Introduction
This document mainly contains examples using recommended styles for Rmarkdown documents. Available styles in summarytools are the same as pander’s:
- simple (default)
- rmarkdown
- grid
- multiline
For freq(), descr() (and ctable(), although with caveats), rmarkdown style is recommended. For dfSummary(), grid is recommended.
Starting with freq(), we’ll review the recommended methods and styles to quickly get satisfying results in Rmarkdown documents.
To see how this vignette is configured, see this section.
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freq()
freq() is best used with `style = ‘rmarkdown’; html rendering is also possible.
Rmarkdown Style
explicit NA's detected - temporarily setting 'report.nas' to FALSE
Frequencies
tobacco$gender
Type: Factor
| F |
489 |
48.90 |
48.90 |
| M |
489 |
48.90 |
97.80 |
| (Missing) |
22 |
2.20 |
100.00 |
| Total |
1000 |
100.00 |
100.00 |
HTML Rendering
explicit NA's detected - temporarily setting 'report.nas' to FALSE
Frequencies
tobacco$gender
Type: Factor
| gender |
Freq |
% |
% Cum. |
| F |
489 |
48.90 |
48.90 |
| M |
489 |
48.90 |
97.80 |
| (Missing) |
22 |
2.20 |
100.00 |
| Total |
1000 |
100.00 |
100.00 |
If you find the table too large, you can use table.classes = 'st-small' - an example is provided further below.
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descr()
descr() is also best used with style = 'rmarkdown', and HTML rendering is also supported.
Rmarkdown Style
Non-numerical variable(s) ignored: gender, age.gr, smoker, diseased, disease
Descriptive Statistics
tobacco
N: 1000
| Mean |
25.73 |
49.60 |
6.78 |
1.00 |
| Std.Dev |
4.49 |
18.29 |
11.88 |
0.08 |
| Min |
8.83 |
18.00 |
0.00 |
0.86 |
| Q1 |
22.93 |
34.00 |
0.00 |
0.86 |
| Median |
25.62 |
50.00 |
0.00 |
1.04 |
| Q3 |
28.65 |
66.00 |
11.00 |
1.05 |
| Max |
39.44 |
80.00 |
40.00 |
1.06 |
| MAD |
4.18 |
23.72 |
0.00 |
0.01 |
| IQR |
5.72 |
32.00 |
11.00 |
0.19 |
| CV |
0.17 |
0.37 |
1.75 |
0.08 |
| Skewness |
0.02 |
-0.04 |
1.54 |
-1.04 |
| SE.Skewness |
0.08 |
0.08 |
0.08 |
0.08 |
| Kurtosis |
0.26 |
-1.26 |
0.90 |
-0.90 |
| N.Valid |
974.00 |
975.00 |
965.00 |
1000.00 |
| Pct.Valid |
97.40 |
97.50 |
96.50 |
100.00 |
HTML Rendering
We’ll use table.classes = ‘st-small’ to show how it affects the table’s size, compared to the freq() table rendered earlier.
Non-numerical variable(s) ignored: gender, age.gr, smoker, diseased, disease
Descriptive Statistics
tobacco
N: 1000
|
BMI |
age |
cigs.per.day |
samp.wgts |
|
Mean |
25.73 |
49.60 |
6.78 |
1.00 |
|
Std.Dev |
4.49 |
18.29 |
11.88 |
0.08 |
|
Min |
8.83 |
18.00 |
0.00 |
0.86 |
|
Q1 |
22.93 |
34.00 |
0.00 |
0.86 |
|
Median |
25.62 |
50.00 |
0.00 |
1.04 |
|
Q3 |
28.65 |
66.00 |
11.00 |
1.05 |
|
Max |
39.44 |
80.00 |
40.00 |
1.06 |
|
MAD |
4.18 |
23.72 |
0.00 |
0.01 |
|
IQR |
5.72 |
32.00 |
11.00 |
0.19 |
|
CV |
0.17 |
0.37 |
1.75 |
0.08 |
|
Skewness |
0.02 |
-0.04 |
1.54 |
-1.04 |
|
SE.Skewness |
0.08 |
0.08 |
0.08 |
0.08 |
|
Kurtosis |
0.26 |
-1.26 |
0.90 |
-0.90 |
|
N.Valid |
974 |
975 |
965 |
1000 |
|
Pct.Valid |
97.40 |
97.50 |
96.50 |
100.00 |
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dfSummary()
Grid Style
Don’t forget to specify plain.ascii = FALSE (or set it as a global option with st_options(plain.ascii = FALSE)), or you won’t get good results.
HTML Rendering
This method also works really well, and not having to specify the tmp.img.dir parameter is a plus.
Managing Lengthy dfSummary() Outputs in Rmarkdown Documents
For data frames containing numerous variables, we can use the max.tbl.height argument to wrap the results in a scrollable window having the specified height, in pixels. For instance:
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This Vignette’s Setup
This vignette uses theme rmarkdown::html_vignette. Its yaml section looks like this:
# ---
# title: "Recommendations for Using summarytools With Rmarkdown"
# author: "Dominic Comtois"
# date: "2020-03-02"
# output:
# rmarkdown::html_vignette:
# css:
# - !expr system.file("rmarkdown/templates/html_vignette/resources/vignette.css", package = "rmarkdown")
# vignette: >
# %\VignetteIndexEntry{Recommendations for Rmarkdown}
# %\VignetteEngine{knitr::rmarkdown}
# %\VignetteEncoding{UTF-8}
# ---
The following summarytools global options have been set. More of them can be useful, but this is a good starting point.
Also, the following knitr chunk options were set this way:
Finally, summarytools’ CSS has been included in the following manner, with chunk option echo = FALSE:
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Final Notes
This is by no way a definitive guide; depending on the themes you use, you could find that other settings yield better results. If you are looking to create a Word or a PDF document, you might want to try different combinations of options.
