In haozhu233/kableExtra: Construct Complex Table with 'kable' and Pipe Syntax

\clearpage

Please see the package documentation site for how to use this package in HTML and more.

Overview

\begin{wrapfigure}{r}{0.2\textwidth}\centering \includegraphics{kableExtra_sm.png} \end{wrapfigure} The goal of kableExtra is to help you build common complex tables and manipulate table styles. It imports the pipe %>% symbol from magrittr and verbalizes all the functions, so basically you can add "layers" to a kable output in a way that is similar with ggplot2 and plotly.

For users who are not very familiar with the pipe operator %>% in R, it is the R version of the fluent interface. The idea is to pass the result along the chain for a more literal coding experience. Basically when we say A %>% B, technically it means sending the results of A to B as B's first argument.

To learn how to generate complex tables in HTML, please visit http://haozhu233.github.io/kableExtra/awesome_table_in_html.html.

Installation

install.packages("kableExtra")

# For dev version
# install.packages("devtools")
devtools::install_github("haozhu233/kableExtra")

Getting Started

Here we are using the first few columns and rows from dataset mtcars

options(kableExtra.latex.load_packages = F)

library(kableExtra)
dt <- mtcars[1:5, 1:6]

Key Update: In the latest version of this package (1.2+), we provide a wrapper function kbl to the original kable function with detailed documentation of all the hidden html/latex options. It also does auto-formatting check in every function call instead of relying on the global environment variable. As a result, it also solves an issue for multi-format R Markdown documents. I encourage you start to use the new kbl function for all its convenience but the support for the original kable function is still there. In this doc, we will use kbl instead of kable.

This paragraph is a little outdated. It's here only for education purpose because it's helpful to understand how kable works under the hood. When you are using kable(), if you don't specify format, by default it will generate a markdown table and let Pandoc handle the conversion from markdown to HTML/PDF. This is the most favorable approach to render most simple tables as it is format independent. If you switch from HTML to pdf, you basically don't need to change anything in your code. However, markdown doesn't support complex table. For example, if you want to have a double-row header table, markdown just cannot provide you the functionality you need. As a result, when you have such a need, you should define format in kable() as either "html" or "latex". You can also define a global option at the beginning using options(knitr.table.format = "html") so you don't repeat the step every time. Starting from kableExtra 0.9.0, when you load this package (library(kableExtra)), it will automatically set up the global option 'knitr.table.format' based on your current environment. Unless you are rendering a PDF, kableExtra will try to render a HTML table for you. You no longer need to manually set either the global option or the format option in each kable() function. I'm still including the explanation above here in this vignette so you can understand what is going on behind the scene. Note that this is only an global option. You can manually set any format in kable() whenever you want. I just hope you can enjoy a peace of mind in most of your time. You can disable this behavior by setting options(kableExtra.auto_format = FALSE) before you load kableExtra.

# If you are using kableExtra < 0.9.0, you are recommended to set a global option first.
# options(knitr.table.format = "latex") 
## If you don't define format here, you'll need put `format = "latex"` 
## in every kable function.

LaTeX packages used in this package

If you are using a recent version of R Markdown, you are recommended to load this package entirely via library(kableExtra) or require(kableExtra) because this package will load all necessary LaTeX packages, such as booktabs or multirow, for you automatically. Note that, if you are calling functions from kableExtra via kableExtra::kable_styling() or if you put library(kableExtra) in a separate R file that is sourced by the R Markdown document, these packages won't be loaded. Furthermore, you can suppress this auto-loading behavior by setting a global option kableExtra.latex.load_packages to be FALSE before you load kableExtra.

# Not evaluated. Illustration purpose
options(kableExtra.latex.load_packages = FALSE)
library(kableExtra)

If you are using R Sweave, beamer, R package vignette template, tufte or some customized R Markdown templates, you can put the following meta data into the YAML section. If you are familiar with LaTeX and you know what you are doing, feel free to remove unnecessary packages from the list.

header-includes:
  - \usepackage{booktabs}
  - \usepackage{longtable}
  - \usepackage{array}
  - \usepackage{multirow}
  - \usepackage{wrapfig}
  - \usepackage{float}
  - \usepackage{colortbl}
  - \usepackage{pdflscape}
  - \usepackage{tabu}
  - \usepackage{threeparttable}
  - \usepackage{threeparttablex}
  - \usepackage[normalem]{ulem}
  - \usepackage{makecell}
  - \usepackage{xcolor}

Note: kableExtra was using xcolor with the table option for alternative row color before 1.0. However, the recent updates in fancyvbr causes a clash in xcolor option. Therefore, we removed the xcolor dependency in version 1.0 and started to rely on colortbl completely.

In reality, most cases, you still need xcolor to define new colors. The tricky part is that, if you are using an older version of rmarkdown, xcolor is not included in the template while in recent version, after rmarkdown started to use the default Pandoc template, xcolor is included by default. To minimize the effort, we chose to load xcolor in the end.

Plain LaTeX

Plain LaTeX table looks relatively ugly in 2017.

# Again, with kableExtra >= 0.9.0, `format = "latex"` is automatically defined
# when this package gets loaded. Otherwise, you still need to define formats
kbl(dt)
# Same: kable(dt, "latex")

LaTeX table with booktabs

Similar to Bootstrap in HTML, in LaTeX, you can also use a trick to make your table look prettier as well. The different part is that, this time you don't need to pipe kable outputs to another function. Instead, you should call booktabs = T directly in kable().

kbl(dt, booktabs = T)

Table Styles

kable_styling in LaTeX uses the same syntax and structure as kable_styling in HTML. However, instead of bootstrap_options, you should specify latex_options instead.

LaTeX options

Similar with bootstap_options, latex_options is also a charter vector with a bunch of options including striped, hold_position and scale_down.

Striped

Even though in the LaTeX world, people usually call it alternative row colors but here I'm using its bootstrap name for consistency. Note that to make it happen, LaTeX package xcolor is required to be loaded. In an environment like rmarkdown::pdf_document (rmarkdown 1.4.0 +), kable_styling will load it automatically if striped is enabled. However, in other cases, you probably need to import that package by yourself.

kbl(dt, booktabs = T) %>%
  kable_styling(latex_options = "striped")

You can also specify which rows you want to striped on via stripe_index. In most case, you might want to turn off the default 5 rows + a space setting in knitr::kable() by setting linesep = "". See this SO answer for details. https://stackoverflow.com/questions/45409750/get-rid-of-addlinespace-in-kable.

kbl(mtcars[1:8, 1:4], booktabs = T, linesep = "") %>%
  kable_styling(latex_options = "striped", stripe_index = c(1,2, 5:6))

Hold position

If you provide a table caption in kbl(), it will put your LaTeX tabular in a table environment, unless you are using longtable. A table environment will automatically find the best place (it thinks) to put your table. However, in many cases, you do want your table to appear in a position you want it to be. In this case, you can use this hold_position options here.

kbl(dt, caption = "Demo table", booktabs = T) %>%
  kable_styling(latex_options = c("striped", "hold_position"))

If you find hold_position is not powerful enough to literally PIN your table in the exact position, you may want to use HOLD_position, which is a more powerful version of this feature. For those who are familiar with LaTeX, hold_position uses [!h] and HOLD_position uses [H] and the float package.

Scale down

When you have a wide table that will normally go out of the page, and you want to scale down the table to fit the page, you can use the scale_down option here. Similarly if you want scale up a table to use the full page width you can use the scale_up option. Having both options available ensures that your table is only scaled in the direction you intended to scale it. You should also note that scale_down does not work with longtable. If your longtable is too wide, you should manually adjust your fontsize or switch to landscape layout.

kbl(cbind(dt, dt, dt), booktabs = T) %>%
  kable_styling(latex_options = c("striped", "scale_down"))

kbl(cbind(dt), booktabs = T) %>%
  kable_styling(latex_options = c("striped", "scale_down"))

kbl(cbind(dt), booktabs = T) %>%
  kable_styling(latex_options = c("striped", "scale_up"))

Repeat header in longtable

In kableExtra 0.3.0 or above, a new option repeat_header was introduced into kable_styling. It will add header rows to longtables spanning multiple pages. For table captions on following pages, it will append "continued" to the caption to differentiate. If you need texts other than "(continued)" (for example, other languages), you can specify it using kable_styling(..., repeat_header_text = "xxx"). If you want to completely replace the table caption instead of appending, you can specify it in the option repeat_header_method.

long_dt <- rbind(mtcars, mtcars) 

kbl(long_dt, longtable = T, booktabs = T, caption = "Longtable") %>%
  add_header_above(c(" ", "Group 1" = 5, "Group 2" = 6)) %>%
  kable_styling(latex_options = c("repeat_header"))

Full width?

If you have a small table and you want it to spread wide on the page, you can try the full_width option. Unlike scale_down, it won't change your font size. You can use column_spec, which will be explained later, together with full_width to achieve the best result.

kbl(dt, booktabs = T) %>%
  kable_styling(full_width = T) %>%
  column_spec(1, width = "8cm")

Position

Table Position only matters when the table doesn't have full_width. You can choose to align the table to center or left side of the page. The default value of position is center.

Note that even though you can select to right align your table but the table will actually be centered. Somehow it is very difficult to right align a table in LaTeX (since it's not very useful in the real world?). If you know how to do it, please send out an issue or PR and let me know.

kbl(dt, booktabs = T) %>%
  kable_styling(position = "center")

Besides these three common options, you can also wrap text around the table using the float-left or float-right options. Note that, like striped, this feature will load another non-default LaTeX package wrapfig which requires rmarkdown 1.4.0 +. If you use rmarkdown version < 1.4.0, you need to load the package through a customized LaTeX template file.

kbl(dt, booktabs = T) %>%
  kable_styling(position = "float_right")

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras sit amet mauris in ex ultricies elementum vel rutrum dolor. Phasellus tempor convallis dui, in hendrerit mauris placerat scelerisque. Maecenas a accumsan enim, a maximus velit. Pellentesque in risus eget est faucibus convallis nec at nulla. Phasellus nec lacinia justo. Morbi fermentum, orci id varius accumsan, nibh neque porttitor ipsum, consectetur luctus risus arcu ac ex. Aenean a luctus augue. Suspendisse et auctor nisl. Suspendisse cursus ultrices quam non vulputate. Phasellus et pharetra neque, vel feugiat erat. Sed feugiat elit at mauris commodo consequat. Sed congue lectus id mattis hendrerit. Mauris turpis nisl, congue eget velit sed, imperdiet convallis magna. Nam accumsan urna risus, non feugiat odio vehicula eget.

Font Size

If one of your tables is huge and you want to use a smaller font size for that specific table, you can use the font_size option.

kbl(dt, booktabs = T) %>%
  kable_styling(font_size = 7)

Column / Row Specification

Column spec

When you have a table with lots of explanatory texts, you may want to specify the column width for different column, since the auto adjust in HTML may not work in its best way while basic LaTeX table is really bad at handling text wrapping. Also, sometimes, you may want to highlight a column (e.g., a "Total" column) by making it bold. In these scenarios, you can use column_spec(). You can find an example below.

text_tbl <- data.frame(
  Items = c("Item 1", "Item 2", "Item 3"),
  Features = c(
    "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin vehicula tempor ex. Morbi malesuada sagittis turpis, at venenatis nisl luctus a. ",
    "In eu urna at magna luctus rhoncus quis in nisl. Fusce in velit varius, posuere risus et, cursus augue. Duis eleifend aliquam ante, a aliquet ex tincidunt in. ", 
    "Vivamus venenatis egestas eros ut tempus. Vivamus id est nisi. Aliquam molestie erat et sollicitudin venenatis. In ac lacus at velit scelerisque mattis. "
  )
)

kbl(text_tbl, booktabs = T) %>%
  kable_styling(full_width = F) %>%
  column_spec(1, bold = T, color = "red") %>%
  column_spec(2, width = "30em")

Key Update: I understand the need of doing conditional formatting and the previous solution cell_spec is relatively hard to use. Therefore in kableExtra 1.2, I improved the functionality of column_spec so it can take vectorized input for most of its arguments (except width, border_left and border_right). It is really easy right now to format a column based on other values.

that_cell <- c(rep(F, 7), T)
mtcars[1:8, 1:8] %>%
  kbl(booktabs = T, linesep = "") %>%
  kable_paper(full_width = F) %>%
  column_spec(2, color = spec_color(mtcars$mpg[1:8]),
              link = "https://haozhu233.github.io/kableExtra") %>%
  column_spec(6, color = "white", 
              background = spec_color(mtcars$drat[1:8], end = 0.7),
              popover = paste("am:", mtcars$am[1:8])) %>%
  column_spec(9, strikeout = that_cell, bold = that_cell,
              color = c(rep("black", 7), "red"))

You can still use the spec_*** helper functions to help you define color. See the documentation below.

Insert Images into Columns

Technically, we are still talking about column_spec here. However, since this topic itself contains its own subtopics, we split it out as a separate section. Since kableExtra 1.2, we introduced the feature of adding images to columns of tables. Here is a quick example.

tbl_img <- data.frame(
  name = c("kableExtra 1", "kableExtra 2"),
  logo = ""
)
tbl_img %>%
  kbl(booktabs = T) %>%
  kable_paper(full_width = F) %>%
  column_spec(2, image = "kableExtra_sm.png")

If you need to specify the size of the images, you need to do it through spec_image.

tbl_img %>%
  kbl(booktabs = T) %>%
  kable_paper(full_width = F) %>%
  column_spec(2, image = spec_image(
    c("kableExtra_sm.png", "kableExtra_sm.png"), 50, 50))

kableExtra also provides a few inline plotting tools. Right now, there are spec_hist, spec_boxplot, and spec_plot. One key feature is that by default, the limits of every subplots are fixed so you can compare across rows.

mpg_list <- split(mtcars$mpg, mtcars$cyl)
disp_list <- split(mtcars$disp, mtcars$cyl)
inline_plot <- data.frame(cyl = c(4, 6, 8), mpg_box = "", mpg_hist = "",
                          mpg_line1 = "", mpg_line2 = "",
                          mpg_points1 = "", mpg_points2 = "", mpg_poly = "")
inline_plot %>%
  kbl(booktabs = TRUE) %>%
  kable_paper(full_width = FALSE) %>%
  column_spec(2, image = spec_boxplot(mpg_list)) %>%
  column_spec(3, image = spec_hist(mpg_list)) %>%
  column_spec(4, image = spec_plot(mpg_list, same_lim = TRUE)) %>%
  column_spec(5, image = spec_plot(mpg_list, same_lim = FALSE)) %>%
  column_spec(6, image = spec_plot(mpg_list, type = "p")) %>%
  column_spec(7, image = spec_plot(mpg_list, disp_list, type = "p")) %>%
  column_spec(8, image = spec_plot(mpg_list, polymin = 5))

There is also a spec_pointrange function specifically designed for forest plots in regression tables. Of course, feel free to use it for other purposes.

coef_table <- data.frame(
  Variables = c("var 1", "var 2", "var 3"),
  Coefficients = c(1.6, 0.2, -2.0),
  Conf.Lower = c(1.3, -0.4, -2.5),
  Conf.Higher = c(1.9, 0.6, -1.4)
) 

data.frame(
  Variable = coef_table$Variables,
  Visualization = ""
) %>%
  kbl(booktabs = T) %>%
  kable_classic(full_width = FALSE) %>%
  column_spec(2, image = spec_pointrange(
    x = coef_table$Coefficients, 
    xmin = coef_table$Conf.Lower, 
    xmax = coef_table$Conf.Higher, 
    vline = 0)
    )

Row spec

Similar with column_spec, you can define specifications for rows. Currently, you can either bold or italicize an entire row. Note that, similar to other row-related functions in kableExtra, for the position of the target row, you don't need to count in header rows or the group labeling rows.

kbl(dt, booktabs = T) %>%
  kable_styling("striped", full_width = F) %>%
  column_spec(7, border_left = T, bold = T) %>%
  row_spec(1, strikeout = T) %>%
  row_spec(3:5, bold = T, color = "white", background = "black")

Header Rows

One special case of row_spec is that you can specify the format of the header row via row_spec(row = 0, ...).

kbl(dt, booktabs = T, align = "c") %>%
  kable_styling(latex_options = "striped", full_width = F) %>%
  row_spec(0, angle = 45)

Cell/Text Specification

Key Update: As said before, if you are using kableExtra 1.2+, you are now recommended to used column_spec to do conditional formatting.

Function cell_spec is introduced in version 0.6.0 of kableExtra. Unlike column_spec and row_spec, this function is designed to be used before the data.frame gets into the kable function. Comparing with figuring out a list of 2 dimensional indexes for targeted cells, this design is way easier to learn and use, and it fits perfectly well with dplyr's mutate and summarize functions. With this design, there are two things to be noted: Since cell_spec generates raw HTML or LaTeX code, make sure you remember to put escape = FALSE in kable. At the same time, you have to escape special symbols including % manually by yourself cell_spec needs a way to know whether you want html or latex. You can specify it locally in function or globally via the options(knitr.table.format = "latex") method as suggested at the beginning. If you don't provide anything, this function will output as HTML by default.

Currently, cell_spec supports features including bold, italic, monospace, text color, background color, align, font size & rotation angle. More features may be added in the future. Please see function documentations as reference.

Conditional logic

It is very easy to use cell_spec with conditional logic. Here is an example.

cs_dt <- mtcars[1:10, 1:2]
cs_dt$car = row.names(cs_dt)
row.names(cs_dt) <- NULL
cs_dt$mpg = cell_spec(cs_dt$mpg, color = ifelse(cs_dt$mpg > 20, "red", "blue"))
cs_dt$cyl = cell_spec(
  cs_dt$cyl, color = "white", align = "c", angle = 45, 
  background = factor(cs_dt$cyl, c(4, 6, 8), c("#666666", "#999999", "#BBBBBB")))
cs_dt <- cs_dt[c("car", "mpg", "cyl")]

kbl(cs_dt, booktabs = T, escape = F) %>%
  kable_paper("striped", full_width = F)

# You can also do this with dplyr and use one pipe from top to bottom
# mtcars[1:10, 1:2] %>%
#   mutate(
#     car = row.names(.),
#     mpg = cell_spec(mpg, "html", color = ifelse(mpg > 20, "red", "blue")),
#     cyl = cell_spec(cyl, "html", color = "white", align = "c", angle = 45, 
#                     background = factor(cyl, c(4, 6, 8), 
#                                         c("#666666", "#999999", "#BBBBBB")))
#   ) %>%
#   select(car, mpg, cyl) %>%
#   kbl(format = "html", escape = F) %>%
#   kable_styling("striped", full_width = F)

Visualize data with Viridis Color

This package also comes with a few helper functions, including spec_color, spec_font_size & spec_angle. These functions can rescale continuous variables to certain scales. For example, function spec_color would map a continuous variable to any viridis color palettes. It offers a very visually impactful representation in a tabular format.

vs_dt <- iris[1:10, ]
vs_dt[1:4] <- lapply(vs_dt[1:4], function(x) {
    cell_spec(x, bold = T, 
              color = spec_color(x, end = 0.9),
              font_size = spec_font_size(x))
})
vs_dt[5] <- cell_spec(vs_dt[[5]], color = "white", bold = T,
    background = spec_color(1:10, end = 0.9, option = "A", direction = -1))
kbl(vs_dt, booktabs = T, escape = F, align = "c") %>%
  kable_classic("striped", full_width = F)
# Or dplyr ver
# iris[1:10, ] %>%
#   mutate_if(is.numeric, function(x) {
#     cell_spec(x, bold = T, 
#               color = spec_color(x, end = 0.9),
#               font_size = spec_font_size(x))
#   }) %>%
#   mutate(Species = cell_spec(
#     Species, color = "white", bold = T,
#     background = spec_color(1:10, end = 0.9, option = "A", direction = -1)
#   )) %>%
#   kable(escape = F, align = "c") %>%
#   kable_styling(c("striped", "condensed"), full_width = F)

Text Specification

If you check the results of cell_spec, you will find that this function does nothing more than wrapping the text with appropriate HTML/LaTeX formatting syntax. The result of this function is just a vector of character strings. As a result, when you are writing a rmarkdown document or write some text in shiny apps, if you need extra markups other than bold or italic, you may use this function to r text_spec("color", color = "red"), r text_spec("change font size ", font_size = 16) or r text_spec("rotate", angle = 30) your text.

An aliased function text_spec is also provided for a more literal writing experience. The only difference is that in LaTeX, unless you specify latex_background_in_cell = FALSE (default is TRUE) in cell_spec, it will define cell background color as \cellcolor{}, which doesn't work outside of a table, while for text_spec, the default value for latex_background_in_cell is FALSE.

sometext <- strsplit(paste0(
  "You can even try to make some crazy things like this paragraph. ", 
  "It may seem like a useless feature right now but it's so cool ",
  "and nobody can resist. ;)"
), " ")[[1]]
text_formatted <- paste(
  text_spec(sometext, color = spec_color(1:length(sometext), end = 0.9),
            font_size = spec_font_size(1:length(sometext), begin = 5, end = 20)),
  collapse = " ")

# To display the text, type `r text_formatted` outside of the chunk

r text_formatted

Grouped Columns / Rows

Add header rows to group columns

Tables with multi-row headers can be very useful to demonstrate grouped data. To do that, you can pipe your kable object into add_header_above(). The header variable is supposed to be a named character with the names as new column names and values as column span. For your convenience, if column span equals to 1, you can ignore the =1 part so the function below can be written as `add_header_above(c(" ", "Group 1" = 2, "Group 2" = 2, "Group 3" = 2)).

kbl(dt, booktabs = T) %>%
  kable_styling() %>%
  add_header_above(c(" " = 1, "Group 1" = 2, "Group 2" = 2, "Group 3" = 2))

In fact, if you want to add another row of header on top, please feel free to do so. Also, since kableExtra 0.3.0, you can specify bold & italic as you do in row_spec().

kbl(dt, booktabs = T) %>%
  kable_styling(latex_options = "striped") %>%
  add_header_above(c(" ", "Group 1" = 2, "Group 2" = 2, "Group 3" = 2)) %>%
  add_header_above(c(" ", "Group 4" = 4, "Group 5" = 2)) %>%
  add_header_above(c(" ", "Group 6" = 6), bold = T, italic = T)

Group rows via labeling

Sometimes we want a few rows of the table being grouped together. They might be items under the same topic (e.g., animals in one species) or just different data groups for a categorical variable (e.g., age < 40, age > 40). With the function pack_rows/group_rows() in kableExtra, this kind of task can be completed in one line. Please see the example below. Note that when you count for the start/end rows of the group, you don't need to count for the header rows nor other group label rows. You only need to think about the row numbers in the "original R dataframe".

kbl(mtcars[1:10, 1:6], caption = "Group Rows", booktabs = T) %>%
  kable_styling() %>%
  pack_rows("Group 1", 4, 7) %>%
  pack_rows("Group 2", 8, 10)

In case some users need it, you can define your own gapping spaces between the group labeling row and previous rows. The default value is 0.5em.

kbl(dt, booktabs = T) %>%
  pack_rows("Group 1", 4, 5, latex_gap_space = "2em")

If you prefer to build multiple groups in one step, you can use the short-hand index option. Basically, you can use it in the same way as you use add_header_above. However, since group_row only support one layer of grouping, you can't add multiple layers of grouping header as you can do in add_header_above.

kbl(mtcars[1:10, 1:6], caption = "Group Rows", booktabs = T) %>%
  kable_styling() %>%
  pack_rows(index=c(" " = 3, "Group 1" = 4, "Group 2" = 3))
# Not evaluated. The code above should have the same result as the first example in this section.

Note that kable has a relatively special feature to handle align and it may bring troubles to you if you are not using it correctly. In the documentation of the align argument of kable, it says:

If length(align) == 1L, the string will be expanded to a vector of individual letters, e.g. 'clc' becomes c('c', 'l', 'c'), unless the output format is LaTeX.

For example,

kbl(mtcars[1:2, 1:2], align = c("cl"))
# \begin{tabular}{l|cl|cl}  # Note the column alignment here
# \hline
#   & mpg & cyl\\
# ...

LaTeX, somehow shows surprisingly high tolerance on that, which is quite unusual. As a result, it won't throw an error if you are just using kable to make some simple tables. However, when you use kableExtra to make some advanced modification, it will start to throw some bugs. As a result, please try to form a habit of using a vector in the align argument for kable (tip: you can use rep function to replicate elements. For example, c("c", rep("l", 10))).

Row indentation

Unlike pack_rows(), which will insert a labeling row, sometimes we want to list a few sub groups under a total one. In that case, add_indent() is probably more appropriate.

kbl(dt, booktabs = T) %>%
  add_indent(c(1, 3, 5))

You can also specify the width of the indentation by the level_of_indent option. At the same time, if you want to indent every column, you can choose to turn on all_cols. Note that if a column is right aligned, you probably won't be able to see the effect.

kbl(dt, booktabs = T, align = "l") %>%
  add_indent(c(1, 3, 5), level_of_indent = 2, all_cols = T)

Group rows via multi-row cell

Function pack_rows is great for showing simple structural information on rows but sometimes people may need to show structural information with multiple layers. When it happens, you may consider using collapse_rows instead, which will put repeating cells in columns into multi-row cells.

In LaTeX, collapse_rows adds some extra hlines to help differentiate groups. You can customize this behavior using the latex_hline argument. You can choose from full (default), major and none.

Vertical alignment of cells (with the default row_group_label_position = "identity")) is controlled by the valign option. You can choose from "top", "middle" (default) and "bottom". Be cautious that the vertical alignment option was only introduced in multirow in 2016. If you are using a legacy LaTeX distribution, you will run into trouble if you set valign to be either "top" or "bottom". Alternatively, use row_group_label_position = "first", which will put the row group labels into the first row without using the \multirow LaTeX command at all.

collapse_rows_dt <- data.frame(C1 = c(rep("a", 10), rep("b", 5)),
                 C2 = c(rep("c", 7), rep("d", 3), rep("c", 2), rep("d", 3)),
                 C3 = 1:15,
                 C4 = sample(c(0,1), 15, replace = TRUE))
kbl(collapse_rows_dt, booktabs = T, align = "c") %>%
  column_spec(1, bold=T) %>%
  collapse_rows(columns = 1:2, latex_hline = "major", row_group_label_position = "first")

Right now, you can't automatically make striped rows based on collapsed rows but you can do it manually via the extra_latex_after option in row_spec. This feature is not officially supported. I'm only document it here if you want to give it a try.

kbl(collapse_rows_dt[-1], align = "c", booktabs = T) %>%
  column_spec(1, bold = T, width = "5em") %>%
  row_spec(c(1:7, 11:12) - 1, extra_latex_after = "\\rowcolor{gray!6}") %>%
  collapse_rows(1, latex_hline = "none")

When there are too many layers, sometimes the table can become too wide. You can choose to stack the first few layers by setting row_group_label_position to stack.

collapse_rows_dt <- expand.grid(
  District = sprintf('District %s', c('1', '2')),
  City = sprintf('City %s', c('1', '2')),
  State = sprintf('State %s', c('a', 'b')),
  Country = sprintf('Country with a long name %s', c('A', 'B'))
) 
collapse_rows_dt <- collapse_rows_dt[c("Country", "State", "City", "District")]
collapse_rows_dt$C1 = rnorm(nrow(collapse_rows_dt))
collapse_rows_dt$C2 = rnorm(nrow(collapse_rows_dt))

kbl(collapse_rows_dt, 
      booktabs = T, align = "c", linesep = '') %>%
  collapse_rows(1:3, row_group_label_position = 'stack') 

To better distinguish different layers, you can format the each layer using row_group_label_fonts. You can also customize the hlines to better differentiate groups.

row_group_label_fonts <- list(
  list(bold = T, italic = T), 
  list(bold = F, italic = F)
  )
kbl(collapse_rows_dt, 
                     booktabs = T, align = "c", linesep = '') %>%
  column_spec(1, bold=T) %>%
  collapse_rows(1:3, latex_hline = 'custom', custom_latex_hline = 1:3, 
                row_group_label_position = 'stack', 
                row_group_label_fonts = row_group_label_fonts) 

Table Footnote

Now it's recommended to use the new footnote function instead of add_footnote to make table footnotes.

Documentations for add_footnote can be found here.

There are four notation systems in footnote, namely general, number, alphabet and symbol. The last three types of footnotes will be labeled with corresponding marks while general won't be labeled. You can pick any one of these systems or choose to display them all for fulfilling the APA table footnotes requirements.

kbl(dt, align = "c") %>%
  kable_styling(full_width = F) %>%
  footnote(general = "Here is a general comments of the table. ",
           number = c("Footnote 1; ", "Footnote 2; "),
           alphabet = c("Footnote A; ", "Footnote B; "),
           symbol = c("Footnote Symbol 1; ", "Footnote Symbol 2")
           )

You can also specify title for each category by using the ***_title arguments. Default value for general_title is "Note: " and "" for the rest three. You can also change the order using footnote_order. You can even display footnote as chunk texts (default is as a list) using footnote_as_chunk. The font format of the titles are controlled by title_format with options including "italic" (default), "bold" and "underline".

kbl(dt, align = "c", booktabs = T) %>%
  footnote(general = "Here is a general comments of the table. ",
           number = c("Footnote 1; ", "Footnote 2; "),
           alphabet = c("Footnote A; ", "Footnote B; "),
           symbol = c("Footnote Symbol 1; ", "Footnote Symbol 2"),
           general_title = "General: ", number_title = "Type I: ",
           alphabet_title = "Type II: ", symbol_title = "Type III: ",
           footnote_as_chunk = T, title_format = c("italic", "underline")
           )

If you need to add footnote marks in a table, you need to do it manually (no fancy) using footnote_marker_***(). Remember that similar with cell_spec, you need to tell this function whether you want it to do it in HTML (default) or LaTeX. You can set it for all using the knitr.table.format global option. Also, if you have ever used footnote_marker_***(), you need to put escape = F in your kable function to avoid escaping of special characters. Note that if you want to use these footnote_marker functions in kableExtra functions like pack_rows (for the row label) or add_header_above, you need to set double_escape = T and escape = F in those functions. I'm trying to find other ways around. Please let me know if you have a good idea and are willing to contribute.

dt_footnote <- dt
names(dt_footnote)[2] <- paste0(names(dt_footnote)[2], 
                                # That "latex" can be eliminated if defined in global
                                footnote_marker_symbol(1, "latex"))
row.names(dt_footnote)[4] <- paste0(row.names(dt_footnote)[4], 
                                footnote_marker_alphabet(1))
kbl(dt_footnote, align = "c", booktabs = T,
      # Remember this escape = F
      escape = F) %>%
  footnote(alphabet = "Footnote A; ",
           symbol = "Footnote Symbol 1; ",
           alphabet_title = "Type II: ", symbol_title = "Type III: ",
           footnote_as_chunk = T)

If your table footnote is very long, please consider to put your table in a ThreePartTable frame. Note that, in kableExtra version <= 0.7.0, we were using threeparttable but since kableExtra 0.8.0, we start to use ThreePartTable from threeparttablex instead. ThreePartTable supports both the longtable and tabu environments.

kbl(dt, align = "c", booktabs = T, caption = "s") %>%
  footnote(general = "Here is a very very very very very very very very very very very very very very very very very very very very long footnote", 
           threeparttable = T)

LaTeX Only Features

Linebreak processor

Unlike in HTML, where you can use <br> at any time, in LaTeX, it's actually quite difficult to make a linebreak in a table. Therefore I created the linebreak function to facilitate this process. Please see the Best Practice for Newline in LaTeX Table for details.

dt_lb <- data.frame(
  Item = c("Hello\nWorld", "This\nis a cat"), 
  Value = c(10, 100)
)
dt_lb$Item = linebreak(dt_lb$Item)

# Or you can use
# dt_lb <- dt_lb %>%
#   mutate_all(linebreak)

dt_lb %>%
  kbl(booktabs = T, escape = F,
      col.names = linebreak(c("Item\n(Name)", "Value\n(Number)"), align = "c"))

At the same time, since kableExtra 0.8.0, all kableExtra functions that have some contents input (such as footnote or pack_rows) will automatically convert \n to linebreaks for you in both LaTeX and HTML.

Table on a Landscape Page

Sometimes when we have a wide table, we want it to sit on a designated landscape page. The new function landscape() can help you on that. Unlike other functions, this little function only serves LaTeX and doesn't have a HTML side.

kbl(dt, caption = "Demo Table (Landscape)[note]", booktabs = T) %>%
  kable_styling(latex_options = c("hold_position")) %>%
  add_header_above(c(" ", "Group 1[note]" = 3, "Group 2[note]" = 3)) %>%
  add_footnote(c("This table is from mtcars", 
                 "Group 1 contains mpg, cyl and disp", 
                 "Group 2 contains hp, drat and wt"), 
               notation = "symbol") %>%
  pack_rows("Group 1", 4, 5) %>%
  landscape()

Decimal Alignment

Decimal alignment has been a requested feature by many LaTeX users. However, since the syntax for either siunitx or dcolumn are a little different, it is sort of difficult to integrate them into the pipeline of this package without breaking other features. If you need this feature, Brandon Bertelsen (@1beb) provided a very nice solution on Github (https://github.com/haozhu233/kableExtra/issues/174, thanks). Here is a working example.

In the header-includes section of the YAML header, include the following settings. If you need different rounding options, you can make changes here.

\usepackage{siunitx}
\newcolumntype{d}{S[table-format=3.2]}

For your table, you need to modify the column names and use d to as the align options.

# not evaluated
k <- mtcars[1:10,1:5]
names(k) <- paste("{", names(k), "}")
kableExtra::kable(
     k, "latex", booktabs = TRUE, longtable = TRUE,  
     align = c("l", rep("d", 4)), linesep = "", escape = FALSE) %>% 
  kable_styling(full_width=FALSE)

Use LaTeX table in HTML or Word

If you want to save a LaTeX table to a image, you may consider using save_kable(). We also provide an as_image() function as a convenience wrapper for save_kable(). It will save the image to a temp location. Note that this feature requires you to have magick installed (install.packages("magick")). Also, if you are planning to use it on Windows, you need to install Ghostscript. This feature may not work if you are using tinytex. If you are using tinytex, please consider using other alternatives to this function.

# Not evaluated. 

# The code below will automatically include the image in the R Markdown document
kbl(dt, booktabs = T) %>%
  column_spec(1, bold = T) %>%
  as_image()

# If you want to save the image locally, just provide a name
kbl(dt, booktabs = T) %>%
  column_spec(1, bold = T) %>%
  save_kable("my_latex_table.png")

From other packages

Since the structure of kable is relatively simple, it shouldn't be too difficult to convert HTML or LaTeX tables generated by other packages to a kable object and then use kableExtra to modify the outputs. If you are a package author, feel free to reach out to me and we can collaborate.

tables

The latest version of tables comes with a toKable() function, which is compatible with functions in kableExtra (>=0.9.0).

xtable

For xtable users, if you want to use kableExtra functions on that, check out this xtable2kable() function shipped with kableExtra 1.0. I personally have been using this function to place table caption below tables and solve some tricky case when I use tufte_handout.

# Not evaluating
xtable::xtable(mtcars[1:4, 1:4], caption = "Hello xtable") %>%
  xtable2kable() %>%
  column_spec(1, color = "red")

haozhu233/kableExtra documentation built on April 13, 2024, 6:49 p.m.