--- title: "Summarytools in R Markdown Documents" author: "Dominic Comtois" date: "`r Sys.Date()`" output: html_document: fig_caption: false toc: true toc_depth: 1 css: assets/vignette.css df_print: default vignette: > %\VignetteIndexEntry{Summarytools in R Markdown Documents} %\VignetteEncoding{UTF-8} %\VignetteDepends{kableExtra} %\VignetteDepends{magrittr} %\VignetteEngine{knitr::rmarkdown} --- ```{r setup, include=FALSE} library(knitr) opts_chunk$set(comment = NA, prompt = FALSE, cache = FALSE, echo = TRUE, results = 'asis') library(summarytools) st_options(bootstrap.css = FALSE, # Already part of the theme so no need for it plain.ascii = FALSE, # One of the essential settings style = "rmarkdown", # Idem. dfSummary.silent = TRUE, # Suppresses messages about temporary files footnote = NA, # Keeping the results minimalist descr.silent = TRUE, # To avoid messages when building / checking subtitle.emphasis = FALSE) # For the vignette theme, this gives better results. # For other themes, using TRUE might be preferable. ``` ```{r, echo=FALSE} st_css(main = TRUE, global = TRUE) ``` # 1. Introduction This document mainly contains examples showing how best to use **summarytools** in *R Markdown* documents. For a more in-depth view of the package's features, please see `vignette("introduction", "summarytools")` - the online version can be found [here](https://cran.r-project.org/package=summarytools/vignettes/introduction.html). ## 1.1 Methods vs Styles Every time we display **summarytools** objects with `print()`, `view()`, or `stview()`, we pick -- explicitly or not -- one of several display methods. Possible display methods are: *pander*, *render*, *viewer*, and *browser*. :::infobox **Disambiguation** To avoid any confusion, here is a small digression on the word *method*. It is a broad term which is also used in the OOP (object oriented programming) lexicon to describe a special kind of function that is linked to a specific class of objects. In R, the `print()` function is called a *generic* function. It is generic because it takes and handles many type of objects as an input. According to the class (or classes) of the object, it will dispatch the object to the particular *print method* dedicated to its class. In that sense, the `print.summarytools()` function *is itself a method*: objects of class "summarytools" are being dispatched to it by the **generic `print()` function**. ::: In this document, the term *method* refers to the *display* method -- **not** the *OOP* concept. It is one of the parameters for `print.summarytools()`, `view()`, and `stview()`. Since methods *viewer* and *browser* are mostly meant for interactive work and rely on the same underlying code as *render*, we will assume for the purpose of this document that there are really only two methods: *pander* and *render*. ### Only the *pander* Method Uses Styles The *pander* method is used by default when results are automatically printed to the console, or when we use `print()` without an explicit `method` argument. The *style* parameter is communicated to **pander** (see `?pander::pander` or visit its [GitHub page](https://github.com/Rapporter/pander) to learn more on this very useful package).
![](assets/lightbulb.svg) When we use any of the *viewer*, *browser*, or *render* methods, the package rather uses **htmltools** to generate results; any specified *styles* are thus ignored.
### **summarytools** styles are **pander** styles Available styles are the ones supported by **pander**: - simple (default, used mainly in R console) - rmarkdown (used by all core functions except `dfSummary()`) - grid (mainly used with `dfSummary()`) - multiline (can be used with `dfSummary()` if you want ASCII graphs only) - jira (recent addition, not thoroughly tested) ## 1.2 General Guidelines **Always** set **results='asis'** either explicitly on a chunk-by-chunk bases or by including `opts_chunk$set(results = 'asis')` in your setup chunk. Also, don't forget to specify **`plain.ascii = FALSE`** in all function calls using the *pander* method. It is advised to set this option, as well as the `style` option in the setup chunk: ```{r, eval=FALSE} st_options(plain.ascii = FALSE, style = "rmarkdown") ``` or include `st_options(plain.ascii = FALSE)` in your setup chunk.
![](assets/exclamation-diamond.svg) If you get repeated, unhelpful warnings, use chunk options `message = FALSE` and/or `warning = FALSE`.
The following table indicates which method / style is better suited for each **summarytools** function in the context of R Markdown documents: | Function | render method | pander method | pander style | |:------------|:-------------:|:-------------:|:-------------| | freq() | ✓ | ✓ | rmarkdown | | ctable() | ✓ | Sub-optimal | rmarkdown | | descr() | ✓ | ✓ | rmarkdown | | dfSummary() | ✓ | ✓ | grid | **Recommended Style When Using *pander* method** For `freq()`, `descr()`, and `ctable()`, _rmarkdown_ style is recommended. For `dfSummary()`, _grid_ is recommended. Note that 'multiline' can also be used, but only ASCII graphs will be displayed. Starting with `freq()`, we'll now review the recommended methods and styles to get satisfying results in *R Markdown* documents. -------------------------------------------------------------------------------- # 2. Using freq() in R Markdown `freq()` is best used with `style = 'rmarkdown'; html rendering is also possible. ## 2.1 Pander Style for freq() With `method="pander"`, "rmarkdown" is the easy winner. ```{r} freq(tobacco$gender, plain.ascii = FALSE, style = 'rmarkdown') ``` ## 2.2 HTML Rendering for freq() There are rarely any problems when using the *render* method to display `freq()` results. ```{r} print(freq(tobacco$gender), method = 'render') ``` If you find the table too large, you can use `table.classes = 'st-small'`: ```{r, message=FALSE} print(descr(tobacco), method = 'render', table.classes = 'st-small') ``` -------------------------------------------------------------------------------- Back to top # 3. Using ctable() in R Markdown ## 3.1 Rmarkdown Style for ctable() Tables with heading spanning over 2 rows are not fully supported in markdown (yet), but the result is getting close to acceptable. This, however, is not true for all themes. That is why the rendering method is preferred. ```{r} ctable(tobacco$gender, tobacco$smoker, plain.ascii = FALSE, style = 'rmarkdown') ``` ## 3.2 HTML Rendering for ctable() For best results, use this method. ```{r ctable_html} print(ctable(tobacco$gender, tobacco$smoker), method = 'render') ``` -------------------------------------------------------------------------------- Back to top # 4. Using descr() in R Markdown `descr()` gives good results with both `style = 'rmarkdown'` and HTML rendering. ## 4.1 Rmarkdown Style for descr() ```{r} descr(tobacco, plain.ascii = FALSE, style = 'rmarkdown') ``` ## 4.2 HTML Rendering for descr() We'll use table.classes = 'st-small' to show how it affects the table's size, compared to the `freq()` table rendered earlier. We'll also use `message = FALSE` as chunk option to avoid the message saying that non-numerical variables have been ignored. ```{r, message=FALSE} print(descr(tobacco), method = 'render', table.classes = 'st-small') ``` -------------------------------------------------------------------------------- Back to top # 5. Using dfSummary() in R Markdown To get optimal results, whichever method you choose, it is always best to omit at least 1, and if possible 2 columns from the output. Also, pick carefully the value of the `graph.magnig` parameter. ## 5.1 Grid Style for dfSummary() 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. (Note that to avoid problems when uploading the package, the following is an imagine, not the actual rendering from this piece of code. This is because CRAN doesn't allow the writing in /tmp or any other directory, except in R's temp directory, for good reasons.) ```{r dfs_grid, eval=FALSE} dfSummary(tobacco, plain.ascii = FALSE, style = 'grid', graph.magnif = 0.85, varnumbers = FALSE, valid.col = FALSE, tmp.img.dir = "/tmp") ``` ### 4.2 HTML Rendering for dfSummary() This method works really well, and not having to specify the `tmp.img.dir` parameter is a plus. ```{r} print(dfSummary(tobacco, varnumbers = FALSE, valid.col = FALSE, graph.magnif = 0.76), method = 'render') ``` ## 4.3 Managing Lengthy dfSummary() Outputs in R Markdown 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. ```{r} print(dfSummary(tobacco, varnumbers = FALSE, valid.col = FALSE, graph.magnif = 0.76), max.tbl.height = 300, method = "render") ```
![](assets/exclamation-diamond.svg) Some users reported getting repeated X11 warnings; those can easily be avoided by using the following chunk expression: `{r, results="asis", warning=FALSE}`.
Back to top -------------------------------------------------------------------------------- # 5. Using Other Formatting Packages As explained in the introductory vignette, `tb()` can be used to convert **summarytools** objects created with `freq()` and `descr()` to simple *tibbles* that packages specialized in table formatting will be able to process. This is particularly helpful with `stby` objects: ```{r} library(kableExtra) library(magrittr) stby(iris, iris$Species, descr, stats = "fivenum") %>% tb() %>% kable(format = "html", digits = 2) %>% collapse_rows(columns = 1, valign = "top") ``` Using `tb(order = 3)` flips the order of the grouping variable(s) and the reported variable(s): ```{r} stby(iris, iris$Species, descr, stats = "fivenum") %>% tb(order = 3) %>% kable(format = "html", digits = 2) %>% collapse_rows(columns = 1, valign = "top") ``` Back to top -------------------------------------------------------------------------------- # 6. Including dfSummaries in PDF Documents Here is a recipe for including fully formatted data frame summaries in pdf documents. There is some work involved, but following the instructions given here should give the expected results. There are basically two parts to this: first, you must create a preamble *tex* file. Second, you must indicate in the *YAML* section of your document where to find this file. ### Included Preamble *Tex* File This is the \LaTeX content that needs to be included as preamble. You can either copy this into your own *tex* file, or use the file that is now included in **summarytools** (as of version 1.0), following the instructions provided below. ```` \usepackage{graphicx} \usepackage[export]{adjustbox} \usepackage{letltxmacro} \LetLtxMacro{\OldIncludegraphics}{\includegraphics} \renewcommand{\includegraphics}[2][]{\raisebox{0.5\height}% {\OldIncludegraphics[valign=t,#1]{#2}}} ```` If you choose to create a *tex* file from the above content, the name of the file is arbitrary -- you can use whatever name you want. Its location is also up to you. I suggest you put it in the same location as your *Rmd* file. Along with the `graph.magnif` parameter for `dfSummary()`, you might need to adjust the 0.5 value used as `raisebox` parameter in the preamble. ### The YAML Section Your document should start with a *YAML* header like this one, supposing the preamble *tex* file is in the same location as your *Rmd* document : ``` --- title: "My PDF With Data Frame Summaries" output: pdf_document: latex_engine: xelatex includes: in_header: - !expr system.file("includes/fig-valign.tex", package = "summarytools") --- ``` If you need to customize the content of the preamble, then your header will look something like this: ``` --- title: "My PDF With Data Frame Summaries" output: pdf_document: latex_engine: xelatex includes: in_header: fig-valign-modified.tex --- ```
![](assets/lightbulb.svg) The *xelatex* engine option is not mandatory, but there are several advantages to it. I use it systematically and recommend you do the same.
### R Code Here is an example setup chunk: ```` ```{r, message=FALSE}`r ''` library(summarytools) st_options( plain.ascii = FALSE, style = "rmarkdown", dfSummary.style = "grid", dfSummary.valid.col = FALSE, dfSummary.graph.magnif = .52, subtitle.emphasis = FALSE, tmp.img.dir = "/tmp" ) ``` ```` And here is a chunk actually creating the summary: ```` ```{r, results='asis', message=FALSE}`r ''` define_keywords(title.dfSummary = "Data Frame Summary in PDF Format") dfSummary(tobacco) ``` ```` ### Remarks Since we redefined the $\LaTeX$ command `includegraphics`, all images included using `[](some-image.png)` will be impacted. In some cases this will likely be problematic. Eventually we will find a more robust solution without such undesired side-effects. If you are well versed in $\LaTeX$ and think you can solve this problem, please get in touch. -------------------------------------------------------------------------------- # 7. This Vignette's Setup This vignette uses theme `rmarkdown::html_vignette`. Its *YAML* section looks like this: ``` --- title: "Summarytools in R Markdown Documents" author: "Dominic Comtois" date: "`r Sys.Date()`" output: html_document: fig_caption: false toc: true toc_depth: 1 css: assets/vignette.css vignette: > %\VignetteIndexEntry{Summarytools in R Markdown Documents} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} %\VignetteDepends{magrittr} %\VignetteDepends{kableExtra} --- ```
The *vignette.css* file is copied from the installed **rmarkdown** package's 'templates/html_vignette/resources' directory. ### Global Options The following **global options** for **knitr** and **summarytools** have been set. Other options might also be useful to optimize content, but this is a good place to start from. ```` ```{r setup, include=FALSE}`r ''` library(knitr) opts_chunk$set(comment=NA, prompt=FALSE, cache=FALSE, echo=TRUE, results='asis') st_options(bootstrap.css = FALSE, # Already part of the theme plain.ascii = FALSE, # Essential setting for Rmd style = "rmarkdown", # Essential setting for Rmd dfSummary.silent = TRUE, # Hides redundant messages footnote = NA, # Keeping the results minimal subtitle.emphasis = FALSE) # For the vignette theme, # this gives better results. # For other themes, using # TRUE might be preferable. ``` ```` Finally, **summarytools CSS** has been included in the following manner: ```` ```{r, echo=FALSE}`r ''` st_css(main = TRUE, global = TRUE) ``` ```` -------------------------------------------------------------------------------- # 8. 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. If you find problems with the recommended settings or if you find better combinations, you are welcome to [open an issue on GitHub](https://github.com/dcomtois/summarytools/issues) to suggest modifications or make a pull request with your own improvements to this vignette. Back to top