Introduction to R Markdown

Learning Objectives

Knitting R Markdown to different formats
Understanding fundamental Markdown syntax
Using code chunks in R Markdown
Using code chunk options
Including plots & tables in R Markdown

Include a first-level header, second-level header, and third-level header in your R Markdown document naming them Section 1, Subsection 1, and Subsubsection 1, respectively.

Section 1

Here is something in R Markdown. R programming is cool.

Subsection 1.1

This is a subsection. It is basically a section of a section.

Subsubsection 1.1.1

This is a subsubsection. Now, this is a section of a section of a section.

Including a Hyperlink

Include a hyperlink in the R Markdown document linking to the Google homepage.

Google is a great resource when coding in R

What would we do without it!

Simple Text Formatting

Include an italicized word or phrase in your R Markdown document.

I like R Markdown because it is cool!

Include a bolded word or phrase in your R Markdown document.

I like R Markdown because it is cool!

Include a word styled showing it is code in your R Markdown document.

The following is a variable x <- 10

Include a superscript and a subscript in your R Markdown document.

Solve the following: y³ + 4log₂4

Code Chunks

# packageName::functionName(arg1 = 3, arg2 = 'linear')
knitr::include_graphics(path = "https://github.com/dilernia/STA418-518/blob/main/uptownFunk.png?raw=true")

Modify `uptownChunk` by setting the echo chunk option to be FALSE.

Creating a Scatterplot

Include the code to create a scatter plot above in a new chunk at the bottom of the R Markdown document.

library(tidyverse)

# Load storms data set
data(storms)

storms |> ggplot(aes(x = pressure, y = wind)) + 
  geom_point()

Inline R Code

# Creating R objects xbar and se
xbar <- 2
se <- 1.3

The following R Markdown syntax: ?/ The 95% confidence interval for the mean is (-0.548, 4.548) produces:

The 95% confidence interval for the mean is (-0.548, 4.548).

Tables

# Seven largest sustained wind speeds recorded
storms_summary <- storms |> 
  group_by(name, year) |> 
  summarize(max_wind_knots = max(wind)) |> 
  ungroup() |> 
  slice_max(max_wind_knots, n = 4)

We can display the table without any helper functions like below.

storms_summary

## # A tibble: 4 × 3
##   name     year max_wind_knots
##   <chr>   <dbl>          <int>
## 1 Allen    1980            165
## 2 Dorian   2019            160
## 3 Gilbert  1988            160
## 4 Wilma    2005            160

kable() function.

library(knitr)

storms_summary |> 
  kable(caption = "Table 1. Storm summary statistics with kable()")

Table 1. Storm summary statistics with kable()
name	year	max_wind_knots
Allen	1980	165
Dorian	2019	160
Gilbert	1988	160
Wilma	2005	160

flextable() function.

library(flextable)

storms_summary |> 
  flextable() |> 
  set_caption(caption = "Table 1. Storm summary statistics with flextable()") |> 
  colformat_double(big.mark = "", digits = 0) |> 
  autofit()

Table 1. Storm summary statistics with flextable()
name	year	max_wind_knots
Allen	1980	165
Dorian	2019	160
Gilbert	1988	160
Wilma	2005	160

gt() function.

library(gt)

storms_summary |> 
  gt() |> 
  tab_header(title = "Table 1. Storm summary statistics with gt()")

name	year	max_wind_knots
Table 1. Storm summary statistics with gt()
Allen	1980	165
Dorian	2019	160
Gilbert	1988	160
Wilma	2005	160

Table themes

Display the storms_summary table applying a complete theme using the gt() function and the gtExtras R package by viewing the available themes here: https://jthomasmock.github.io/gtExtras/reference/index.html

library(gt)
library(gtExtras)

storms_summary |> 
  gt() |> 
  gt_theme_dark() |>
  tab_header(title = "Table 1. Storm summary statistics with gt()")

name	year	max_wind_knots
Table 1. Storm summary statistics with gt()
Allen	1980	165
Dorian	2019	160
Gilbert	1988	160
Wilma	2005	160

Display the storms_summary table applying a complete theme using the flextable() function by viewing the available themes here: https://davidgohel.github.io/flextable/reference/index.html#flextable-themes.

library(flextable)

storms_summary |> 
  flextable() |> 
  theme_zebra() |>
  set_caption(caption = "Table 1. Storm summary statistics with flextable()") |> 
  colformat_double(big.mark = "", digits = 0) |> 
  autofit()

Table 1. Storm summary statistics with flextable()
name	year	max_wind_knots
Allen	1980	165
Dorian	2019	160
Gilbert	1988	160
Wilma	2005	160