In ddsjoberg/gtsummary: Presentation-Ready Data Summary and Analytic Result Tables

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()

# 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() 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 others are supported 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 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 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.

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 data set.

# 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}.

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, 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.

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.

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.

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 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*"))

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()

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().

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.

Supported Models {#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.

broom.helpers::supported_models %>%
  gt::gt() %>%
  gt::cols_label(model = gt::md("Model"), notes = gt::md("Details")) %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = 11, 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)
  )

ddsjoberg/gtsummary documentation built on Nov. 3, 2023, 11:42 a.m.