Palmer Penguins

Replacing Flowers with Flightless Arctic Birds

Table of Contents

• Introduction
• Source
• The Penguins
• Data Dictionary
• Data in Python
• History

Introduction

This page presents information about the Palmer Penguins dataset which will be used throughout the CS 307 notes.

A duck walks into a drugstore to purchase some lip balm.

While checking out, the cashier asks: “Will that be cash or credit?”

The duck responds: “Put it on my bill.”

– As told by Andrew “Andy” Glaysher, BS Media Studies, 2009

Source

The Palmer Penguins data were originally collected and made available by Dr. Kristen Gorman and the Palmer Station, Antarctica LTER, a member of the Long Term Ecological Research Network.

• Gorman KB, Williams TD, Fraser WR (2014). Ecological sexual dimorphism and environmental variability within a community of Antarctic penguins (genus Pygoscelis). PLoS ONE 9(3):e90081. https://doi.org/10.1371/journal.pone.0090081

The data as used here is derived from the palmerpenguins Python package that is a port of the palmerpenguins R package. Use the load_penguins() function from either package to obtain the data as originally published via these packages, however, that is not the data you should use for lab in CS 307.

• Horst, AM, Hill, AP, & Gorman, KB (2020). palmerpenguins: Palmer Archipelago (Antarctica) penguin data. R package version 0.1. 0. https://allisonhorst.github.io/palmerpenguins/. doi: 10.5281/zenodo.3960218.

The Penguins

Meet the Palmer Penguins: Chinstrap, Gentoo¹, and Adelie! Artwork by Allison Horst.

In lab, we will focus on the length and depth of the penguins’ bills. We’ll attempt to use these measurements to predict the species of each penguin.

Data Dictionary

The Palmer Penguins dataset includes size measurements for adult foraging penguins near Palmer Station, Antarctica. The data includes measurements for penguin species, island in Palmer Archipelago, size (flipper length, body mass, bill dimensions), and sex.

This dictionary is a modification of the original reference page from the R package with modifications appropriate for the data as presented in Python.

species

• a string denoting penguin species (Adélie, Chinstrap and Gentoo)

island

• a string denoting island in Palmer Archipelago, Antarctica (Biscoe, Dream or Torgersen)

bill_length_mm

• a number denoting bill length (millimeters)

bill_depth_mm

• a number denoting bill depth (millimeters)

flipper_length_mm

• a number denoting flipper length (millimeters)

body_mass_g

• a number denoting body mass (grams)

sex

• a string denoting penguin sex (female, male)

year

• an integer denoting the study year (2007, 2008, or 2009)

Data in Python

The Palmer Penguins data can be access in Python using the palmerpenguins package.

from palmerpenguins import load_penguins
from palmerpenguins import load_penguins_raw

/home/runner/work/cs307-notes/cs307-notes/.venv/lib/python3.13/site-packages/palmerpenguins/penguins.py:2: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources

The load_penguins function returns a Pandas DataFrame containing the data described in the above data dictionary.

penguins = load_penguins()
penguins

	species	island	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	sex	year
0	Adelie	Torgersen	39.10	18.70	181.00	3,750.00	male	2007
1	Adelie	Torgersen	39.50	17.40	186.00	3,800.00	female	2007
2	Adelie	Torgersen	40.30	18.00	195.00	3,250.00	female	2007
3	Adelie	Torgersen	NaN	NaN	NaN	NaN	NaN	2007
4	Adelie	Torgersen	36.70	19.30	193.00	3,450.00	female	2007
...	...	...	...	...	...	...	...	...
339	Chinstrap	Dream	55.80	19.80	207.00	4,000.00	male	2009
340	Chinstrap	Dream	43.50	18.10	202.00	3,400.00	female	2009
341	Chinstrap	Dream	49.60	18.20	193.00	3,775.00	male	2009
342	Chinstrap	Dream	50.80	19.00	210.00	4,100.00	male	2009
343	Chinstrap	Dream	50.20	18.70	198.00	3,775.00	female	2009

344 rows × 8 columns

import seaborn as sns
import matplotlib.pyplot as plt

joint = sns.jointplot(
    data=penguins,
    x="bill_length_mm",
    y="bill_depth_mm",
    hue="species",
    edgecolor="k",
    alpha=0.75,
    space=0,
)
joint.set_axis_labels(
    xlabel="Bill Length (mm)",
    ylabel="Bill Depth (mm)",
)
joint.ax_joint.legend(
    title="Species",
    loc="lower left",
)
plt.show()

The original data can be loaded via the load_penguins_raw, but this data is used infrequently.

History

As you move through your journey as a data scientist, you’ll like encounter the Palmer Penguins dataset with some frequency. An interesting question is, why?

In many ways, the Palmer Penguins data is meant to replace the even more ubiquitous Iris flower data. This again leads to the question, why? In many ways, it is a better dataset because it is useful for everything that the Iris data was, but also more.

The Palmer Penguins data…

• uses a permissive CC0 license.
• uses understandable variables.
• has complete metadata and documentation.
• is a manageable, but less trivial size than the Iris data.
• is real world, not simulated data.
• includes addition feature variables, including categorical variables, as well as missing data, providing more opportunity for usage and learning.

This reasoning is expanded upon in the R Journal article introducing the dataset.

All that is wonderful, but there was another compelling reason to move away from the Iris data, eugenics. How on earth are flowers related to eugenics?

If you study statistics for any length of time, you’ll start to notice that many methods and theories can be traced to one person, Ronald Aylmer (R.A.) Fisher.²

Like many of his contemporaries, Fisher’s interest in statistics and biology cannot be separated from his interest in and study of eugenics. While this is a very unfortunate part of the history of statistics, it cannot simply be ignored. Many of the most foundational statistical methods were developed by researchers and scientists at least interested in if not pursuing eugenics. If you were not already of the mind that statistical methodology should be applied with great care and ethical consideration, hopefully this history will change your perspective.

But how does this all relate to flowers? Well, the Iris data often goes by another name: Fisher’s Iris data set.³ If we stopped using all of Fisher’s creations in statistics, we might not be left with much. But this particular artifact was also published in the Annals of Eugenics.

For additional reading and background:

• Nature Heredity: The outstanding scientist, R.A. Fisher: his views on eugenics and race
• The New Statesman: RA Fisher and the science of hatred
• Andrew Gelman: Commentary on “RA Fisher and the science of hatred”

Footnotes

1. Linux users might recognize the Gentoo name.

2. Interestingly, among his many faults, Fisher did not believe that smoking caused cancer. Especially at the time, his argument was not completely without merit, but his thoughts on the topic were used to combat the arguments made by the Surgeon General’s report in the 1960s making the claim that smoking caused cancer..

3. The data was actually gather by Edgar Anderson, so you will also see it referred to as Anderson’s Iris data set.