palmerpenguins: Palmer Archipelago (Antarctica) Penguin Data
The data set is from the package palmerpenguins (v0.1.1) and contains the recorded bill lengths and sex of penguins living on three islands in the Palmer Archipelago, Antarctica. It was made available by Allison Horst, Alison Hill, and Kristen Gorman under the license CC0 1.0. For educational purposes, we added the fictitious column cuteness.
Important 1: Consider Legal Restrictions Before Sharing
Everything you put into the project folder will be shared publicly. For reasons of reproducibility, this should include the data you analyze. Of course, you should only share them to the extent you are allowed to. Besides copyright and similar rights, you need to take into account applicable privacy laws (e.g., the GDPR for European citizens) and contractual obligations (e.g., with your data provider).
Privacy laws and contractual obligations may require you to create an anonymized or synthetic data set1, in which case you should provide a reference to a repository where the originally measured data can be obtained from. For further information, you can watch the talk “Data anonymity” by Felix Schönbrodt recorded during the LMU Open Science Center Summer School 2023 and have a look at the accompanying slides. Another resource to look at is the presentation “Creating reproducible packages when data are confidential” by Vilhuber (2024).
Let’s take a first look at our data:
dat <-read.csv("data.csv")str(dat)
R Console
'data.frame': 344 obs. of 9 variables: $ species : int 1 1 1 1 1 1 1 1 1 1 ... $ island : int 3 3 3 3 3 3 3 3 3 3 ... $ bill_length_mm : num 39.1 39.5 40.3 -99 36.7 39.3 38.9 39.2 34.1 42 ... $ bill_depth_mm : num 18.7 17.4 18 -99 19.3 20.6 17.8 19.6 18.1 20.2 ... $ flipper_length_mm: int 181 186 195 -99 193 190 181 195 193 190 ... $ body_mass_g : int 3750 3800 3250 -99 3450 3650 3625 4675 3475 4250 ... $ sex : int 2 1 1 -99 1 2 1 2 -99 -99 ... $ year : int 2007 2007 2007 2007 2007 2007 2007 2007 2007 2007 ... $ cuteness : int 2 3 7 3 7 8 7 2 1 10 ...
We can see that the variables species, island, and sex are stored as integers:
species
1 = Adelie
2 = Chinstrap
3 = Gentoo
island
1 = Biscoe
2 = Dream
3 = Torgersen
sex
1 = female
2 = male
Further, missing values are stored as -99. We need to document this information somewhere!
Add a Data Dictionary
Whether or not distributing the data set, it is important to document the meaning (e.g., units) and values of its variables. This is typically done with a data dictionary (also called a codebook).
The recommendation for data dictionaries vary between fields – both in terms of the recommended content (i.e., what exactly should be documented) and the technical implementation (i.e., which file formats should be used).
For the purpose of this exercise, we keep it easy and propose that you manually create a file with the data dictionary (e.g., as a table in .xlsx, .docx, .ods, or as a Markdown table), documenting only the bare minimum.
Tip 1: Creating data dictionaries using R
Our in-depth supplementary material “Generation of Data Dictionaries Using R” explains how you can create a data dictionary with R. This advanced chapter also contains a section on how to create machine-readable data dictionaries.
A bare minimum data dictionary
Most standards for data dictionaries require at least this information for each variable in your data set:
name: Column name of the variable in the data set
label: Short title for the variable
description: Brief description of what the variable measures or represents
item_text: Exact wording of a question in a survey
values: A mapping of stored answers to their meanings (especially for categorical variables). For example: 1 = male, 2 = female, 9 = missing
units: The units of measurement (only for numeric variables). For example: kg, USD, years
Here’s an example from a different data set, with one row for each variable:
name
label
description
item_text
values
units
gender
Gender
self‑identified gender
1 = male, 2 = female, 3 = other, 9 = missing
age
Age
age in years
-99 = Not answered
years
blood_pressure
Blood Pressure (systolic)
systolic blood pressure
-99 = Not answered
mmHg
life_satisfaction
Life Satisfaction
5-point scale
How satisfied are you with your life?
1 = very dissatisfied, 2 = dissatisfied, 3 = neutral, 4 = satisfied, 5 = very satisfied, -99 = not answered
You can download this example data dictionary as an ODS file here.
Depending on the type of data, it may also be necessary to describe sampling procedures (e.g., selection criteria), measurement instruments (e.g., established questionnaires), appropriate weighting, already applied preprocessing steps, or contact information.
Practical Exercise: Add your own data dictionary
Now it’s your turn. Fill in the missing information (denoted by a bold question mark “?”) in the following data dictionary.
Practical Exercise: Add Data Citation and Attribution
All data relied upon should be cited in the manuscript to allow for precise identification and access. Please add an appropriate citation for the data set to the manuscript where it says “cite data here”.
Copy the following BibTeX entry to the file Bibliography.bib:
Bibliography.bib
@Manual{horst2020,title = {palmerpenguins: Palmer Archipelago (Antarctica) Penguin Data},author = {Allison Horst and Alison Hill and Kristen Gorman},year = {2022},note = {R package version 0.1.1},url = {https://allisonhorst.github.io/palmerpenguins/},}
Then, find the line in the manuscript that says “cite data here” and replace it with a sentence such as the following:
Manuscript.qmd
The analyzed data are by @horst2020.
Render the document to check that the citation is displayed properly.
Terminal
quarto render Manuscript.qmd
While citation happens in the manuscript for reasons of academic integrity and reproducibility, to comply with any licenses you also may need to provide attribution within your project folder. Even though the data file we use here does not require attribution, we recommend adding a short paragraph to LICENSE.txt:
LICENSE.txt
The penguins data stored in "data.csv" by Allison Horst, Alison Hill, and Kristen Gorman available from <https://allisonhorst.github.io/palmerpenguins/> are licensed under CC0 1.0: <https://creativecommons.org/publicdomain/zero/1.0/>
Wrap up
Congrats! You documented your data set and cited it correctly.
To finalize this step, you can go through the commit routine:
