datasummary_skim: Quick overview of numeric or categorical variables

In vincentarelbundock/gtsummary: Summary Tables and Plots for Statistical Models and Data: Beautiful, Customizable, and Publication-Ready

Quick overview of numeric or categorical variables

Description

This function was inspired by the excellent skimr package for R. See the Details and Examples sections below, and the vignettes on the modelsummary website:

• https://modelsummary.com/

• https://modelsummary.com/articles/datasummary.html

Usage

datasummary_skim(
  data,
  output = "default",
  type = "all",
  fmt = 1,
  title = NULL,
  notes = NULL,
  align = NULL,
  escape = TRUE,
  by = NULL,
  fun_numeric = list(Unique = NUnique, `Missing Pct.` = PercentMissing, Mean = Mean, SD =
    SD, Min = Min, Median = Median, Max = Max, Histogram = function(x) ""),
  ...
)

Arguments

data	A data.frame (or tibble)
output	filename or object type (character string) Supported filename extensions: .docx, .html, .tex, .md, .txt, .csv, .xlsx, .png, .jpg Supported object types: "default", "html", "markdown", "latex", "latex_tabular", "typst", "data.frame", "tinytable", "gt", "kableExtra", "huxtable", "flextable", "DT", "jupyter". The "modelsummary_list" value produces a lightweight object which can be saved and fed back to the modelsummary function. The "default" output format can be set to "tinytable", "kableExtra", "gt", "flextable", "huxtable", "DT", or "markdown" If the user does not choose a default value, the packages listed above are tried in sequence. Session-specific configuration: options("modelsummary_factory_default" = "gt") Persistent configuration: config_modelsummary(output = "markdown") Warning: Users should not supply a file name to the output argument if they intend to customize the table with external packages. See the 'Details' section. LaTeX compilation requires the booktabs and siunitx packages, but siunitx can be disabled or replaced with global options. See the 'Details' section.
type	String. Variables to summarize: "all", "numeric", "categorical", "dataset"
fmt	how to format numeric values: integer, user-supplied function, or modelsummary function. Integer: Number of decimal digits User-supplied functions: Any function which accepts a numeric vector and returns a character vector of the same length. modelsummary functions: fmt = fmt_significant(2): Two significant digits (at the term-level) fmt = fmt_sprintf("%.3f"): See ?sprintf fmt = fmt_identity(): unformatted raw values
title	string. Cross-reference labels should be added with Quarto or Rmarkdown chunk options when applicable. When saving standalone LaTeX files, users can add a label such as ⁠\\label{tab:mytable}⁠ directly to the title string, while also specifying escape=FALSE.
notes	list or vector of notes to append to the bottom of the table.
align	A string with a number of characters equal to the number of columns in the table (e.g., align = "lcc"). Valid characters: l, c, r, d. "l": left-aligned column "c": centered column "r": right-aligned column "d": dot-aligned column. For LaTeX/PDF output, this option requires at least version 3.0.25 of the siunitx LaTeX package. See the LaTeX preamble help section below for commands to insert in your LaTeX preamble.
escape	boolean TRUE escapes or substitutes LaTeX/HTML characters which could prevent the file from compiling/displaying. TRUE escapes all cells, captions, and notes. Users can have more fine-grained control by setting escape=FALSE and using an external command such as: modelsummary(model, "latex") |> tinytable::format_tt(tab, j=1:5, escape=TRUE)
by	Character vector of grouping variables to compute statistics over.
fun_numeric	Named list of funtions to apply to each column of data. If fun_numeric includes "Histogram" or "Density", inline plots are inserted.
...	all other arguments are passed through to the table-making functions tinytable::tt, kableExtra::kbl, gt::gt, DT::datatable, etc. depending on the output argument. This allows users to pass arguments directly to datasummary in order to affect the behavior of other functions behind the scenes.

Global Options

The behavior of modelsummary can be modified by setting global options. For example:

• options(modelsummary_model_labels = "roman")

The rest of this section describes each of the options above.

Model labels: default column names

These global option changes the style of the default column headers:

• options(modelsummary_model_labels = "roman")

• options(modelsummary_panel_labels = "roman")

The supported styles are: "model", "panel", "arabic", "letters", "roman", "(arabic)", "(letters)", "(roman)"

The panel-specific option is only used when shape="rbind"

Table-making packages

modelsummary supports 6 table-making packages: tinytable, kableExtra, gt, flextable, huxtable, and DT. Some of these packages have overlapping functionalities. To change the default backend used for a specific file format, you can use ' the options function:

options(modelsummary_factory_html = 'kableExtra') options(modelsummary_factory_word = 'huxtable') options(modelsummary_factory_png = 'gt') options(modelsummary_factory_latex = 'gt') options(modelsummary_factory_latex_tabular = 'kableExtra')

Table themes

Change the look of tables in an automated and replicable way, using the modelsummary theming functionality. See the vignette: https://modelsummary.com/articles/appearance.html

• modelsummary_theme_gt

• modelsummary_theme_kableExtra

• modelsummary_theme_huxtable

• modelsummary_theme_flextable

• modelsummary_theme_dataframe

Model extraction functions

modelsummary can use two sets of packages to extract information from statistical models: the easystats family (performance and parameters) and broom. By default, it uses easystats first and then falls back on broom in case of failure. You can change the order of priorities or include goodness-of-fit extracted by both packages by setting:

options(modelsummary_get = "easystats")

options(modelsummary_get = "broom")

options(modelsummary_get = "all")

Formatting numeric entries

By default, LaTeX tables enclose all numeric entries in the ⁠\num{}⁠ command from the siunitx package. To prevent this behavior, or to enclose numbers in dollar signs (for LaTeX math mode), users can call:

options(modelsummary_format_numeric_latex = "plain")

options(modelsummary_format_numeric_latex = "mathmode")

A similar option can be used to display numerical entries using MathJax in HTML tables:

options(modelsummary_format_numeric_html = "mathjax")

LaTeX preamble

When creating LaTeX via the tinytable backend (default in version 2.0.0 and later), it is useful to include the following commands in the LaTeX preamble of your documents. Note that they are added automatically when compiling Rmarkdown or Quarto documents (except when the modelsummary() calls are cached).

\usepackage{tabularray}
\usepackage{float}
\usepackage{graphicx}
\usepackage[normalem]{ulem}
\UseTblrLibrary{booktabs}
\UseTblrLibrary{siunitx}
\newcommand{\tinytableTabularrayUnderline}[1]{\underline{#1}}
\newcommand{\tinytableTabularrayStrikeout}[1]{\sout{#1}}
\NewTableCommand{\tinytableDefineColor}[3]{\definecolor{#1}{#2}{#3}}

References

Arel-Bundock V (2022). “modelsummary: Data and Model Summaries in R.” Journal of Statistical Software, 103(1), 1-23. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v103.i01")}.'

Examples

dat <- mtcars
dat$vs <- as.logical(dat$vs)
dat$cyl <- as.factor(dat$cyl)
datasummary_skim(dat)
datasummary_skim(dat, type = "categorical")

vincentarelbundock/gtsummary documentation built on Nov. 6, 2024, 11:07 p.m.