Penguins Dataset Overview – iris alternative in R

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

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

island a factor 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 an integer denoting flipper length (millimeters)

body_mass_g an integer denoting body mass (grams)

sex a 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},
##   }