Tables with memoiR • memoiR

The purpose here is to print a dataframe as a formated table.

Many packages are dedicated to tables but few of them meet the requirements of memoiR:

Support of numbered captions for cross-references (such as “Table 1: caption”).
Support of HTML, LaTeX (ultimately PDF) and hopefully Word outputs.
Support of 2-column LaTeX documents.
Support of maths in all formats.

kableExtra is memoiR’s first choice because it supports LaTeX better than the others. huxtable is an alternative if Word support is needed.

kableExtra

Basic use

bookdown was built with the kable() function¹, completed by the kableExtra package.

This basic example shows how to produce a simple, well-formatted table. The label of the code chunk is cars.

library("kableExtra")
mtcars[1:5, 1:6] |>
  kbl(
    caption = "Demo table", 
    booktabs = TRUE
  ) |>
  kable_styling()

Table 1: Demo table
	mpg	cyl	disp	hp	drat	wt
Mazda RX4	21.0	6	160	110	3.90	2.620
Mazda RX4 Wag	21.0	6	160	110	3.90	2.875
Datsun 710	22.8	4	108	93	3.85	2.320
Hornet 4 Drive	21.4	6	258	110	3.08	3.215
Hornet Sportabout	18.7	8	360	175	3.15	3.440

The kableExtra::kbl() function replaces knitr::kable() starting from version 1.2 of kableExtra to avoid incorrect caption format. A consequence is that the table caption can’t be included in the chunk header with option tab.cap which works only with kable(). The table caption is thus in the argument caption of kbl(). Formatted captions, possibly with maths, can be used with text references²:

add the reference somewhere in the text (just above the code chunk is a good place), such as

(ref:cars) Caption with _italics_ and maths: $\pi$

call the reference in the chunk with caption = "Caption with italics and maths: \(\pi\).". Note that knitr shows the value of the text reference in the chunk below.

library("kableExtra")
mtcars[1:5, 1:6] |>
  kbl(
    caption = "Caption with italics and maths: \(\pi\).", 
    booktabs = TRUE
  ) |>
  kable_styling()

Table 2: Caption with *italics* and maths: \(\pi\).
	mpg	cyl	disp	hp	drat	wt
Mazda RX4	21.0	6	160	110	3.90	2.620
Mazda RX4 Wag	21.0	6	160	110	3.90	2.875
Datsun 710	22.8	4	108	93	3.85	2.320
Hornet 4 Drive	21.4	6	258	110	3.08	3.215
Hornet Sportabout	18.7	8	360	175	3.15	3.440

Argument booktabs = TRUE provides clean horizontal rules and should always be used.

Last, kable_styling() formats the table for printing. It has many arguments that are not detailed here: read the documentation of the package³. More details are given in the document templates of memoiR, including the code to place tables in a single column or across the full page in the Stylish Article template.

Cross references (such as table 2) are called by table \@ref(tab:cars): the name of the code snippet (“cars” here) is prefixed by tab:.

Limitations

kableExtra used to produce clean tables in Word with a workaround⁴ that was included in previous versions of memoiR but this no longer the case since its version 1. Tables are rendered with a single cell per row.

The solution is to produce the HTML version of the document, copy its tables and paste them into the Word version⁵.

huxtable

Basic use

huxtable works perfectly with memoiR after adding the LaTeX packages in the preamble section of the YAML header. Run huxtable::report_latex_dependencies() and copy all of them to obtain something like

preamble: >
  \usepackage{array}
  \usepackage{caption}
  ...

Add huxtable in the vector of packages to install in the “Options” chunk:

# Add necessary packages here
packages <- c("tidyverse", "huxtable")

Tables are produced by as_hux() and formatting is made possible by a large set of functions.

library("huxtable")

## Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
##   object 'type_sum.accel' not found

mtcars[1:5, 1:6] |>
  as_hux() |>
  set_header_rows(1, value = TRUE) |> 
  style_headers(bold = TRUE) |> 
  theme_article() |>
  set_caption("Made by huxtable")

Table 3: Made by **huxtable**
mpg	cyl	disp	hp	drat	wt
21	6	160	110	3.9	2.62
21	6	160	110	3.9	2.88
22.8	4	108	93	3.85	2.32
21.4	6	258	110	3.08	3.21
18.7	8	360	175	3.15	3.44

Read its documentation⁶.

Limitations

Word output is correct, unlike kableExtra, but LaTeX support is more limited. In Stylish Articles, tables are always printed in full width. There seems to be no way to make them fit a single column.

gt

gt is the a promising table package, developped by the RStudio team with an approach similar to that of ggplot2, i.e. the definition of a grammar of tables.

It has been focusing on HTML output and somehow neglected LaTeX in its first versions. LaTeX support was improved in version 0.11 but it can’t be used in memoiR yet because the numbered captions are not correct when the document is rendered with bookdown::html_document2(), as shown below.

library("gt")

## 
## Attaching package: 'gt'

## The following object is masked from 'package:huxtable':
## 
##     fmt_percent

mtcars[1:5, 1:6] |>
  gt(
    caption = "Demo table"
  )

(\#tab:gt)Demo table
mpg	cyl	disp	hp	drat	wt
21.0	6	160	110	3.90	2.620
21.0	6	160	110	3.90	2.875
22.8	4	108	93	3.85	2.320
21.4	6	258	110	3.08	3.215
18.7	8	360	175	3.15	3.440

flextable

flextable supports all output formats but it does not produce standard table captions. Even though they are numbered and support cross-referencing, they rely on their own style, which makes them different from figure captions. This requires extra work to harmonize the documents.

More problematic, knitting to PDF fails with memoiR templates because the LaTeX templates are not compatible.

In conclusion, flextable is not supported.