Tables

Introduction

First, load {tidyverse}, {papaja}, and {palmerpenguins}.

library(tidyverse)
library(papaja)
library(palmerpenguins)

Now let’s build a data frame that will be our table.

(penguins_means <- penguins |> 
   summarise(.by = c(island, species),
             bill_length = mean(bill_length_mm, na.rm = TRUE),
             bill_depth = mean(bill_depth_mm, na.rm = TRUE),
             flipper_length = mean(flipper_length_mm, na.rm = TRUE)) |> 
  arrange(island))

# A tibble: 5 × 5
  island    species   bill_length bill_depth flipper_length
  <fct>     <fct>           <dbl>      <dbl>          <dbl>
1 Biscoe    Adelie           39.0       18.4           189.
2 Biscoe    Gentoo           47.5       15.0           217.
3 Dream     Adelie           38.5       18.3           190.
4 Dream     Chinstrap        48.8       18.4           196.
5 Torgersen Adelie           39.0       18.4           191.

Tables by `{knitr}`

The {knitr} package uses the kable() function to format tables.

library(knitr)
kable(penguins_means)

island	species	bill_length	bill_depth	flipper_length
Biscoe	Adelie	38.97500	18.37045	188.7955
Biscoe	Gentoo	47.50488	14.98211	217.1870
Dream	Adelie	38.50179	18.25179	189.7321
Dream	Chinstrap	48.83382	18.42059	195.8235
Torgersen	Adelie	38.95098	18.42941	191.1961

Column and row names

You can control column names and row names with col.names and row.names.

kable(penguins_means, 
      col.names = c("Island", "Species", "Bill length (mm)", 
                    "Bill depth (mm)", "Flipper length (mm)"))

Island	Species	Bill length (mm)	Bill depth (mm)	Flipper length (mm)
Biscoe	Adelie	38.97500	18.37045	188.7955
Biscoe	Gentoo	47.50488	14.98211	217.1870
Dream	Adelie	38.50179	18.25179	189.7321
Dream	Chinstrap	48.83382	18.42059	195.8235
Torgersen	Adelie	38.95098	18.42941	191.1961

Column alignment

By default, character columns are left aligned and numeric columns are right aligned. You can set alignment manually with the align argument with l = left, c = center, and r = right. You can just pass a character string with a series of those letters.

kable(penguins_means,
      col.names = c("Island", "Species", "Bill length (mm)", 
                    "Bill depth (mm)", "Flipper length (mm)"), 
      align = "rclcr")

Island	Species	Bill length (mm)	Bill depth (mm)	Flipper length (mm)
Biscoe	Adelie	38.97500	18.37045	188.7955
Biscoe	Gentoo	47.50488	14.98211	217.1870
Dream	Adelie	38.50179	18.25179	189.7321
Dream	Chinstrap	48.83382	18.42059	195.8235
Torgersen	Adelie	38.95098	18.42941	191.1961

Digit rounding

Round the digits for all numeric data columns with digits argument.

penguins_means |> 
  kable(digits = 2)

island	species	bill_length	bill_depth	flipper_length
Biscoe	Adelie	38.98	18.37	188.80
Biscoe	Gentoo	47.50	14.98	217.19
Dream	Adelie	38.50	18.25	189.73
Dream	Chinstrap	48.83	18.42	195.82
Torgersen	Adelie	38.95	18.43	191.20

If you want different digits for different columns, you can pass a vector to the digits argument.

penguins_means |> 
  kable(digits = c(0, 0, 1, 2, 3))

island	species	bill_length	bill_depth	flipper_length
Biscoe	Adelie	39.0	18.37	188.795
Biscoe	Gentoo	47.5	14.98	217.187
Dream	Adelie	38.5	18.25	189.732
Dream	Chinstrap	48.8	18.42	195.824
Torgersen	Adelie	39.0	18.43	191.196

Table titles

Add a title to the table with the caption argument. The good news is that we can cross-reference easily (Table @ref(tab:title-table)). The bad news is that with captions, tables in PDFs are automatically placed at the top of the page. We’ll see how to fix this later.

kable(penguins_means,
      col.names = c("Island", "Species", "Bill length (mm)", 
                    "Bill depth (mm)", "Flipper length (mm)"), 
      caption = "Penguin body measurements by island and species")

Penguin body measurements by island and species
Island	Species	Bill length (mm)	Bill depth (mm)	Flipper length (mm)
Biscoe	Adelie	38.97500	18.37045	188.7955
Biscoe	Gentoo	47.50488	14.98211	217.1870
Dream	Adelie	38.50179	18.25179	189.7321
Dream	Chinstrap	48.83382	18.42059	195.8235
Torgersen	Adelie	38.95098	18.42941	191.1961

Supplementing kable with `{kableExtra}`

The kable() function is intentionally simple to use and therefore does not have a lot of additional functionality. The {kableExtra} package supplements the kable() functionality with additional formatting options by adding additional functions after the kable() function call using the |> pipe (a bit like how ggplot() works). Check out Create Awesome LaTeX Table with knitr::kable and kableExtra.

# install.packages("kableExtra")
library(kableExtra)

General styling

The kable_styling() function formats a number of things such as font size, table width, and table alignment. I’ll also add latex_options = "hold_position" to keep the table in the text. Otherwise, it puts it at the top of the page.

kable(penguins_means,
      caption = "Penguin body measurements by island and species",
      col.names = c("Island", "Species", "Bill length (mm)", 
                    "Bill depth (mm)", "Flipper length (mm)"),
      digits = 2,
      booktabs = TRUE) |>
  kable_styling(font_size = 15, 
                latex_options = "hold_position")

Penguin body measurements by island and species
Island	Species	Bill length (mm)	Bill depth (mm)	Flipper length (mm)
Biscoe	Adelie	38.98	18.37	188.80
Biscoe	Gentoo	47.50	14.98	217.19
Dream	Adelie	38.50	18.25	189.73
Dream	Chinstrap	48.83	18.42	195.82
Torgersen	Adelie	38.95	18.43	191.20

Labels spanning rows

If you want to label groups of rows, use pack_rows(). Let’s get rid of the island column and label the islands explicitly.

penguins_means2 <- penguins_means |>
  select(-island)

kable(penguins_means2,
      digits = 2, 
      booktabs = TRUE)

species	bill_length	bill_depth	flipper_length
Adelie	38.98	18.37	188.80
Gentoo	47.50	14.98	217.19
Adelie	38.50	18.25	189.73
Chinstrap	48.83	18.42	195.82
Adelie	38.95	18.43	191.20

kable(penguins_means2,
      digits = 2, 
      booktabs = TRUE,
      col.names = c("", "Bill length (mm)", "Bill depth (mm)", 
                    "Flipper length (mm)")
      ) |>
  pack_rows("Biscoe", start_row = 1, end_row = 2) |>
  pack_rows("Dream", start_row = 3, end_row = 4) |>
  pack_rows("Torgersen", start_row = 5, end_row = 5)

	Bill length (mm)	Bill depth (mm)	Flipper length (mm)
Biscoe
Adelie	38.98	18.37	188.80
Gentoo	47.50	14.98	217.19
Dream
Adelie	38.50	18.25	189.73
Chinstrap	48.83	18.42	195.82
Torgersen
Adelie	38.95	18.43	191.20

Notice that we removed the first column name with "".

Labels spanning columns

You can labels groups of columns with the add_header_above() function. Let’s rearrange the data into wide format to illustrate this.

(wide_means <- penguins_means |>
   unite(island_species, island:species) |>
   pivot_wider(id_cols = !bill_depth:flipper_length,
               names_from = island_species, 
               values_from = bill_length))

# A tibble: 1 × 5
  Biscoe_Adelie Biscoe_Gentoo Dream_Adelie Dream_Chinstrap Torgersen_Adelie
          <dbl>         <dbl>        <dbl>           <dbl>            <dbl>
1          39.0          47.5         38.5            48.8             39.0

kable(wide_means,
      digits = 2, 
      booktabs = TRUE)

Biscoe_Adelie	Biscoe_Gentoo	Dream_Adelie	Dream_Chinstrap	Torgersen_Adelie
38.98	47.5	38.5	48.83	38.95

Now that the data are in wide format, we can add the column names by specifying the species then add the headers.

kable(wide_means,
      digits = 2, 
      booktabs = TRUE, 
      col.names = c("Adelie", "Gentoo", "Adelie", 
                    "Chinstrap", "Adelie")) |>
  add_header_above(c("Biscoe" = 2, "Dream" = 2, "Torgersen" = 1))

Biscoe		Dream		Torgersen
Adelie	Gentoo	Adelie	Chinstrap	Adelie
38.98	47.5	38.5	48.83	38.95

Table footnotes

Add table notes with the footnote() function.

kable(penguins_means,
      digits = 2, 
      booktabs = TRUE,
      caption = "Penguin body measurements by island and species",
      col.names = c("Island*", "Species", "Bill length (mm)", 
                    "Bill depth (mm)", "Flipper length (mm)")) |>
  kable_styling(latex_options = "hold_position") |>
  footnote(general = "Source: Gorman et al. (2014)",
           symbol = "Not all species are found on all islands.",
           footnote_as_chunk = TRUE)

Penguin body measurements by island and species
Island*	Species	Bill length (mm)	Bill depth (mm)	Flipper length (mm)
Biscoe	Adelie	38.98	18.37	188.80
Biscoe	Gentoo	47.50	14.98	217.19
Dream	Adelie	38.50	18.25	189.73
Dream	Chinstrap	48.83	18.42	195.82
Torgersen	Adelie	38.95	18.43	191.20
Note: Source: Gorman et al. (2014)
^* Not all species are found on all islands.

Landscape

Rotate wide tables with landscape() function.

kable(penguins_means,
      digits = 2, 
      booktabs = TRUE,
      caption = "Penguin body measurements by island and species",
      col.names = c("Island*", "Species", "Bill length (mm)", 
                    "Bill depth (mm)", "Flipper length (mm)")) |>
  kable_styling(latex_options = "hold_position") |>
  footnote(general = "Source: Gorman et al. (2014)",
           symbol = "Not all species are found on all islands.",
           footnote_as_chunk = TRUE) |> 
  landscape()

Penguin body measurements by island and species
Island*	Species	Bill length (mm)	Bill depth (mm)	Flipper length (mm)
Biscoe	Adelie	38.98	18.37	188.80
Biscoe	Gentoo	47.50	14.98	217.19
Dream	Adelie	38.50	18.25	189.73
Dream	Chinstrap	48.83	18.42	195.82
Torgersen	Adelie	38.95	18.43	191.20
Note: Source: Gorman et al. (2014)
^* Not all species are found on all islands.

Tables by `{papaja}`

The {papaja} package uses the kable() function to format tables in APA format with the apa_table() function. You can use many of the same arguments that are available in the kable() function. You can control where the table is placed (here, top, bottom) with the placement argument. You can add a general footnote with the note argument.

apa_table(penguins_means,
          caption = "Penguin body measurements by island and species",
          col.names = c("Island", "Species", "Bill length (mm)", 
                        "Bill depth (mm)", "Flipper length (mm)"),
          placement = "h",
          note = "Source: Gorman et al. (2014)")

(#tab:unnamed-chunk-18) Penguin body measurements by island and species
Island	Species	Bill length (mm)	Bill depth (mm)	Flipper length (mm)
Biscoe	Adelie	38.98	18.37	188.80
Biscoe	Gentoo	47.50	14.98	217.19
Dream	Adelie	38.50	18.25	189.73
Dream	Chinstrap	48.83	18.42	195.82
Torgersen	Adelie	38.95	18.43	191.20

Note. Source: Gorman et al. (2014)

Notice the alignment is different, with everything left aligned. Let’s right align the means.

apa_table(penguins_means, 
          caption = "Penguin body measurements by island and species",
          col.names = c("Island", "Species", "Bill length (mm)", 
                        "Bill depth (mm)", "Flipper length (mm)"),
          align = c("l", "l", "r", "r", "r"),
          placement = "h",
          note = "Source: Gorman et al. (2014)")

(#tab:unnamed-chunk-19) Penguin body measurements by island and species
Island	Species	Bill length (mm)	Bill depth (mm)	Flipper length (mm)
Biscoe	Adelie	38.98	18.37	188.80
Biscoe	Gentoo	47.50	14.98	217.19
Dream	Adelie	38.50	18.25	189.73
Dream	Chinstrap	48.83	18.42	195.82
Torgersen	Adelie	38.95	18.43	191.20

Note. Source: Gorman et al. (2014)

You can rotate to landscape orientation with the landscape = TRUE argument.

apa_table(penguins_means, 
          caption = "Penguin body measurements by island and species",
          col.names = c("Island", "Species", "Bill length (mm)", 
                        "Bill depth (mm)", "Flipper length (mm)"),
          align = c("l", "l", "r", "r", "r"),
          placement = "h",
          note = "Source: Gorman et al. (2014)",
          landscape = TRUE)

(#tab:unnamed-chunk-20) Penguin body measurements by island and species
Island	Species	Bill length (mm)	Bill depth (mm)	Flipper length (mm)
Biscoe	Adelie	38.98	18.37	188.80
Biscoe	Gentoo	47.50	14.98	217.19
Dream	Adelie	38.50	18.25	189.73
Dream	Chinstrap	48.83	18.42	195.82
Torgersen	Adelie	38.95	18.43	191.20

Note. Source: Gorman et al. (2014)

APA-formatted statistics by `{papaja}`

{papaja} also includes apa_print(), which extracts statistical values in APA format.

Linear regression

penguin_lm <- lm(bill_length_mm ~ sex, data = penguins)
summary(penguin_lm)


Call:
lm(formula = bill_length_mm ~ sex, data = penguins)

Residuals:
     Min       1Q   Median       3Q      Max 
-11.2548  -4.7548   0.8452   4.3030  15.9030 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  42.0970     0.4003 105.152  < 2e-16 ***
sexmale       3.7578     0.5636   6.667 1.09e-10 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 5.143 on 331 degrees of freedom
  (11 observations deleted due to missingness)
Multiple R-squared:  0.1184,    Adjusted R-squared:  0.1157 
F-statistic: 44.45 on 1 and 331 DF,  p-value: 1.094e-10

apa_print(penguin_lm)

$estimate
$estimate$Intercept
[1] "$b = 42.10$, 95\\% CI $[41.31, 42.88]$"

$estimate$sexmale
[1] "$b = 3.76$, 95\\% CI $[2.65, 4.87]$"

$estimate$modelfit
$estimate$modelfit$r2
[1] "$R^2 = .12$, 90\\% CI $[0.07, 0.18]$"

$estimate$modelfit$r2_adj
[1] "$R^2_{adj} = .12$"

$estimate$modelfit$aic
[1] "$\\mathrm{AIC} = 2,039.61$"

$estimate$modelfit$bic
[1] "$\\mathrm{BIC} = 2,051.03$"



$statistic
$statistic$Intercept
[1] "$t(331) = 105.15$, $p < .001$"

$statistic$sexmale
[1] "$t(331) = 6.67$, $p < .001$"

$statistic$modelfit
$statistic$modelfit$r2
[1] "$F(1, 331) = 44.45$, $p < .001$"



$full_result
$full_result$Intercept
[1] "$b = 42.10$, 95\\% CI $[41.31, 42.88]$, $t(331) = 105.15$, $p < .001$"

$full_result$sexmale
[1] "$b = 3.76$, 95\\% CI $[2.65, 4.87]$, $t(331) = 6.67$, $p < .001$"

$full_result$modelfit
$full_result$modelfit$r2
[1] "$R^2 = .12$, 90\\% CI $[0.07, 0.18]$, $F(1, 331) = 44.45$, $p < .001$"



$table
A data.frame with 6 labelled columns:

       term estimate       conf.int statistic  df p.value
1 Intercept    42.10 [41.31, 42.88]    105.15 331  < .001
2   Sexmale     3.76   [2.65, 4.87]      6.67 331  < .001

term     : Predictor 
estimate : $b$ 
conf.int : 95\\% CI 
statistic: $t$ 
df       : $\\mathit{df}$ 
p.value  : $p$ 
attr(,"class")
[1] "apa_results" "list"

apa_table(apa_print(penguin_lm)$table,
          caption = "Linear regression results",
          placement = "h")

(#tab:lm-table) Linear regression results
Predictor	\(b\)	95% CI	\(t\)	\(\mathit{df}\)	\(p\)
Intercept	42.10	[41.31, 42.88]	105.15	331	< .001
Sexmale	3.76	[2.65, 4.87]	6.67	331	< .001

Let’s clean up those predictor names.

penguin_lm_table <- apa_print(penguin_lm)$table |>
  mutate(term = str_replace(term, "Sexmale", "Sex"))
apa_table(penguin_lm_table,
          caption = "Linear regression results",
          placement = "h")

(#tab:unnamed-chunk-22) Linear regression results
term	\(b\)	95% CI	\(t\)	\(\mathit{df}\)	\(p\)
Intercept	42.10	[41.31, 42.88]	105.15	331	< .001
Sex	3.76	[2.65, 4.87]	6.67	331	< .001

How could we name the first column Predictor instead of term?

Other table packages

{gt} RStudio’s grammar of tables (logically like ggplot2)
{flextable} Good Word output but a bit tricky to work with
{huxtable} Very flexible but tricky to work with

Introduction

Tables by {knitr}

Column and row names

Column alignment

Digit rounding

Table titles

Supplementing kable with {kableExtra}

General styling

Labels spanning rows

Labels spanning columns

Table footnotes

Landscape

Tables by {papaja}

APA-formatted statistics by {papaja}

Linear regression

Other table packages

Tables by `{knitr}`

Supplementing kable with `{kableExtra}`

Tables by `{papaja}`

APA-formatted statistics by `{papaja}`