`datasummary`: Crosstabs, frequencies, correlations, balance (a.k.a. "table 1"), and more

datasummary is a function from the modelsummary package. It allows us to create data summaries, frequency tables, crosstabs, correlation tables, balance tables (aka “Table 1”), and more. It has many benefits:

• Easy to use.
• Extremely flexible.
• Many output formats: HTML, LaTeX, Microsoft Word and Powerpoint, Text/Markdown, PDF, RTF, or Image files.
• Embed tables in Rmarkdown or knitr dynamic documents.
• Customize the appearance of tables with the gt, kableExtra or flextable packages. The possibilities are endless!

This tutorial will show how to draw tables like these (and more!):

Background

datasummary is built around the fantastic tables package for R. It is a thin “wrapper” which adds convenience functions and arguments; a user-interface consistent with modelsummary; cleaner html output; and the ability to export tables to more formats, including gt tables, flextable objects, and Microsoft Word documents.

datasummary is a general-purpose table-making tool. It allows us to build (nearly) any summary table we want by using simple 2-sided formulae. For example, in the expression x + y ~ mean + sd, the left-hand side of the formula identifies the variables or statistics to display as rows, and the right-hand side defines the columns. Below, we will see how variables and statistics can be “nested” with the * operator to produce tables like the ones above.

In addition to datasummary, the modelsummary package includes a “family” of companion functions named datasummary_*. These functions facilitate the production of standard, commonly used tables. This family currently includes:

• datasummary(): Flexible function to create custom tables using 2-sided formulae.
• datasummary_balance(): Group characteristics (e.g., control vs. treatment)
• datasummary_correlation(): Table of correlations.
• datasummary_skim(): Quick summary of a dataset.
• datasummary_df(): Create a table from any dataframe.
• datasummary_crosstab(): Cross tabulations of categorical variables.

In the next three sections, we illustrate how to use datasummary_balance, datasummary_correlation, datasummary_skim, and datasummary_crosstab. Then, we dive into datasummary itself to highlight its ease and flexibility.

datasummary_skim

The first datasummary companion function is called datasummary_skim. It was heavily inspired by one of my favorite data exploration tools for R: the skimr package. The goal of this function is to give us a quick look at the data.

To illustrate, we download data from the cool new palmerpenguins package by Alison Presmanes Hill and Allison Horst. These data were collected at the Palmer Station in Antarctica by Gorman, Williams & Fraser (2014), and they include 3 categorical variables and 4 numeric variables.

library(modelsummary)
library(tidyverse)

url <- 'https://vincentarelbundock.github.io/Rdatasets/csv/palmerpenguins/penguins.csv'
penguins <- read.csv(url, na.strings = "")

To summarize the numeric variables in the dataset, we type:

datasummary_skim(penguins)

To summarize the categorical variables in the dataset, we type:

datasummary_skim(penguins, type = "categorical")

		N	%
species	Adelie	152	44.2
	Chinstrap	68	19.8
	Gentoo	124	36.0
island	Biscoe	168	48.8
	Dream	124	36.0
	Torgersen	52	15.1
sex	female	165	48.0
	male	168	48.8
	NA	11	3.2

Later in this tutorial, it will become clear that datasummary_skim is just a convenience “template” built around datasummary, since we can achieve identical results with the latter. For example, to produce a text-only version of the tables above, we can type:

datasummary(All(penguins) ~ Mean + SD + Histogram,
            data = penguins,
            output = 'markdown')

|                  |    Mean|     SD|  Histogram|
|:-----------------|-------:|------:|----------:|
|bill_length_mm    |   43.92|   5.46|  ▁▅▆▆▆▇▇▂▁|
|bill_depth_mm     |   17.15|   1.97| ▃▄▄▄▇▆▇▅▂▁|
|flipper_length_mm |  200.92|  14.06|  ▂▅▇▄▁▄▄▂▁|
|body_mass_g       | 4201.75| 801.95| ▁▄▇▅▄▄▃▃▂▁|

Printing histograms will not work on all computers. If you have issues with this feature, try changing your computer’s locale, or try using a different display font.

The datasummary_skim function does not currently allow users to summarize continuous and categorical variables together in a single table, but the datasummary_balance function described in the next section can do so.

datasummary_balance

The expressions “balance table” or “Table 1” refer to a type of table which is often printed in the opening pages of a scientific peer-reviewed article. Typically, this table includes basic descriptive statistics about different subsets of the study population. For instance, analysts may want to compare the socio-demographic characteristics of members of the “control” and “treatment” groups in a randomized control trial, or the flipper lengths of male and female penguins. In addition, balance tables often include difference in means tests.

To illustrate how to build a balance table using the datasummary_balance function, we download data about a job training experiment studies in Lalonde (1986). Then, we clean up the data by renaming and recoding a few variables.

# Download and read data
training <- 'https://vincentarelbundock.github.io/Rdatasets/csv/Ecdat/Treatment.csv'
training <- read.csv(training, na.strings = "")

# Rename and recode variables
training <- training %>%
            mutate(`Earnings Before` = re75 / 1000,
                   `Earnings After` = re78 / 1000,
                   Treatment = ifelse(treat == TRUE, 'Treatment', 'Control'),
                   Married = ifelse(married == TRUE, 'Yes', 'No')) %>%
            select(`Earnings Before`,
                   `Earnings After`,
                   Treatment,
                   Ethnicity = ethn,
                   Age = age,
                   Education = educ,
                   Married)

Now, we execute the datasummary_balance function. If the estimatr package is installed, datasummary_balance will calculate the difference in means and test statistics.

caption <- 'Descriptive statistics about participants in a job training experiment. The earnings are displayed in 1000s of USD. This table was created using the "datasummary" function from the "modelsummary" package for R.'
reference <- 'Source: Lalonde (1986) American Economic Review.'

library(modelsummary)
datasummary_balance(~Treatment,
                    data = training,
                    title = caption,
                    notes = reference)

Note that if the dataset includes columns called “blocks”, “clusters”, or “weights”, this information will automatically be taken into consideration by estimatr when calculating the difference in means and the associated statistics.

Users can also use the ~ 1 formula to indicate that they want to summarize all the data instead of splitting the analysis across subgroups:

datasummary_balance(~ 1, data = training)

		Mean	Std. Dev.
Earnings Before		17.9	13.9
Earnings After		20.5	15.6
Age		34.2	10.5
Education		12.0	3.1
		N	Pct.
Treatment	Control	2490	93.1
	Treatment	185	6.9
Ethnicity	black	780	29.2
	hispanic	92	3.4
	other	1803	67.4
Married	No	483	18.1
	Yes	2192	81.9

datasummary_correlation

The datasummary_correlation accepts a dataframe or tibble, it identifies all the numeric variables, and calculates the correlation between each of those variables:

datasummary_correlation(mtcars)

	mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
mpg	1	.	.	.	.	.	.	.	.	.	.
cyl	-.85	1	.	.	.	.	.	.	.	.	.
disp	-.85	.90	1	.	.	.	.	.	.	.	.
hp	-.78	.83	.79	1	.	.	.	.	.	.	.
drat	.68	-.70	-.71	-.45	1	.	.	.	.	.	.
wt	-.87	.78	.89	.66	-.71	1	.	.	.	.	.
qsec	.42	-.59	-.43	-.71	.09	-.17	1	.	.	.	.
vs	.66	-.81	-.71	-.72	.44	-.55	.74	1	.	.	.
am	.60	-.52	-.59	-.24	.71	-.69	-.23	.17	1	.	.
gear	.48	-.49	-.56	-.13	.70	-.58	-.21	.21	.79	1	.
carb	-.55	.53	.39	.75	-.09	.43	-.66	-.57	.06	.27	1

The values displayed in this table are equivalent to those obtained by calling: cor(x, use='pairwise.complete.obs').

datasummary_crosstab

A cross tabulation is often useful to explore the association between two categorical variables.

library(modelsummary)
url <- 'https://vincentarelbundock.github.io/Rdatasets/csv/palmerpenguins/penguins.csv'
penguins <- read.csv(url, na.strings = "")

datasummary_crosstab(species ~ sex, data = penguins)

species		female	male	All
Adelie	N	73	73	152
	% row	48.0	48.0	100.0
Chinstrap	N	34	34	68
	% row	50.0	50.0	100.0
Gentoo	N	58	61	124
	% row	46.8	49.2	100.0
All	N	165	168	344
	% row	48.0	48.8	100.0

You can create multi-level crosstabs by specifying interactions using the * operator:

datasummary_crosstab(species ~ sex * island, data = penguins)

species		female			male			All
		Biscoe	Dream	Torgersen	Biscoe	Dream	Torgersen
Adelie	N	22	27	24	22	28	23	152
	% row	14.5	17.8	15.8	14.5	18.4	15.1	100.0
Chinstrap	N	0	34	0	0	34	0	68
	% row	0.0	50.0	0.0	0.0	50.0	0.0	100.0
Gentoo	N	58	0	0	61	0	0	124
	% row	46.8	0.0	0.0	49.2	0.0	0.0	100.0
All	N	80	61	24	83	62	23	344
	% row	23.3	17.7	7.0	24.1	18.0	6.7	100.0

By default, the cell counts and row percentages are shown for each cell, and both row and column totals are calculated. To show cell percentages or column percentages, or to drop row and column totals, adjust the statistic argument. This argument accepts a formula that follows the datasummary “language”. To understand exactly how it works, you may find it useful to skip to the datasummary tutorial in the next section. Example:

datasummary_crosstab(species ~ sex,
                     statistic = 1 ~ Percent("col"),
                     data = penguins)

species		female	male
Adelie	% col	44.2	43.5
Chinstrap	% col	20.6	20.2
Gentoo	% col	35.2	36.3
All	% col	100.0	100.0

See ?datasummary_crosstab for more details.

datasummary

datasummary tables are specified using a 2-sided formula, divided by a tilde ~. The left-hand side describes the rows; the right-hand side describes the columns. To illustrate how this works, we will again be using the palmerpenguins dataset:

To display the flipper_length_mm variable as a row and the mean as a column, we type:

datasummary(flipper_length_mm ~ Mean,
            data = penguins)

	Mean
flipper_length_mm	200.92

To flip rows and columns, we flip the left and right-hand sides of the formula:

datasummary(Mean ~ flipper_length_mm,
            data = penguins)

	flipper_length_mm
Mean	200.92

Custom summary functions

The Mean function is a shortcut supplied by modelsummary, and it is equivalent to mean(x,na.rm=TRUE). Since the flipper_length_mm variable includes missing observation, using the mean formula (with default na.rm=FALSE) would produce a missing/empty cell:

datasummary(flipper_length_mm ~ mean,
            data = penguins)

	mean
flipper_length_mm

modelsummary supplies these functions: Mean, SD, Min, Max, Median, P0, P25, P50, P75, P100, Histogram, and a few more (see the package documentation).

Users are also free to create and use their own custom summaries. Any R function which takes a vector and produces a single value is acceptable. For example, the Range functions return a numerical value, and the MinMax returns a string:

Range <- function(x) max(x, na.rm = TRUE) - min(x, na.rm = TRUE)

datasummary(flipper_length_mm ~ Range,
            data = penguins)

	Range
flipper_length_mm	59.00

MinMax <- function(x) paste0('[', min(x, na.rm = TRUE), ', ', max(x, na.rm = TRUE), ']')

datasummary(flipper_length_mm ~ MinMax,
            data = penguins)

	MinMax
flipper_length_mm	[172, 231]

Concatenating with +

To include more rows and columns, we use the + sign:

datasummary(flipper_length_mm + body_mass_g ~ Mean + SD,
            data = penguins)

	Mean	SD
flipper_length_mm	200.92	14.06
body_mass_g	4201.75	801.95

Sometimes, it can be cumbersome to list all variables separated by + signs. The All() function is a useful shortcut:

datasummary(All(penguins) ~ Mean + SD,
            data = penguins)

	Mean	SD
rownames	172.50	99.45
bill_length_mm	43.92	5.46
bill_depth_mm	17.15	1.97
flipper_length_mm	200.92	14.06
body_mass_g	4201.75	801.95
year	2008.03	0.82

By default, All selects all numeric variables. This behavior can be changed by modifying the function’s arguments. See ?All for details.

Nesting with *

datasummary can nest variables and statistics inside categorical variables using the * symbol. When applying the the * operator to factor, character, or logical variables, columns or rows will automatically be nested. For instance, if we want to display separate means for each value of the variable sex, we use mean * sex:

datasummary(flipper_length_mm + body_mass_g ~ mean * sex,
            data = penguins)

	female	male
flipper_length_mm	197.36	204.51
body_mass_g	3862.27	4545.68

We can use parentheses to nest several terms inside one another, using a call of this form: x * (y + z). Here is an example with nested columns:

datasummary(body_mass_g ~ sex * (mean + sd),
            data = penguins)

	female		male
	mean	sd	mean	sd
body_mass_g	3862.27	666.17	4545.68	787.63

Here is an example with nested rows:

datasummary(sex * (body_mass_g + flipper_length_mm) ~ mean + sd,
            data = penguins)

sex		mean	sd
female	body_mass_g	3862.27	666.17
	flipper_length_mm	197.36	12.50
male	body_mass_g	4545.68	787.63
	flipper_length_mm	204.51	14.55

The order in which terms enter the formula determines the order in which labels are displayed. For example, this shows island above sex:

datasummary(flipper_length_mm + body_mass_g ~ mean * island * sex,
            data = penguins)

	Biscoe		Dream		Torgersen
	female	male	female	male	female	male
flipper_length_mm	205.69	213.29	190.02	196.31	188.29	194.91
body_mass_g	4319.38	5104.52	3446.31	3987.10	3395.83	4034.78

This shows sex above island values:

datasummary(flipper_length_mm + body_mass_g ~ mean * sex * island,
            data = penguins)

	female			male
	Biscoe	Dream	Torgersen	Biscoe	Dream	Torgersen
flipper_length_mm	205.69	190.02	188.29	213.29	196.31	194.91
body_mass_g	4319.38	3446.31	3395.83	5104.52	3987.10	4034.78

By default, datasummary omits column headers with a single value/label across all columns, except for the header that sits just above the data. If the header we want to see is not displayed, we may want to reorder the terms of the formula. To show all headers, set sparse_header=FALSE:

datasummary(flipper_length_mm + body_mass_g ~ mean * sex * island,
            data = penguins,
            sparse_header = FALSE)

	female			male
	Biscoe	Dream	Torgersen	Biscoe	Dream	Torgersen
flipper_length_mm	205.69	190.02	188.29	213.29	196.31	194.91
body_mass_g	4319.38	3446.31	3395.83	5104.52	3987.10	4034.78

When using sparse_header=FALSE, it is often useful to insert Heading() * in the table formula, in order to rename or omit some of the labels manually. Type ?tables::Heading for details and examples.

Renaming with =

Personally, I prefer to rename variables and values before drawing my tables, using backticks when variable names include whitespace. For example,

tmp <- penguins %>%
       select(`Flipper length (mm)` = flipper_length_mm,
              `Body mass (g)` = body_mass_g)

datasummary(`Flipper length (mm)` + `Body mass (g)` ~ Mean + SD,
            data = tmp)

	Mean	SD
Flipper length (mm)	200.92	14.06
Body mass (g)	4201.75	801.95

However, thanks to the tables package, datasummary offers two additional mechanisms to rename. First, we can wrap a term in parentheses and use the equal = sign: (NewName=OldName):

datasummary((`Flipper length (mm)` = flipper_length_mm) + (`Body mass (g)` = body_mass_g) ~
            island * ((Avg. = Mean) + (Std.Dev. = SD)),
            data = penguins)

	Biscoe		Dream		Torgersen
	Avg.	Std.Dev.	Avg.	Std.Dev.	Avg.	Std.Dev.
Flipper length (mm)	209.71	14.14	193.07	7.51	191.20	6.23
Body mass (g)	4716.02	782.86	3712.90	416.64	3706.37	445.11

Second, we can use the Heading() function:

datasummary(Heading("Flipper length (mm)") * flipper_length_mm + Heading("Body mass (g)") * body_mass_g ~ island * (Mean + SD),
            data = penguins)

	Biscoe		Dream		Torgersen
	Mean	SD	Mean	SD	Mean	SD
Flipper length (mm)	209.71	14.14	193.07	7.51	191.20	6.23
Body mass (g)	4716.02	782.86	3712.90	416.64	3706.37	445.11

The Heading function also has a nearData argument which can be useful in cases where some rows are nested but others are not. Compare the last row of these two tables:

datasummary(sex * (flipper_length_mm + bill_length_mm) + Heading("Body mass (g)") * body_mass_g ~ Mean + SD,
            data = penguins)

sex		Mean	SD
female	flipper_length_mm	197.36	12.50
	bill_length_mm	42.10	4.90
male	flipper_length_mm	204.51	14.55
	bill_length_mm	45.85	5.37
	Body mass (g)	4201.75	801.95

datasummary(sex * (flipper_length_mm + bill_length_mm) + Heading("Body mass (g)", nearData=FALSE) * body_mass_g ~ Mean + SD,
            data = penguins)

sex		Mean	SD
female	flipper_length_mm	197.36	12.50
	bill_length_mm	42.10	4.90
male	flipper_length_mm	204.51	14.55
	bill_length_mm	45.85	5.37
Body mass (g)		4201.75	801.95

Counts and Percentages

The tables package allows datasummary to use neat tricks to produce frequency tables:

1. Add a N to the right-hand side of the equation.
2. Add Percent() to the right-hand side to calculate the percentage of observations in each cell.
3. Add 1 to the left-hand side to include a row with the total number of observations:

datasummary(species * sex + 1 ~ N + Percent(),
            data = penguins)

species	sex	N	Percent
Adelie	female	73	21.22
	male	73	21.22
Chinstrap	female	34	9.88
	male	34	9.88
Gentoo	female	58	16.86
	male	61	17.73
	All	344	100.00

Note that the Percent() function accepts a denom argument to determine if percentages should be calculated row or column-wise, or if they should take into account all cells.

Weighted percentages

The Percent() pseudo-function also accepts a fn argument, which must be a function which accepts two vectors: x is the values in the current cell, and y is all the values in the whole dataset. The default fn is:

datasummary(species * sex + 1 ~ N + Percent(fn = function(x, y) 100 * length(x) / length(y)),
            output = "markdown",
            data = penguins)

species	sex	N	Percent
Adelie	female	73	21.22
	male	73	21.22
Chinstrap	female	34	9.88
	male	34	9.88
Gentoo	female	58	16.86
	male	61	17.73
	All	344	100.00

The code above takes the number of elements in the cell length(x) and divides it by the number of total elements length(y).

Now, let’s say we want to display percentages weighted by one of the variables of the dataset. This can often be useful with survey weights, for example. Here, we use an arbitrary column of weights called flipper_length_mm:

wtpct <- function(x, y) sum(x, na.rm = TRUE) / sum(y, na.rm = TRUE) * 100
datasummary(species * sex + 1 ~ N + flipper_length_mm * Percent(fn = wtpct),
            output = "markdown",
            data = penguins)

species	sex	N	Percent
Adelie	female	73	19.95
	male	73	20.44
Chinstrap	female	34	9.49
	male	34	9.89
Gentoo	female	58	17.95
	male	61	19.67
	All	344	100.00

In each cell we now have the sum of weights in that cell, divided by the total sum of weights in the column.

Custom percentages

Here is another simple illustration of Percent function mechanism in action, where we combine counts and percentages in a simple nice label:

dat <- mtcars
dat$cyl <- as.factor(dat$cyl)

fn <- function(x, y) {
    out <- sprintf(
        "%s (%.1f%%)",
        length(x),
        length(x) / length(y) * 100)
}
datasummary(
    cyl ~ Percent(fn = fn),
    data = dat)

cyl	Percent
4	11 (34.4%)
6	7 (21.9%)
8	14 (43.8%)

Factor

The * nesting operator that we used above works automatically for factor, character, and logical variables. Sometimes, it is convenient to use it with other types of variables, such as binary numeric variables. In that case, we can wrap the variable name inside a call to Factor(). This allows us to treat a variable as factor, without having to modify it in the original data. For example, in the mtcars data, there is a binary numeric variable call am. We nest statistics within categories of am by typing:

datasummary(mpg + hp ~ Factor(am) * (mean + sd),
            data = mtcars)

	0		1
	mean	sd	mean	sd
mpg	17.15	3.83	24.39	6.17
hp	160.26	53.91	126.85	84.06

Arguments: na.rm=TRUE

We can pass any argument to the summary function by including a call to Arguments(). For instance, there are missing values in the flipper_length_mm variable of the penguins dataset. Therefore, the standard mean function will produce no result, because its default argument is na.rm=FALSE. We can change that by calling:

datasummary(flipper_length_mm ~ mean + mean*Arguments(na.rm=TRUE),
            data = penguins)

	mean	mean
flipper_length_mm		200.92

Notice that there is an empty cell (NA) under the normal mean function, but that the mean call with Arguments(na.rm=TRUE) produced a numeric result.

We can pass the same arguments to multiple functions using the parentheses:

datasummary(flipper_length_mm ~ (mean + sd) * Arguments(na.rm=TRUE),
            data = penguins)

	mean	sd
flipper_length_mm	200.92	14.06

Note that the shortcut functions that modelsummary supplies use na.rm=TRUE by default, so we can use them directly without arguments, even when there are missing values:

datasummary(flipper_length_mm ~ Mean + Var + P75 + Range,
            data = penguins)

	Mean	Var	P75	Range
flipper_length_mm	200.92	197.73	213.00	59.00

Arguments: Weighted Mean

You can use the Arguments mechanism to do various things, such as calculating weighted means:

newdata <- data.frame(
  x = rnorm(20),
  w = rnorm(20),
  y = rnorm(20))

datasummary(x + y ~ weighted.mean * Arguments(w = w),
            data = newdata, output = "markdown")

	weighted.mean
x	0.70
y	-0.47

Which produces the same results as:

weighted.mean(newdata$x, newdata$w)

## [1] 0.6985158

weighted.mean(newdata$y, newdata$w)

## [1] -0.4710503

But different results from:

mean(newdata$x)

## [1] -0.04014939

mean(newdata$y)

## [1] -0.2950554

Empty cells

Sometimes, if we nest too much and the dataset is not large/diverse enough, we end up with empty cells. In that case, we add *DropEmpty() to the formula:

datasummary(island * species * body_mass_g ~ sex * (Mean + SD),
            data = penguins)

island	species		female		male
			Mean	SD	Mean	SD
Biscoe	Adelie	body_mass_g	3369.32	343.47	4050.00	355.57
	Chinstrap	body_mass_g
	Gentoo	body_mass_g	4679.74	281.58	5484.84	313.16
Dream	Adelie	body_mass_g	3344.44	212.06	4045.54	330.55
	Chinstrap	body_mass_g	3527.21	285.33	3938.97	362.14
	Gentoo	body_mass_g
Torgersen	Adelie	body_mass_g	3395.83	259.14	4034.78	372.47
	Chinstrap	body_mass_g
	Gentoo	body_mass_g

datasummary(island * species * body_mass_g ~ sex * (Mean + SD) * DropEmpty(),
            data = penguins)

island	species		female		male
			Mean	SD	Mean	SD
Biscoe	Adelie	body_mass_g	3369.32	343.47	4050.00	355.57
	Gentoo	body_mass_g	4679.74	281.58	5484.84	313.16
Dream	Adelie	body_mass_g	3344.44	212.06	4045.54	330.55
	Chinstrap	body_mass_g	3527.21	285.33	3938.97	362.14
Torgersen	Adelie	body_mass_g	3395.83	259.14	4034.78	372.47

Logical subsets

Cool stuff is possible with logical subsets:

datasummary((bill_length_mm > 44.5) + (bill_length_mm <= 44.5) ~ Mean * flipper_length_mm,
            data = penguins)

bill_length_mm > 44.5	209.68
bill_length_mm <= 44.5	192.45

See the tables package documentation for more details and examples.

output

All functions in the datasummary_* family accept the same output argument. Tables can be saved to several file formats:

f <- flipper_length_mm ~ island * (mean + sd)
datasummary(f, data = penguins, output = 'table.html')
datasummary(f, data = penguins, output = 'table.tex')
datasummary(f, data = penguins, output = 'table.docx')
datasummary(f, data = penguins, output = 'table.pptx')
datasummary(f, data = penguins, output = 'table.md')
datasummary(f, data = penguins, output = 'table.rtf')
datasummary(f, data = penguins, output = 'table.jpg')
datasummary(f, data = penguins, output = 'table.png')

They can be returned in human-readable data.frames, markdown, html, or LaTeX code to the console:

datasummary(f, data = penguins, output = 'data.frame')
datasummary(f, data = penguins, output = 'markdown')
datasummary(f, data = penguins, output = 'html')
datasummary(f, data = penguins, output = 'latex')

datasummary can return objects compatible with the gt, kableExtra, flextable, huxtable, and DT table creation and customization packages:

datasummary(f, data = penguins, output = 'gt')
datasummary(f, data = penguins, output = 'kableExtra')
datasummary(f, data = penguins, output = 'flextable')
datasummary(f, data = penguins, output = 'huxtable')
datasummary(f, data = penguins, output = 'DT')

Please note that hierarchical or “nested” column labels are only available for these output formats: kableExtra, gt, html, rtf, and LaTeX. When saving tables to other formats, nested labels will be combined to a “flat” header.

fmt

The fmt argument allows us to set the printing format of numeric values. It accepts a single number representing the number of digits after the period, or a string to be passed to the sprintf function. For instance, setting fmt="%.4f" will keep 4 digits after the dot (see ?sprintf for more options):

datasummary(flipper_length_mm ~ Mean + SD,
            fmt = 4,
            data = penguins)

	Mean	SD
flipper_length_mm	200.9152	14.0617

We can set the formatting on a term-by-term basis by using the same Arguments function that we used to handle missing values in the previous section. The shortcut functions that ship with modelsummary (e.g., Mean, SD, Median, P25) all include a fmt argument:

datasummary(flipper_length_mm ~ Mean * Arguments(fmt = "%.4f") + SD * Arguments(fmt = "%.1f"),
            data = penguins)

	Mean	SD
flipper_length_mm	200.9152	14.1

If we do not want datasummary to format numbers, and we want to keep the numerical values instead of formatted strings, set fmt=NULL. This can be useful when post-processing tables with packages like gt, which allow us to transform cells based on their numerical content (this gt table will be omitted from PDF output):

library(gt)

datasummary(All(mtcars) ~ Mean + SD,
            data = mtcars,
            fmt = NULL,
            output = 'gt') %>%
    tab_style(style = cell_fill(color = "pink"),
              locations = cells_body(rows = Mean > 10, columns = 2))

	Mean	SD
mpg	20.090625	6.0269481
cyl	6.187500	1.7859216
disp	230.721875	123.9386938
hp	146.687500	68.5628685
drat	3.596563	0.5346787
wt	3.217250	0.9784574
qsec	17.848750	1.7869432
vs	0.437500	0.5040161
am	0.406250	0.4989909
gear	3.687500	0.7378041
carb	2.812500	1.6152000

Please note that the N() function is supplied by the upstream tables package, and does not have a fmt argument. Fortunately, it is easy to override the built-in function to use custom formatting:

tmp <- data.frame(X = sample(letters[1:3], 1e6, replace = TRUE))
N <- \(x) format(length(x), big.mark = ",")
datasummary(X ~ N, data = tmp)

X	N
a	332,358
b	334,065
c	333,577

title, notes

datasummary includes the same title and notes arguments as in modelsummary:

datasummary(All(penguins) ~ Mean + SD,
            data = penguins,
            title = 'Statistics about the famous Palmer Penguins.',
            notes = c('A note at the bottom of the table.'))

Statistics about the famous Palmer Penguins.

	Mean	SD
rownames	172.50	99.45
bill_length_mm	43.92	5.46
bill_depth_mm	17.15	1.97
flipper_length_mm	200.92	14.06
body_mass_g	4201.75	801.95
year	2008.03	0.82
A note at the bottom of the table.

align

We can align columns using the align argument. align should be a string of length equal to the number of columns, and which includes only the letters “l”, “c”, or “r”:

datasummary(flipper_length_mm + bill_length_mm ~ Mean + SD + Range,
            data = penguins,
            align = 'lrcl')

	Mean	SD	Range
flipper_length_mm	200.92	14.06	59.00
bill_length_mm	43.92	5.46	27.50

add_rows

new_rows <- data.frame('Does',
                       2,
                       'plus',
                       2,
                       'equals',
                       5,
                       '?')
datasummary(flipper_length_mm + body_mass_g ~ species * (Mean + SD),
            data = penguins,
            add_rows = new_rows)

	Adelie		Chinstrap		Gentoo
	Mean	SD	Mean	SD	Mean	SD
flipper_length_mm	189.95	6.54	195.82	7.13	217.19	6.48
body_mass_g	3700.66	458.57	3733.09	384.34	5076.02	504.12
Does	2.00	plus	2.00	equals	5.00	?

add_columns

new_cols <- data.frame('New Stat' = runif(2))
datasummary(flipper_length_mm + body_mass_g ~ species * (Mean + SD),
            data = penguins,
            add_columns = new_cols)

	Adelie		Chinstrap		Gentoo		New.Stat
	Mean	SD	Mean	SD	Mean	SD
flipper_length_mm	189.95	6.54	195.82	7.13	217.19	6.48	0.02
body_mass_g	3700.66	458.57	3733.09	384.34	5076.02	504.12	0.26

Histograms

The datasummary family of functions allow users to display in-line spark-style histograms to describe the distribution of the variables. For example, the datasummary_skim produces such a histogram:

tmp <- mtcars[, c("mpg", "hp")]
datasummary_skim(tmp)

	Unique (#)	Missing (%)	Mean	SD	Min	Median	Max
mpg	25	0	20.1	6.0	10.4	19.2	33.9
hp	22	0	146.7	68.6	52.0	123.0	335.0

Each of the histograms in the table above is actually an SVG image, produced by the kableExtra package. For this reason, the histogram will not appear when users use a different output backend, such as gt, flextable, or huxtable.

The datasummary function is incredibly flexible, but it does not include a histogram option by default. Here is a simple example of how one can customize the output of datasummary. We proceed in 4 steps:

1. Normalize the variables and store them in a list
2. Create the table with datasummary, making sure to include 2 “empty” columns. In the example, we use a simple function called emptycol to fill those columns with empty strings.
3. Add the histograms or boxplots using functions from the kableExtra package.

tmp <- mtcars[, c("mpg", "hp")]

# create a list with individual variables
# remove missing and rescale
tmp_list <- lapply(tmp, na.omit)
tmp_list <- lapply(tmp_list, scale)

# create a table with `datasummary`
# add a histogram with column_spec and spec_hist
# add a boxplot with colun_spec and spec_box
emptycol = function(x) " "
datasummary(mpg + hp ~ Mean + SD + Heading("Boxplot") * emptycol + Heading("Histogram") * emptycol,
    output = "kableExtra",
    data = tmp) %>%
    kableExtra::column_spec(column = 4, image = spec_boxplot(tmp_list)) %>%
    kableExtra::column_spec(column = 5, image = spec_hist(tmp_list))

If you want a simpler solution, you can try the Histogram function which works in datasummary automatically and comes bundled with modelsummary. The downside of this function is that it uses Unicode characters to create the histogram. This kind of histogram may not display well with certain typefaces or on some operating systems (Windows!).

datasummary(mpg + hp ~ Mean + SD + Histogram, data = tmp)

	Mean	SD	Histogram
mpg	20.09	6.03	▂▅▇▇▆▃▁▁▂▂
hp	146.69	68.56	▅▅▇▂▆▂▃▁▁

Missing values

At least 3 distinct issues can arise related to missing values.

Functions and na.rm

An empty cell can appear in the table when a statistical function returns NA instead of a numeric value. In those cases, you should:

1. Make sure that your statistical function (e.g., mean or sd) uses na.rm=TRUE by default
2. Use the Arguments strategy to set na.rm=TRUE (see the Arguments section of this vignette).
3. Use a convenience function supplied by modelsummary, where na.rm is TRUE by default: Mean, SD, P25, etc.

Empty crosstab cells

An empty cell can appear in the table when a crosstab is deeply nested, and there are no observations for a given combination of covariates. In those cases, you can use the * DropEmpty pseudo-function. See the “Empty cells” section of this vignette for examples.

Factors

By default, the factor function in R does not assign a distinct factor level to missing values: the factor function’s exclude argument is set to NA by default. To ensure that NAs appear in your table, make sure you set exclude=NULL when you create the factor.

Internally, the datasummary_balance and datasummary_crosstab functions convert logical and character variables to factor with the exclude=NULL argument. This means that NAs will appear in the table as distinct rows/columns. If you do not want NAs to appear in your table, convert them to factors yourself ahead of time. For example:

mycars <- mtcars[, c("cyl", "mpg", "hp", "vs")]
mycars$cyl[c(1, 3, 6, 8)] <- NA
mycars$cyl_nona <- factor(mycars$cyl)
mycars$cyl_na <- factor(mycars$cyl, exclude = NULL)

datasummary_crosstab(cyl_nona ~ vs, data = mycars)

cyl_nona		0	1	All
4	N	1	8	9
	% row	11.1	88.9	100.0
6	N	2	3	5
	% row	40.0	60.0	100.0
8	N	14	0	14
	% row	100.0	0.0	100.0
All	N	18	14	32
	% row	56.2	43.8	100.0

datasummary_crosstab(cyl_na ~ vs, data = mycars)

cyl_na		0	1	All
4	N	1	8	9
	% row	11.1	88.9	100.0
6	N	2	3	5
	% row	40.0	60.0	100.0
8	N	14	0	14
	% row	100.0	0.0	100.0
NA	N	1	3	4
	% row	25.0	75.0	100.0
All	N	18	14	32
	% row	56.2	43.8	100.0

Appearance

In the Appearance Vignette we saw how to customize the tables produced by the modelsummary function. The same customization possibilities are also available for all functions in the datasummary_* family of functions. Indeed, we can customize the tables produced by datasummary using the functions provided by gt, kableExtra, flextable, huxtable, and DT. For instance, to customize tables using kableExtra, we can do:

datasummary(All(penguins) ~ sex * (Mean + SD),
            data = penguins,
            output = 'kableExtra') %>%
  kableExtra::row_spec(3, background = 'cyan', color = 'red')

To customize a table using the gt package, we can:

library(gt)

adelie <- function(x) web_image('https://user-images.githubusercontent.com/987057/85402702-20b1d280-b52a-11ea-9950-f3a03133fd45.png', height = 100)
gentoo <- function(x) web_image('https://user-images.githubusercontent.com/987057/85402718-27404a00-b52a-11ea-9ad3-dd7562f6438d.png', height = 100)
chinstrap <- function(x) web_image('https://user-images.githubusercontent.com/987057/85402708-23acc300-b52a-11ea-9a77-de360a0d1f7d.png', height = 100)

cap <- 'Flipper lengths (mm) of the famous penguins of Palmer Station, Antarctica.'
f <- (`Species` = species) ~ (` ` = flipper_length_mm) * (`Distribution` = Histogram) + flipper_length_mm * sex * ((`Avg.` = Mean)*Arguments(fmt='%.0f') + (`Std. Dev.` = SD)*Arguments(fmt='%.1f'))
datasummary(f,
            data = penguins,
            output = 'gt',
            title = cap,
            notes = 'Artwork by @allison_horst',
            sparse_header = TRUE) %>%
    text_transform(locations = cells_body(columns = 1, rows = 1), fn = adelie) %>%
    text_transform(locations = cells_body(columns = 1, rows = 2), fn = chinstrap) %>%
    text_transform(locations = cells_body(columns = 1, rows = 3), fn = gentoo) %>%
    tab_style(style = list(cell_text(color = "#FF6700", size = 'x-large')), locations = cells_body(rows = 1)) %>%
    tab_style(style = list(cell_text(color = "#CD51D1", size = 'x-large')), locations = cells_body(rows = 2)) %>%
    tab_style(style = list(cell_text(color = "#007377", size = 'x-large')), locations = cells_body(rows = 3)) %>%
    tab_options(table_body.hlines.width = 0, table.border.top.width = 0, table.border.bottom.width = 0) %>%
    cols_align('center', columns = 3:6)

Flipper lengths (mm) of the famous penguins of Palmer Station, Antarctica.

Species	Distribution	Female		Male
		Avg.	Std. Dev.	Avg.	Std. Dev.
	▁▃▆▇▃▅▂	188	5.6	192	6.6
	▁▄▃▇▆▄▃▁▂	192	5.8	200	6.0
	▂▅▅▇▃▅▂▁▃	213	3.9	222	5.7
Artwork by @allison_horst