library("modelsummary")
dat <- mtcars
dat$vs <- as.logical(dat$vs)
dat$cyl <- as.factor(dat$cyl)
datasummary_skim(dat)
datasummary_skim(dat, type = "categorical")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 = getOption("modelsummary_output", default = "default"),
type = getOption("modelsummary_type", default = "all"),
fmt = 1,
title = getOption("modelsummary_title", default = NULL),
notes = getOption("modelsummary_notes", default = NULL),
align = getOption("modelsummary_align", default = NULL),
escape = getOption("modelsummary_escape", default = TRUE),
by = getOption("modelsummary_by", default = NULL),
fun_numeric = getOption("modelsummary_fun_numeric", default = 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)
|
type
|
String. Variables to summarize: "all", "numeric", "categorical", "dataset" |
fmt
|
how to format numeric values: integer, user-supplied function, or
|
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.,
|
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 numeric column of data. If fun_numeric includes "Histogram" or "Density", inline plots are inserted. This argument is only used when type=“numeric” or “all”.
|
…
|
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.
|
Version 2.0.0, kableExtra, and tinytable
Since version 2.0.0, modelsummary uses tinytable as its default table-drawing backend. Learn more at: https://vincentarelbundock.github.io/tinytable/",
Revert to kableExtra for one session:
options(modelsummary_factory_default = ‘kableExtra’) options(modelsummary_factory_latex = ‘kableExtra’) options(modelsummary_factory_html = ‘kableExtra’)
Global Options
The behavior of modelsummary can be modified by setting global options. In particular, most of the arguments for most of the package’s functions cna be set using global options. For example:
-
options(modelsummary_output = “modelsummary_list”) -
options(modelsummary_statistic = ‘({conf.low}, {conf.high})’) -
options(modelsummary_stars = TRUE)
Options not specific to given arguments are listed below.
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 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. doi:10.18637/jss.v103.i01.’