Penguins Dataset Overview – iris alternative in R (2024)

Installation

palmerpenguins is yet to make it to CRAN, so you can install it from Github

remotes::install_github("allisonhorst/palmerpenguins")

Accessing Data

After successful installation, you can find out that there are two datasets attached with the package – penguins and penguins_raw. You can check out their help page (?penguins_raw) to understand more about respective datasets.

Loading Library

library(tidyverse)library(palmerpenguins)

Meta – Glimpse of penguins dataset

penguins dataset has got the following 7 columns and 344 columns

names(penguins)## [1] "species" "island" "bill_length_mm" ## [4] "bill_depth_mm" "flipper_length_mm" "body_mass_g" ## [7] "sex"

Of the 7 columns, 3 are categorical (species,island,sex) and the rest are numeric.

glimpse(penguins)## Rows: 344## Columns: 7## $ species <fct> Adelie, Adelie, Adelie, Adelie, Adelie, Adelie, Ade…## $ island <fct> Torgersen, Torgersen, Torgersen, Torgersen, Torgers…## $ bill_length_mm <dbl> 39.1, 39.5, 40.3, NA, 36.7, 39.3, 38.9, 39.2, 34.1,…## $ bill_depth_mm <dbl> 18.7, 17.4, 18.0, NA, 19.3, 20.6, 17.8, 19.6, 18.1,…## $ flipper_length_mm <int> 181, 186, 195, NA, 193, 190, 181, 195, 193, 190, 18…## $ body_mass_g <int> 3750, 3800, 3250, NA, 3450, 3650, 3625, 4675, 3475,…## $ sex <fct> male, female, female, NA, female, male, female, mal…

Penguins Data Column Definition

speciesa factor denoting penguin species (Adélie, Chinstrap and Gentoo)

islanda factor denoting island in Palmer Archipelago, Antarctica (Biscoe, Dream or Torgersen)

bill_length_mma number denoting bill length (millimeters)

bill_depth_mma number denoting bill depth (millimeters)

flipper_length_mman integer denoting flipper length (millimeters)

body_mass_gan integer denoting body mass (grams)

sexa factor denoting penguin sex (female, male)

Missing Values

A good thing about penguins over iris is that, It’s got missing values NA. It’s quite an important thing to be present while using for educational purposes!

penguins %>% #group_by(species) %>% select(everything()) %>% summarise_all(funs(sum(is.na(.)))) %>% pivot_longer(cols = 1:7, names_to = 'columns', values_to = 'NA_count') %>% arrange(desc(NA_count)) %>% ggplot(aes(y = columns, x = NA_count)) + geom_col(fill = 'darkorange') + geom_label(aes(label = NA_count)) +# scale_fill_manual(values = c("darkorange","purple","cyan4")) + theme_minimal() + labs(title = 'Penguins - NA Count')## Warning: `funs()` is deprecated as of dplyr 0.8.0.## Please use a list of either functions or lambdas: ## ## # Simple named list: ## list(mean = mean, median = median)## ## # Auto named with `tibble::lst()`: ## tibble::lst(mean, median)## ## # Using lambdas## list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))## This warning is displayed once every 8 hours.## Call `lifecycle::last_warnings()` to see where this warning was generated.

Simple Scatter Plot

Like iris, You can simply make a scatter plot using base-R’s plot()

plot(penguins)

### Bar Plot

In this Bar plot, We can visualize the count of each species in the penguins dataset

penguins %>% count(species) %>% ggplot() + geom_col(aes(x = species, y = n, fill = species)) + geom_label(aes(x = species, y = n, label = n)) + scale_fill_manual(values = c("darkorange","purple","cyan4")) + theme_minimal() + labs(title = 'Penguins Species & Count')

### Bar Plot for each Species

In this Bar Plot, We can visualize Species distribution of each Sex (with faceted plot)

penguins %>% drop_na() %>% count(sex, species) %>% ggplot() + geom_col(aes(x = species, y = n, fill = species)) + geom_label(aes(x = species, y = n, label = n)) + scale_fill_manual(values = c("darkorange","purple","cyan4")) + facet_wrap(~sex) + theme_minimal() + labs(title = 'Penguins Species ~ Gender')

Correlation Matrix

penguins %>% select_if(is.numeric) %>% drop_na() %>% cor() ## bill_length_mm bill_depth_mm flipper_length_mm body_mass_g## bill_length_mm 1.0000000 -0.2350529 0.6561813 0.5951098## bill_depth_mm -0.2350529 1.0000000 -0.5838512 -0.4719156## flipper_length_mm 0.6561813 -0.5838512 1.0000000 0.8712018## body_mass_g 0.5951098 -0.4719156 0.8712018 1.0000000

Scatter Plot – Penguins Size Relation wrt Species

In this scatter plot, we’ll try to visualize relationship between flipper_length_mm and body_mass_g with respect to each species.

library(tidyverse)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_minimal()

Scatter Plot – Penguins Size Relation wrt Island

library(tidyverse)ggplot(data = penguins, aes(x = flipper_length_mm, y = body_mass_g)) + geom_point(aes(color = island, 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 each island", x = "Flipper length (mm)", y = "Body mass (g)", color = "Penguin island", shape = "Penguin species") + theme_minimal()

References

• palmerpenguin – Github
• palmerpenguin – Documentation

citation('palmerpenguins')## ## To cite palmerpenguins in publications use:## ## 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## ## A BibTeX entry for LaTeX users is## ## @Article{,## title = {Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis)},## author = {Gorman KB and Williams TD and Fraser WR},## journal = {PLoS ONE},## year = {2014},## volume = {9(3)},## number = {e90081},## pages = {-13},## url = {https://doi.org/10.1371/journal.pone.0090081},## }