tabyls: a tidy, fully-featured approach to counting things"

In janitor: Simple Tools for Examining and Cleaning Dirty Data

knitr::opts_chunk$set(collapse = T, comment = "#>")

Motivation: why tabyl?

Analysts do a lot of counting. Indeed, it's been said that "data science is mostly counting things." But the base R function for counting, table(), leaves much to be desired:

• It doesn't accept data.frame inputs (and thus doesn't play nicely with the %>% pipe)
• It doesn't output data.frames
• Its results are hard to format. Compare the look and formatting choices of an R table to a Microsoft Excel PivotTable or even the table formatting provided by SPSS.

tabyl() is an approach to tabulating variables that addresses these shortcomings. It's part of the janitor package because counting is such a fundamental part of data cleaning and exploration.

tabyl() is tidyverse-aligned and is primarily built upon the dplyr and tidyr packages.

How it works

On its surface, tabyl() produces frequency tables using 1, 2, or 3 variables. Under the hood, tabyl() also attaches a copy of these counts as an attribute of the resulting data.frame.

The result looks like a basic data.frame of counts, but because it's also a tabyl containing this metadata, you can use adorn_ functions to add additional information and pretty formatting.

The adorn_ functions are built to work on tabyls, but have been adapted to work with similar, non-tabyl data.frames that need formatting.

Examples

This vignette demonstrates tabyl in the context of studying humans in the starwars dataset from dplyr:

library(dplyr)
humans <- starwars %>%
  filter(species == "Human")

One-way tabyl

Tabulating a single variable is the simplest kind of tabyl:

library(janitor)

t1 <- humans %>%
  tabyl(eye_color)

t1

When NA values are present, tabyl() also displays "valid" percentages, i.e., with missing values removed from the denominator. And while tabyl() is built to take a data.frame and column names, you can also produce a one-way tabyl by calling it directly on a vector:

x <- c("big", "big", "small", "small", "small", NA)
tabyl(x)

Most adorn_ helper functions are built for 2-way tabyls, but those that make sense for a 1-way tabyl do work:

t1 %>%
  adorn_totals("row") %>%
  adorn_pct_formatting()

Two-way tabyl

This is often called a "crosstab" or "contingency" table. Calling tabyl on two columns of a data.frame produces the same result as the common combination of dplyr::count(), followed by tidyr::pivot_wider() to wide form:

t2 <- humans %>%
  tabyl(gender, eye_color)

t2

Since it's a tabyl, we can enhance it with adorn_ helper functions. For instance:

t2 %>%
  adorn_percentages("row") %>%
  adorn_pct_formatting(digits = 2) %>%
  adorn_ns()

Adornments have options to control axes, rounding, and other relevant formatting choices (more on that below).

Three-way tabyl

Just as table() accepts three variables, so does tabyl(), producing a list of tabyls:

t3 <- humans %>%
  tabyl(eye_color, skin_color, gender)

# the result is a tabyl of eye color x skin color, split into a list by gender
t3 

If the adorn_ helper functions are called on a list of data.frames - like the output of a three-way tabyl call - they will call purrr::map() to apply themselves to each data.frame in the list:

library(purrr)
humans %>%
  tabyl(eye_color, skin_color, gender, show_missing_levels = FALSE) %>%
  adorn_totals("row") %>%
  adorn_percentages("all") %>%
  adorn_pct_formatting(digits = 1) %>%
  adorn_ns %>%
  adorn_title

This automatic mapping supports interactive data analysis that switches between combinations of 2 and 3 variables. That way, if a user starts with humans %>% tabyl(eye_color, skin_color), adds some adorn_ calls, then decides to split the tabulation by gender and modifies their first line to humans %>% tabyl(eye_color, skin_color, gender), they don't have to rewrite the subsequent adornment calls to use map().

However, if feels more natural to call these with map() or lapply(), that is still supported. For instance, t3 %>% lapply(adorn_percentages) would produce the same result as t3 %>% adorn_percentages.

Other features of tabyls

• When called on a factor, tabyl will show missing levels (levels not present in the data) in the result
  • This can be suppressed if not desired
• NA values can be displayed or suppressed
• tabyls print without displaying row numbers

You can call chisq.test() and fisher.test() on a two-way tabyl to perform those statistical tests, just like on a base R table() object.

The adorn_* functions

These modular functions build on a tabyl to approximate the functionality of a PivotTable in Microsoft Excel. They print elegant results for interactive analysis or for sharing in a report, e.g., with knitr::kable(). For example:

humans %>%
  tabyl(gender, eye_color) %>%
  adorn_totals(c("row", "col")) %>%
  adorn_percentages("row") %>% 
  adorn_pct_formatting(rounding = "half up", digits = 0) %>%
  adorn_ns() %>%
  adorn_title("combined") %>%
  knitr::kable()

The adorn functions are:

• adorn_totals(): Add totals row, column, or both.
• adorn_percentages(): Calculate percentages along either axis or over the entire tabyl
• adorn_pct_formatting(): Format percentage columns, controlling the number of digits to display and whether to append the % symbol
• adorn_rounding(): Round a data.frame of numbers (usually the result of adorn_percentages), either using the base R round() function or using janitor's round_half_up() to round all ties up (thanks, StackOverflow).
  • e.g., round 10.5 up to 11, consistent with Excel's tie-breaking behavior.
  • This contrasts with rounding 10.5 down to 10 as in base R's round(10.5).
  • adorn_rounding() returns columns of class numeric, allowing for graphing, sorting, etc. It's a less-aggressive substitute for adorn_pct_formatting(); these two functions should not be called together.
• adorn_ns(): add Ns to a tabyl. These can be drawn from the tabyl's underlying counts, which are attached to the tabyl as metadata, or they can be supplied by the user.
• adorn_title(): add a title to a tabyl (or other data.frame). Options include putting the column title in a new row on top of the data.frame or combining the row and column titles in the data.frame's first name slot.

These adornments should be called in a logical order, e.g., you probably want to add totals before percentages are calculated. In general, call them in the order they appear above.

BYOt (Bring Your Own tabyl)

You can also call adorn_ functions on other data.frames, not only the results of calls to tabyl(). E.g., mtcars %>% adorn_totals("col") %>% adorn_percentages("col") performs as expected, despite mtcars not being a tabyl.

This can be handy when you have a data.frame that is not a simple tabulation generated by tabyl but would still benefit from the adorn_ formatting functions.

A simple example: calculate the proportion of records meeting a certain condition, then format the results.

percent_above_165_cm <- humans %>%
  group_by(gender) %>%
  summarise(pct_above_165_cm = mean(height > 165, na.rm = TRUE), .groups = "drop")

percent_above_165_cm %>%
  adorn_pct_formatting()

You can control which columns are adorned by using the ... argument. It accepts the tidyselect helpers. That is, you can specify columns the same way you would using dplyr::select().

For instance, say you have a numeric column that should not be included in percentage formatting and you wish to exempt it. Here, only the proportion column is adorned:

mtcars %>%
  count(cyl, gear) %>%
  rename(proportion = n) %>%
  adorn_percentages("col", na.rm = TRUE, proportion) %>%
  adorn_pct_formatting(,,,proportion) # the commas say to use the default values of the other arguments

Here we specify that only two consecutive numeric columns should be totaled (year is numeric but should not be included):

cases <- data.frame(
  region = c("East", "West"),
  year = 2015,
  recovered = c(125, 87),
  died = c(13, 12)
)

cases %>%
    adorn_totals(c("col", "row"), fill = "-", na.rm = TRUE, name = "Total Cases", recovered:died)

Here's a more complex example that uses a data.frame of means, not counts. We create a table containing the mean of a 3rd variable when grouped by two other variables, then use adorn_ functions to round the values and append Ns. The first part is pretty straightforward:

library(tidyr) # for spread()
mpg_by_cyl_and_am <- mtcars %>%
  group_by(cyl, am) %>%
  summarise(mpg = mean(mpg), .groups = "drop") %>%
  spread(am, mpg)

mpg_by_cyl_and_am

Now to adorn_ it. Since this is not the result of a tabyl() call, it doesn't have the underlying Ns stored in the core attribute, so we'll have to supply them:

mpg_by_cyl_and_am %>%
  adorn_rounding() %>%
  adorn_ns(
    ns = mtcars %>% # calculate the Ns on the fly by calling tabyl on the original data
      tabyl(cyl, am)
  ) %>%
  adorn_title("combined", row_name = "Cylinders", col_name = "Is Automatic")

If needed, Ns can be manipulated in their own data.frame before they are appended. Here a tabyl with values in the thousands has its Ns formatted to include the separating character , as typically seen in American numbers, e.g., 3,000.

First we create the tabyl to adorn:

set.seed(1)
raw_data <- data.frame(sex = rep(c("m", "f"), 3000),
                age = round(runif(3000, 1, 102), 0))
raw_data$agegroup = cut(raw_data$age, quantile(raw_data$age, c(0, 1/3, 2/3, 1)))

comparison <- raw_data %>%
  tabyl(agegroup, sex, show_missing_levels = F) %>%
  adorn_totals(c("row", "col")) %>%
  adorn_percentages("col") %>%
  adorn_pct_formatting(digits = 1)

comparison

At this point, the Ns are unformatted:

comparison %>%
  adorn_ns()

Now we format them to insert the thousands commas. A tabyl's raw Ns are stored in its "core" attribute. Here we retrieve those with attr(), then apply the base R function format() to all numeric columns. Lastly, we append these Ns using adorn_ns().

formatted_ns <- attr(comparison, "core") %>% # extract the tabyl's underlying Ns
  adorn_totals(c("row", "col")) %>% # to match the data.frame we're appending to
  dplyr::mutate_if(is.numeric, format, big.mark = ",")

comparison %>%
  adorn_ns(position = "rear", ns = formatted_ns)

Questions? Comments?

File an issue on GitHub if you have suggestions related to tabyl() and its adorn_ helpers or encounter problems while using them.

janitor documentation built on Feb. 16, 2023, 10:16 p.m.