Demo Website - Example of R codes

Below is an example to illustrate how to include executable code.

R Code:

Code

1 + 1

[1] 2

Data Visualizations

Generate Example graphs using the penguins data from palmerpenguins using R and GGPlot2

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 dataset contain data for 344 penguins. There are 3 different species of penguins in this dataset, collected from 3 islands in the Palmer Archipelago, Antarctica.

Artwork

You are invited to use this accompanying artwork when you use or teach with palmerpenguins! Please cite with "Artwork by @allison_horst".

Meet the Palmer penguins

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!):

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")
OR
remotes::install_github("mohitshrestha/automaton")

Code

# To install the released version from CRAN use:
# install.packages("ggplot2")
# install.packages("palmerpenguins")

# To install the development version from GitHub use:
# install.packages("remotes")
# remotes::install_github("allisonhorst/palmerpenguins")
# remotes::install_github("mohitshrestha/automaton")

library(ggplot2)
library(palmerpenguins)
ggplot2::theme_set(ggplot2::theme_minimal())

Dataset `Penguins` are fun to Summarize and Visualize!

Code

library(tidyverse)
library(gt)

penguins |> 
    count(species) |> 
    gt()

species	n
Adelie	152
Chinstrap	68
Gentoo	124

Code

penguins |>
    summarize(
        across(where(is.numeric), mean, na.rm = TRUE),
        .by = c(species)
    ) |> 
    gt() |> 
    fmt_number(
        columns = contains("mm") | contains("g")
    ) |> 
    fmt_integer(
        columns = contains("year"),
        sep_mark = ""
    )

species	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	year
Adelie	38.79	18.35	189.95	3,700.66	2008
Gentoo	47.50	14.98	217.19	5,076.02	2008
Chinstrap	48.83	18.42	195.82	3,733.09	2008

Generate Visualizations

Penguin body mass versus flipper length

Code

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) +
  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

Penguin flipper length versus bill length

Code

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) +
  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

Penguin bill length versus depth

Code

bill_len_dep <- ggplot(data = penguins,
                         aes(x = bill_length_mm,
                             y = bill_depth_mm,
                             group = species)) +
  geom_point(aes(color = species, 
                 shape = species),
             size = 3,
             alpha = 0.8) +
  geom_smooth(method = "lm", se = FALSE, aes(color = species)) +
  scale_color_manual(values = c("darkorange","purple","cyan4")) +
  labs(title = "Penguin bill dimensions",
       subtitle = "Bill length and depth for Adelie, Chinstrap and Gentoo Penguins at Palmer Station LTER",
       x = "Bill length (mm)",
       y = "Bill depth (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")

bill_len_dep

Histogram: Penguin flipper lengths

Code

flipper_hist <- ggplot(data = penguins, aes(x = flipper_length_mm)) +
  geom_histogram(aes(fill = species), 
                 alpha = 0.5, 
                 position = "identity",
                 bins = 30) +
  scale_fill_manual(values = c("darkorange","purple","cyan4")) +
  labs(x = "Flipper length (mm)",
       y = "Frequency",
       title = "Penguin flipper lengths")

flipper_hist

BoxPlot & Jitter: Penguin flipper lengths

Code

flipper_box <- ggplot(data = penguins, aes(x = species, y = flipper_length_mm)) +
  geom_boxplot(aes(color = species), width = 0.3, show.legend = FALSE) +
  geom_jitter(aes(color = species), alpha = 0.5, show.legend = FALSE, position = position_jitter(width = 0.2, seed = 0)) +
  scale_color_manual(values = c("darkorange","purple","cyan4")) +
  labs(x = "Species",
       y = "Flipper length (mm)",
       title = "Penguin flipper lengths")

flipper_box

Histogram: Penguin Body mass

Code

mass_hist <- ggplot(data = penguins, aes(x = body_mass_g)) +
  geom_histogram(aes(fill = species), 
                 alpha = 0.5, 
                 position = "identity") +
  scale_fill_manual(values = c("darkorange","purple","cyan4")) +
  labs(x = "Body mass (g)",
       y = "Frequency",
       title = "Penguin body mass")

mass_hist

Scatterplot: Penguin flipper and body mass by sex

Code

flipper_length_body_mass <- ggplot(penguins, aes(x = flipper_length_mm,
                                                 y = body_mass_g)) +
    geom_point(aes(color = sex)) +
    scale_color_manual(values = c("darkorange","cyan4"), na.translate = FALSE) +
    labs(title = "Penguin flipper and body mass",
         subtitle = "Dimensions for male and female Adelie, Chinstrap and Gentoo Penguins at Palmer Station LTER",
         x = "Flipper length (mm)",
         y = "Body mass (g)",
         color = "Penguin sex") +
    theme(legend.position = "bottom",
          plot.title.position = "plot",
          plot.caption = element_text(hjust = 0, face= "italic"),
          plot.caption.position = "plot") +
    facet_wrap(~species)

flipper_length_body_mass

Interactive Visualization

Plotly: Scatterplot Penguin flipper and body mass by sex

Code

library(plotly)
library(ggplot2)
library(palmerpenguins)
ggplot2::theme_set(ggplot2::theme_minimal())

flipper_length_body_mass <- ggplot(penguins, aes(x = flipper_length_mm,
                                                 y = body_mass_g)) +
    geom_point(aes(color = sex)) +
    scale_color_manual(values = c("darkorange","cyan4"), na.translate = FALSE) +
    labs(title = "Penguin flipper and body mass",
         subtitle = "Dimensions for male and female Adelie, Chinstrap and Gentoo Penguins at Palmer Station LTER",
         x = "Flipper length (mm)",
         y = "Body mass (g)",
         color = "Penguin sex") +
    theme(legend.position = "bottom",
          plot.title.position = "plot",
          plot.caption = element_text(hjust = 0, face= "italic"),
          plot.caption.position = "plot") +
    facet_wrap(~species)

ggplotly(flipper_length_body_mass,
         tooltip = c("x", "y", "color"))

Citation

Code

citation("palmerpenguins")

To cite palmerpenguins in publications use:

  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.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {palmerpenguins: Palmer Archipelago (Antarctica) penguin data},
    author = {Allison Marie Horst and Alison Presmanes Hill and Kristen B Gorman},
    year = {2020},
    note = {R package version 0.1.0},
    doi = {10.5281/zenodo.3960218},
    url = {https://allisonhorst.github.io/palmerpenguins/},
  }

Reuse

https://creativecommons.org/licenses/by-sa/4.0/

Citation

BibTeX citation:

@online{shrestha,
  author = {Shrestha, Mohit},
  title = {Example of {R} Codes},
  url = {https://mohitshrestha.github.io/posts/example_r_codes},
  langid = {en}
}

For attribution, please cite this work as:

Shrestha, Mohit. n.d. “Example of R Codes.” https://mohitshrestha.github.io/posts/example_r_codes.

Data Visualizations

About the data

Artwork

Meet the Palmer penguins

Bill dimensions

Installation

Dataset Penguins are fun to Summarize and Visualize!

Generate Visualizations

Penguin body mass versus flipper length

Penguin flipper length versus bill length

Penguin bill length versus depth

Histogram: Penguin flipper lengths

BoxPlot & Jitter: Penguin flipper lengths

Histogram: Penguin Body mass

Scatterplot: Penguin flipper and body mass by sex

Interactive Visualization

Plotly: Scatterplot Penguin flipper and body mass by sex

Citation

Reuse

Citation

Dataset `Penguins` are fun to Summarize and Visualize!