# Tutorial: tbl_regression

#### Last Updated: September 13, 2020

## Introduction

The `tbl_regression()` 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()`, `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.

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 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}.

    # install.packages("gtsummary")
    library(gtsummary)

## Example data set

In this vignette we’ll be using the `trial` data set which is included in the {gtsummary package}.

- This data set contains information from 200 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 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.

Variable | Class | Label
--- | --- | ---
`trt` | character | Chemotherapy Treatment
`age` | numeric | Age
`marker` | numeric | Marker Level (ng/mL)
`stage` | factor | T Stage
`grade` | factor | Grade
`response` | integer | Tumor Response
`death` | integer | Patient Died
`ttdeath` | numeric | Months to Death/Censor
Includes mix of continuous, dichotomous, and categorical variables

## 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` data set.

    # build logistic regression model
    m1 <- glm(response ~ age + stage, trial, family = binomial)

    # view raw model results
    summary(m1)$coefficients
    #>                Estimate Std. Error    z value   Pr(>|z|)
    #> (Intercept) -1.48622424 0.62022844 -2.3962530 0.01656365
    #> age          0.01939109 0.01146813  1.6908683 0.09086195
    #> stageT2     -0.54142643 0.44000267 -1.2305071 0.21850725
    #> stageT3     -0.05953479 0.45042027 -0.1321761 0.89484501
    #> stageT4     -0.23108633 0.44822835 -0.5155549 0.60616530

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

    tbl_regression(m1, exponentiate = TRUE)

Characteristic | OR1 | 95% CI1 | p-value
--- | --- | --- | ---
Age | 1.02 | 1.00, 1.04 | 0.091
T Stage |  |  |
T1 | — | — |
T2 | 0.58 | 0.24, 1.37 | 0.2
T3 | 0.94 | 0.39, 2.28 | 0.9
T4 | 0.79 | 0.33, 1.90 | 0.6
1 OR = Odds Ratio, CI = Confidence Interval

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, 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
2. Add additional data/information to a summary table with `add_*()` functions
3. Modify summary table appearance with the {gtsummary} functions
4. Modify table appearance with {gt} package functions

### Modifying function arguments

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

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

### {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.

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

### {gtsummary} functions to format table

The {gtsummary} package comes with functions specifically made to modify and format summary tables.

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} functions to format table

The {gt} package 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.

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

Characteristic | OR1 | 95% CI1 | p-value
--- | --- | --- | ---
Age | 1.02 | 1.00, 1.04 | 0.091
T Stage |  |  |
T1 | — | — |
T2 | 0.58 | 0.24, 1.37 | 0.2
T3 | 0.94 | 0.39, 2.28 | 0.9
T4 | 0.79 | 0.33, 1.90 | 0.6
This data is simulated
1 OR = Odds Ratio, CI = Confidence Interval

### 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

    # 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()

Characteristic | OR1 | 95% CI1 | p-value
--- | --- | --- | ---
Age | 1.02 | 1.00, 1.04 | 0.087
T Stage |  |  | 0.62
T1 | — | — |
T2 | 0.58 | 0.24, 1.37 |
T3 | 0.94 | 0.39, 2.28 |
T4 | 0.79 | 0.33, 1.90 |
1 OR = Odds Ratio, CI = Confidence Interval

## Univariate Regression

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()`.

    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()
    #> add_q: Adjusting p-values with
    #> `stats::p.adjust(x$table_body$p.value, method = "fdr")`

Characteristic | N | Event N | OR1 | 95% CI1 | p-value | q-value2
--- | --- | --- | --- | --- | --- | ---
Age | 183 | 58 | 1.02 | 1.00, 1.04 | 0.091 | 0.18
Grade | 193 | 61 |  |  | 0.93 | 0.93
I |  |  | — | — |  |
II |  |  | 0.95 | 0.45, 2.00 |  |
III |  |  | 1.10 | 0.52, 2.29 |  |
1 OR = Odds Ratio, CI = Confidence Interval
2 False discovery rate correction for multiple testing

## Setting Default 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.

## Supported Models

Below is a listing of known and tested models supported by `tbl_regression()`. If a model follows a standard format and has a tidier, it’s likely to be supported as well, even if not listed below.

Model | Details
--- | ---
`biglm::bigglm()` |
`biglmm::bigglm()` |
`brms::brm()` | `broom.mixed` package required
`cmprsk::crr()` | Limited support. It is recommended to use `tidycmprsk::crr()` instead.
`fixest::feglm()` | May fail with R <= 4.0.
`fixest::femlm()` | May fail with R <= 4.0.
`fixest::feNmlm()` | May fail with R <= 4.0.
`fixest::feols()` | May fail with R <= 4.0.
`gam::gam()` |
`geepack::geeglm()` |
`glmmTMB::glmmTMB()` | `broom.mixed` package required
`lavaan::lavaan()` | Limited support for categorical variables
`lfe::felm()` |
`lme4::glmer()` | `broom.mixed` package required
`lme4::glmer.nb()` | `broom.mixed` package required
`lme4::lmer()` | `broom.mixed` package required
`logitr::logitr()` | Requires logitr >= 0.8.0
`MASS::glm.nb()` |
`MASS::polr()` |
`mgcv::gam()` | Use default tidier `broom::tidy()` for smooth terms only, or `gtsummary::tidy_gam()` to include parametric terms
`mice::mira` | Limited support. If `mod` is a `mira` object, use `tidy_plus_plus(mod, tidy_fun = function(x, ...) mice::pool(x) %>% mice::tidy(...))`
`multgee::nomLORgee()` | Experimental support. Use `tidy_multgee()` as `tidy_fun`.
`multgee::ordLORgee()` | Experimental support. Use `tidy_multgee()` as `tidy_fun`.
`nnet::multinom()` |
`ordinal::clm()` | Limited support for models with nominal predictors.
`ordinal::clmm()` | Limited support for models with nominal predictors.
`parsnip::model_fit` | Supported as long as the type of model and the engine is supported.
`plm::plm()` |
`rstanarm::stan_glm()` | `broom.mixed` package required
`stats::aov()` | Reference rows are not relevant for such models.
`stats::glm()` |
`stats::lm()` |
`stats::nls()` | Limited support
`survey::svycoxph()` |
`survey::svyglm()` |
`survey::svyolr()` |
`survival::clogit()` |
`survival::coxph()` |
`survival::survreg()` |
`tidycmprsk::crr()` |
`VGAM::vglm()` | Limited support. It is recommended to use `tidy_parameters()` as `tidy_fun`.