In allisonhorst/palmerpenguins: Palmer Archipelago (Antarctica) Penguin Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "75%",
  warning = FALSE,
  message = FALSE,
  fig.retina = 2,
  fig.align = 'center'
)
library(tidyverse)
library(palmerpenguins)

palmerpenguins

The goal of palmerpenguins is to provide a great dataset for data exploration & visualization, as an alternative to iris.

flipper_bill <- ggplot(data = penguins,
                         aes(x = flipper_length_mm,
                             y = bill_length_mm)) +
  geom_point(aes(color = species, 
                 shape = species),
             size = 3,
             alpha = 0.8) +
  geom_smooth(method = "lm", se = FALSE, aes(color = species)) +
  theme_minimal() +
  scale_color_manual(values = c("darkorange","purple","cyan4")) +
  labs(title = "Flipper and bill length",
       subtitle = "Dimensions for Adelie, Chinstrap and Gentoo Penguins at Palmer Station LTER",
       x = "Flipper length (mm)",
       y = "Bill length (mm)",
       color = "Penguin species",
       shape = "Penguin species") +
  theme(legend.position = c(0.85, 0.15),
        plot.title.position = "plot",
        plot.caption = element_text(hjust = 0, face= "italic"),
        plot.caption.position = "plot")

flipper_bill

Installation

You can install the released version of palmerpenguins from CRAN with:

install.packages("palmerpenguins")

To install the development version from GitHub use:

# install.packages("remotes")
remotes::install_github("allisonhorst/palmerpenguins")

About the data

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

The palmerpenguins package contains two datasets.

library(palmerpenguins)
data(package = 'palmerpenguins')

One is called penguins, and is a simplified version of the raw data; see ?penguins for more info:

head(penguins)

The second dataset is penguins_raw, and contains all the variables and original names as downloaded; see ?penguins_raw for more info.

head(penguins_raw)

Both datasets contain data for r nrow(penguins) penguins. There are r length(unique(penguins$species)) different species of penguins in this dataset, collected from r length(unique(penguins$island)) islands in the Palmer Archipelago, Antarctica.

str(penguins)

We gratefully acknowledge Palmer Station LTER and the US LTER Network. Special thanks to Marty Downs (Director, LTER Network Office) for help regarding the data license & use.

Examples

You can find these and more code examples for exploring palmerpenguins in vignette("examples").

Penguins are fun to summarize! For example:

library(tidyverse)
penguins %>% 
  count(species)
penguins %>% 
  group_by(species) %>% 
  summarize(across(where(is.numeric), mean, na.rm = TRUE))

Penguins are fun to visualize! For example:

mass_flipper <- ggplot(data = penguins, 
                       aes(x = flipper_length_mm,
                           y = body_mass_g)) +
  geom_point(aes(color = species, 
                 shape = species),
             size = 3,
             alpha = 0.8) +
  theme_minimal() +
  scale_color_manual(values = c("darkorange","purple","cyan4")) +
  labs(title = "Penguin size, Palmer Station LTER",
       subtitle = "Flipper length and body mass for Adelie, Chinstrap, and Gentoo Penguins",
       x = "Flipper length (mm)",
       y = "Body mass (g)",
       color = "Penguin species",
       shape = "Penguin species") +
  theme(legend.position = c(0.2, 0.7),
        plot.title.position = "plot",
        plot.caption = element_text(hjust = 0, face= "italic"),
        plot.caption.position = "plot")

mass_flipper

flipper_hist <- ggplot(data = penguins, aes(x = flipper_length_mm)) +
  geom_histogram(aes(fill = species), 
                 alpha = 0.5, 
                 position = "identity") +
  scale_fill_manual(values = c("darkorange","purple","cyan4")) +
  theme_minimal() +
  labs(x = "Flipper length (mm)",
       y = "Frequency",
       title = "Penguin flipper lengths")

flipper_hist

Artwork

You can download palmerpenguins art (useful for teaching with the data) in vignette("art"). If you use this artwork, please cite with: "Artwork by @allison_horst".

Meet the Palmer penguins

knitr::include_graphics("man/figures/lter_penguins.png", dpi = 300)

Bill dimensions

The culmen is the upper ridge of a bird's bill. In the simplified penguins data, culmen length and depth are renamed as variables bill_length_mm and bill_depth_mm to be more intuitive.

For this penguin data, the culmen (bill) length and depth are measured as shown below (thanks Kristen Gorman for clarifying!):

knitr::include_graphics("man/figures/culmen_depth.png", dpi = 300)

License

Data are available by CC-0 license in accordance with the Palmer Station LTER Data Policy and the LTER Data Access Policy for Type I data.

Citation

To cite the palmerpenguins package, please use:

citation("palmerpenguins")

Additional data use information

Anyone interested in publishing the data should contact Dr. Kristen Gorman about analysis and working together on any final products. From Gorman et al. (2014): "Individuals interested in using these data are expected to follow the US LTER Network’s Data Access Policy, Requirements and Use Agreement: https://lternet.edu/data-access-policy/."

References

Data originally published in:

• 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

Data citations:

Adélie penguins:

• Palmer Station Antarctica LTER and K. Gorman, 2020. Structural size measurements and isotopic signatures of foraging among adult male and female Adélie penguins (Pygoscelis adeliae) nesting along the Palmer Archipelago near Palmer Station, 2007-2009 ver 5. Environmental Data Initiative. https://doi.org/10.6073/pasta/98b16d7d563f265cb52372c8ca99e60f (Accessed 2020-06-08).

Gentoo penguins:

• Palmer Station Antarctica LTER and K. Gorman, 2020. Structural size measurements and isotopic signatures of foraging among adult male and female Gentoo penguin (Pygoscelis papua) nesting along the Palmer Archipelago near Palmer Station, 2007-2009 ver 5. Environmental Data Initiative. https://doi.org/10.6073/pasta/7fca67fb28d56ee2ffa3d9370ebda689 (Accessed 2020-06-08).

Chinstrap penguins:

• Palmer Station Antarctica LTER and K. Gorman, 2020. Structural size measurements and isotopic signatures of foraging among adult male and female Chinstrap penguin (Pygoscelis antarcticus) nesting along the Palmer Archipelago near Palmer Station, 2007-2009 ver 6. Environmental Data Initiative. https://doi.org/10.6073/pasta/c14dfcfada8ea13a17536e73eb6fbe9e (Accessed 2020-06-08).

allisonhorst/palmerpenguins documentation built on Sept. 20, 2024, 12:05 p.m.