Data dictionary

A data dictionary is (usually) a table defining each variable in a dataset, often including information like data type (continuous, categorical, etc.) and a description of its values. It’s helpful for collaborators, others trying to reproduce your analyses, and of course future-you.

Data dictionary in R

I first started creating data dictionaries based on a free Coding Club I attended on creating an R package, given by Lisa DeBruine.

You’ll need the package dplyr from the tidyverse.

library(tidyverse)

I prefer to load packages in using the function p_load from the pacman package. It will install and load packages that you don’t already have installed, otherwise it simply loads a package.

# install.packages("pacman")
pacman::p_load(tidyverse)

Step 1: Load in data

df_penguins <- palmerpenguins::penguins

Step 2: Get variable names

dput(names(df_penguins))

c("species", "island", "bill_length_mm", "bill_depth_mm", "flipper_length_mm", 
"body_mass_g", "sex", "year")

Copy list of names (without c( and )) and place them in tribble() from dplyr. Add varible headers ~variable and ~description, or whatever you like.

tribble(
  ~ "variable", ~ "description",
  "species", "island", "bill_length_mm", "bill_depth_mm", "flipper_length_mm", 
"body_mass_g", "sex", "year"
)

Highlight the variable names, and use the keyboard shortcut Cmd/Ctrl+Shift+A to format the list, making a single row for each. Then add "", after each variable name. Now we’ve got all our variable names, which will appear under the header variable, and an empty string where we can write the variable description that will appear under the heading despcription. Try printing this to see how the table looks.

tribble(
  ~ "variable", ~ "description",
  "species", "",
  "island",  "",
  "bill_length_mm",  "",
  "bill_depth_mm",  "",
  "flipper_length_mm",  "",
  "body_mass_g",  "",
  "sex",  "",
  "year",  ""
)

Step 3: Create table

Fill in all the variable descriptions. Then feed the tibble through your favourite table formatter. I’ll use kable() from knitr and kable_styling() from kableExtra for some extra HTML formatting. You might also try gt() from the gt package.

dplyr::tribble(
  ~ "variable", ~ "description",
  "species", "penguin species",
  "island",  "island penguin lives on",
  "bill_length_mm",  "length of bill in millimeters",
  "bill_depth_mm",  "depth of bill in millimeters",
  "flipper_length_mm",  "length of flipper in millimeters",
  "body_mass_g",  "penguin weight in grams",
  "sex",  "penguin sex",
  "year",  "year of data collection"
) |> 
  knitr::kable() |> 
  kableExtra::kable_styling()

variable	description
species	penguin species
island	island penguin lives on
bill_length_mm	length of bill in millimeters
bill_depth_mm	depth of bill in millimeters
flipper_length_mm	length of flipper in millimeters
body_mass_g	penguin weight in grams
sex	penguin sex
year	year of data collection

Table caption

If this table will be printed in a PDF or HTML output, you might want to add a table label (label: tbl-...) and table caption (tbl-cap: ...). Then you can also cross reference the table using @tbl-.... For example, Table 1 has a label and caption. I’ve printed the code chunk options so you can see exactly how I achieved this.

```{r}
#| eval: true
#| label: tbl-penguins-dictionary
#| tbl-cap: Data dictionary for penguins data from palmerpenguins
dplyr::tribble(
  ~ "variable", ~ "description",
  "species", "penguin species",
  "island",  "island penguin lives on",
  "bill_length_mm",  "length of bill in millimeters",
  "bill_depth_mm",  "depth of bill in millimeters",
  "flipper_length_mm",  "length of flipper in millimeters",
  "body_mass_g",  "penguin weight in grams",
  "sex",  "penguin sex",
  "year",  "year of data collection"
) |> 
  knitr::kable() |> 
  kableExtra::kable_styling()
```

Table 1: Data dictionary for penguins data from palmerpenguins

variable	description
species	penguin species
island	island penguin lives on
bill_length_mm	length of bill in millimeters
bill_depth_mm	depth of bill in millimeters
flipper_length_mm	length of flipper in millimeters
body_mass_g	penguin weight in grams
sex	penguin sex
year	year of data collection