Jared White 2024-03-12
© Jared White, 2024. This work is licensed under a Creative Commons Attribution 4.0 International License.
The Palmer Penguins data is one of the many standard datasets that is available within CRAN, and is commonly used to demonstrate the capabilities of analysis and visualization with the R TidyVerse package.
library(tidyverse)
library(janitor)
library(palmerpenguins)
pallete1 <- c("royalblue1", "forestgreen", "salmon")
pallete2 <- c("#b69574", "#efe0bf")
scale_color_manual(values = pallete1)## <ggproto object: Class ScaleDiscrete, Scale, gg>
## aesthetics: colour
## axis_order: function
## break_info: function
## break_positions: function
## breaks: waiver
## call: call
## clone: function
## dimension: function
## drop: TRUE
## expand: waiver
## get_breaks: function
## get_breaks_minor: function
## get_labels: function
## get_limits: function
## get_transformation: function
## guide: legend
## is_discrete: function
## is_empty: function
## labels: waiver
## limits: NULL
## make_sec_title: function
## make_title: function
## map: function
## map_df: function
## n.breaks.cache: NULL
## na.translate: TRUE
## na.value: grey50
## name: waiver
## palette: function
## palette.cache: NULL
## position: left
## range: environment
## rescale: function
## reset: function
## train: function
## train_df: function
## transform: function
## transform_df: function
## super: <ggproto object: Class ScaleDiscrete, Scale, gg>
# the data is already very clean, but does have 11 NAs, which are dropped.
df <- penguins %>% clean_names() %>% drop_na()fyr <- min(penguins$year)
lyr <- max(penguins$year)bm_fl_cor <- df %>% group_by(island, species) %>% summarise(correlation = cor(body_mass_g, flipper_length_mm), avg_bm = mean(body_mass_g), avg_fl = mean(flipper_length_mm))
head(bm_fl_cor)## # A tibble: 5 × 5
## # Groups: island [3]
## island species correlation avg_bm avg_fl
## <fct> <fct> <dbl> <dbl> <dbl>
## 1 Biscoe Adelie 0.526 3710. 189.
## 2 Biscoe Gentoo 0.711 5092. 217.
## 3 Dream Adelie 0.433 3701. 190.
## 4 Dream Chinstrap 0.642 3733. 196.
## 5 Torgersen Adelie 0.459 3709. 192.
# standard deviations of summary values
sd_bm_fl_cor <- sd(bm_fl_cor$correlation)
sd_avg_bm <- sd(bm_fl_cor$avg_bm)
sd_avg_fl <- sd(bm_fl_cor$avg_fl)This is one of the most widely created correlation visuals in R. It shows a positive correlation between the total body mass of penguins in grams and the length of their flippers in millimeters. This specific series of scatterplots also identifies the difference between the three species’ size and native islands.
# need to create dfs for custom annotations per species...
plot1_ann_gent <- data.frame(island = c("Biscoe"), label = c("Corr = 0.71"))
plot1_ann_chin <- data.frame(island = c("Dream"), label = c("Corr = 0.64"))
plot1_ann_adel <- data.frame(island = c("Biscoe", "Dream", "Torgersen"), label = c("Corr = 0.53", "Corr = 0.43", "Corr = 0.45"))
ggplot(data = df)+
# Gam Smoothing is used
geom_smooth(mapping = aes(x=flipper_length_mm, y=body_mass_g), color = 'black', method = "gam" )+
# Jitter and color+shape is used to help with overplotting
geom_jitter(aes(x=flipper_length_mm, y=body_mass_g,
color = species, shape = species)) +
# Separate the plots by native island.
facet_wrap(~ island) +
# Adding the custom annotation values and labels
geom_text(x = 190, y = 5750, aes(label = label), data = plot1_ann_gent, color = 'royalblue1', fontface = "bold") +
geom_text(x = 190, y = 5000, aes(label = label), data = plot1_ann_chin, color = 'forestgreen', fontface = "bold") +
geom_text(x = 215, y = 3250, aes(label = label), data = plot1_ann_adel, color = 'salmon', fontface = "bold") +
labs(title = "Flipper Length and Body Mass by Island and Species", x = "Flipper Length (mm)", y = "Body Mass (g)", caption = paste0("Palmer's Penguins, ", fyr, " to ", lyr))
As these plots illustrate, Adelie penguins inhabit all three islands, whereas Gentoos and Chinstraps occupy only one island each - Biscoe and Dream respectively. Notably, although Adelies exhibit the lowest correlation between body mass and flipper length overall, the correlation within this species is noticeably higher on the island that is shared with the species having the highest correlation (Biscoe, which is also inhabited by Gentoo penguins). This raises interesting questions about environmental adaptation and possible cross-breeding which could be the subject of future research. While cross-breeding between penguin species is relatively rare, there have been recently observed and documented cases of this occurring.
Sources: Nature.com, Feb 13, 2024, BouldersBeachPenguins.com
sp_sex_summary <- df %>% group_by(species, sex) %>% summarise(count = n())
ggplot(data = sp_sex_summary) + geom_col(mapping = aes(x = species, y = count, fill = sex, color = species)) +
scale_fill_grey(start = 0.7, end = 0.4) +
geom_text(aes(label = count, x = species, y = ifelse(sex =="male", count-(.2*count), count+(.8*count))), color = "black", fontface = "bold") +
labs(title = "Number of Observations by Species and Sex", caption = paste0("Palmer's Penguins, ", fyr, " to ", lyr), y = "Observations", fill = "Sex")
The representation of male and female Gentoos differs slightly, likely due to a slight sampling bias rather than reflecting the true composition of the entire population.
According to This Research Article on the hydrodynamic performance of penguin wings, published June of 2023: “Results indicate that feathering is the primary contributor to thrust generation.” Feathering is the angling of the wings for optimal hydrodynamic performance. Additionally, the publication states: “Spatial analysis of the thrust shows that the outer three-fifths of the wing are the primary source of thrust, contributing 85.4% of thrust generation at optimal feathering amplitude.” Since the flipper width is not included in the dataset, it is not possible to calculate the total wing area. However, the cited publication does detail a full computer simulation of penguin hydrodynamics. The following ratio is a very rough approximation of this model given the data available:
Since the outer 60% of the flipper generates 85.4% of the total thrust, 51.24% of the total flipper length is divided by the body mass. This figure is then multiplied by 10 to create a rounded Swim Power from flipper length : Body Mass ratio.
df_sr <- df %>% mutate(sp_ratio = round(10*((flipper_length_mm*.5124)/body_mass_g), digits = 2))
df_sr_summary <- df_sr %>% group_by(species) %>% summarise(avg_sp_ratio = round(mean(sp_ratio), digits = 4))
ggplot(data = df_sr_summary) + geom_col(aes(x = species, y = avg_sp_ratio, fill = species)) +
geom_text(aes(x = species, y = avg_sp_ratio-(.2*avg_sp_ratio), label = avg_sp_ratio, fontface = 'bold'), color = "black") +
labs(title = "Swim Power from Flipper Length to Body Mass per Species", caption = paste0("Palmer's Penguins, ", fyr, " to ", lyr), y = "Swim Power : Body Mass", x = "Species")
Despite having the lowest Swim Power from Flipper Length : Body Mass Ratio, Gentoo penguins are the fastest average swimmers out of the three species included in the dataset. This demonstrates the effectiveness of optimal feathering on hydrodynamics. Additionally, the formula for this ratio does not account for the size of the penguins’ air sacs or many other relevant factors.
R Core Team (2023). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). “Welcome to the tidyverse.” Journal of Open Source Software, 4(43), 1686. doi: 10.21105/joss.01686 (URL: https://doi.org/10.21105/joss.01686).
Sam Firke (2023). janitor: Simple Tools for Examining and Cleaning Dirty Data. R package version 2.2.0. https://CRAN.R-project.org/package=janitor
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.
Borecki, P., Rosenberger, J., Mucha, A. et al. Breeding behavior analysis in a large captive colony of African penguins (Spheniscus demersus) and its implications for population management and conservation. Sci Rep 14, 3589 (2024). https://doi.org/10.1038/s41598-024-54105-w
https://bouldersbeachpenguins.com/can-penguins-crossbreed/ © 2024 bouldersbeachpenguins.com - A project by Jan Pretorius
Zhanzhou Hao, Bo Yin, Prasert Prapamonthon, Guowei Yang; Hydrodynamic performance of a penguin wing: Effect of feathering and flapping. Physics of Fluids 1 June 2023; 35 (6): 061907. https://doi.org/10.1063/5.0147776