg.com/gtsummary/reference/tbl_regression.html) function takes a **regression model object** in **R** and returns a **formatted table of regression model results** that is publication-ready.
It is a simple way to summarize and present your analysis results using **R**!
Like [`tbl_summary()`](https://www.danieldsjoberg.com/gtsummary/reference/tbl_summary.html), `tbl_regression()` creates highly customizable analytic tables with sensible defaults. 

This vignette will walk a reader through the `tbl_regression()` function, and the various functions available to modify and make additions to an existing formatted regression table.

<img src = "https://github.com/ddsjoberg/gtsummary/raw/main/data-raw/misc_files/tbl_mvregression_demo.gif" alt = "animated" width = "100%">

*Behind the scenes:* `tbl_regression()` uses `broom::tidy()` to perform the initial model formatting, and can accommodate many different model types (e.g. `lm()`, `glm()`, `survival::coxph()`, `survival::survreg()` and other are [vetted models](https://www.danieldsjoberg.com/gtsummary/reference/vetted_models.html) known to work with {gtsummary}).
It is also possible to specify your own function to tidy the model results if needed.  

## Setup

Before going through the tutorial, install and load {gtsummary}.

```{r message = FALSE, warning=FALSE}
# install.packages("gtsummary")
library(gtsummary)
```

## Example data set

In this vignette we'll be using the [**`trial`**](https://www.danieldsjoberg.com/gtsummary/reference/trial.html) data set which is included in the {gtsummary package}.

* This data set contains information from `r nrow(trial)` patients who received one of two types of chemotherapy (Drug A or Drug B).

* The outcomes are tumor response and death.  

* Each variable in the data frame has been assigned an **attribute label** (i.e. `attr(trial$trt, "label") == "Chemotherapy Treatment")` with the **[labelled](http://larmarange.github.io/labelled/)** package, which we highly recommend using. These labels are displayed in the {gtsummary} output table by default. Using {gtsummary} on a data frame without labels will simply print variable names, or there is an option to add labels later.

```{r, echo = FALSE}
trial %>%
  purrr::imap_dfr(
    ~tibble::tibble(Variable = glue::glue("`{.y}`"), 
                    Class = class(.x),
                    Label = attr(.x, "label"))) %>%
  gt::gt() %>%
  gt::tab_source_note("Includes mix of continuous, dichotomous, and categorical variables") %>%
  gt::fmt_markdown(columns = c(Variable)) %>%
  gt::cols_align("left") %>%
  gt_compact_fun()
```

## Basic Usage

The default output from `tbl_regression()` is meant to be publication ready.  

* Let's start by creating a **logistic regression model** to **predict tumor response** using the variables age and grade from the [`trial`](https://www.danieldsjoberg.com/gtsummary/reference/trial.html) data set. 
```{r, message=FALSE}
# build logistic regression model
m1 <- glm(response ~ age + stage, trial, family = binomial)

# view raw model results
summary(m1)$coefficients
```

* We will then a **regression model table** to summarize and present these results in just one line of code from {gtsummary}. 

```{r, message=FALSE}
tbl_regression(m1, exponentiate = TRUE)
```

Note the sensible defaults with this basic usage (that can be customized later):

* The model was recognized as logistic regression with coefficients exponentiated, so the **header displayed "OR"** for odds ratio. 

* **Variable types** are automatically detected and **reference rows** are added for categorical variables.

* **Model estimates** and **confidence intervals** are **rounded** and formatted.

* Because the variables in the data set were [labelled](http://larmarange.github.io/labelled/), the **labels were carried through** into the {gtsummary} output table.  Had the data not been labelled, the default is to display the variable name.

* Variable levels are **indented** and **footnotes** added.

## Customize Output

There are four primary ways to customize the output of the regression model table.

1. Modify `tbl_regression()` function input arguments
1. Add additional data/information to a summary table with `add_*()` functions
1. Modify summary table appearance with the {gtsummary} functions
1. Modify table appearance with {gt} package functions

### Modifying function arguments

The `tbl_regression()` function includes many arguments for modifying the appearance.

```{r, echo = FALSE}
tibble::tribble(
  ~Argument,          ~Description,
  "`label=`",            "modify variable labels in table", 
  "`exponentiate=`",     "exponentiate model coefficients",
  "`include=`",          "names of variables to include in output. Default is all variables",
  "`show_single_row=`",  "By default, categorical variables are printed on multiple rows. If a variable is dichotomous and you wish to print the regression coefficient on a single row, include the variable name(s) here.", 
  "`conf.level=`",       "confidence level of confidence interval",  
  "`intercept=`",        "indicates whether to include the intercept",  
  "`estimate_fun=`",     "function to round and format coefficient estimates",  
  "`pvalue_fun=`",       "function to round and format p-values",
  "`tidy_fun=`",         "function to specify/customize tidier function"
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = c(Argument)) %>%
  gt_compact_fun()
```

### {gtsummary} functions to add information

The {gtsummary} package has built-in functions for adding to results from `tbl_regression()`.
The following functions add columns and/or information to the regression table.

```{r echo = FALSE}
tibble::tribble(
  ~Function,                     ~Description,
  "`add_global_p()`",           "adds the global p-value for a categorical variables",  
  "`add_glance_source_note()`", "adds statistics from `broom::glance()` as source note",
  "`add_vif()`",                "adds column of the variance inflation factors (VIF)",
  "`add_q()`",                  "add a column of q values to control for multiple comparisons"   
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = c(Function)) %>%
  gt_compact_fun()
```

### {gtsummary} functions to format table

The {gtsummary} package comes with functions specifically made to modify and format summary tables.  
```{r echo = FALSE}
tibble::tribble(
  ~Function,                     ~Description,
  "`modify_header()`",           "update column headers",   
  "`modify_footnote()`",         "update column footnote",   
  "`modify_spanning_header()`",  "update spanning headers",   
  "`modify_caption()`",          "update table caption/title",   
  "`bold_labels()`",             "bold variable labels",  
  "`bold_levels()`",             "bold variable levels",  
  "`italicize_labels()`",        "italicize variable labels",  
  "`italicize_levels()`",        "italicize variable levels",  
  "`bold_p()`",                  "bold significant p-values"
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = c(Function)) %>%
  gt_compact_fun()
```

### {gt} functions to format table

The [{gt} package](https://gt.rstudio.com/index.html) is packed with many great functions for modifying table output---too many to list here.
Review the package's website for a full listing.

To use the {gt} package functions with {gtsummary} tables, the regression table must first be converted into a {gt} object.
To this end, use the `as_gt()` function after modifications have been completed with {gtsummary} functions.

```{r}
m1 %>%
  tbl_regression(exponentiate = TRUE) %>%
  as_gt() %>%
  gt::tab_source_note(gt::md("*This data is simulated*"))
```

### Example

There are formatting options available, such as adding bold and italics to text.
In the example below,  
  - Coefficients are **exponentiated** to give odds ratios  
  - **Global p-values** for Stage are reported
  - Large p-values are rounded to **two decimal places**  
  - P-values less than 0.10 are **bold** 
  - Variable labels are **bold**  
  - Variable levels are **italicized**  

```{r, eval=TRUE}
# format results into data frame with global p-values
m1 %>%
  tbl_regression(
    exponentiate = TRUE, 
    pvalue_fun = ~style_pvalue(.x, digits = 2),
  ) %>% 
  add_global_p() %>%
  bold_p(t = 0.10) %>%
  bold_labels() %>%
  italicize_levels()
```

## Univariate Regression {#tbl_uvregression}

The `tbl_uvregression()` function produces a table of univariate regression models.
The function is a wrapper for `tbl_regression()`, and as a result, accepts nearly identical function arguments.
The function's results can be modified in similar ways to `tbl_regression()`. 

```{r tbl_uvregression}
trial %>%
  select(response, age, grade) %>%
  tbl_uvregression(
    method = glm,
    y = response,
    method.args = list(family = binomial),
    exponentiate = TRUE,
    pvalue_fun = ~style_pvalue(.x, digits = 2)
  ) %>%
  add_global_p() %>%  # add global p-value 
  add_nevent() %>%    # add number of events of the outcome
  add_q() %>%         # adjusts global p-values for multiple testing
  bold_p() %>%        # bold p-values under a given threshold (default 0.05)
  bold_p(t = 0.10, q = TRUE) %>% # now bold q-values under the threshold of 0.10
  bold_labels()
```

## Setting Default Options {#options}

The {gtsummary} regression functions and their related functions have sensible defaults for rounding and formatting results.
If you, however, would like to change the defaults there are a few options.
The default options can be changed using the {gtsummary} themes function `set_gtsummary_theme()`.
The package includes pre-specified themes, and you can also create your own.
Themes can control baseline behavior, for example, how p-values are rounded, coefficients are rounded, default headers, confidence levels, etc.
For details on creating a theme and setting personal defaults, visit the [themes vignette](https://www.danieldsjoberg.com/gtsummary/articles/themes.html).
