Overview

This is an example R Markdown document that is designed to give you a brief overview of how to write a document.

You can always read about this subject more online:

• https://rmarkdown.rstudio.com/

• https://bookdown.org/yihui/rmarkdown/

The RStudio Cheatsheat for R Markdown is found here:
https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf

This particular example is meant to be compiled to an HTML file.

While it would also compile to a PDF document using LaTeX, there are some bonus settings and slight tricks that are unique only to LaTeX documents. I will demonstrate this in another example file.

Header Level 1

Headers start new chapters/sections and subsections

General Text

To insert a break between paragraphs, include a single completely blank line.

To force a line break, put two blank
spaces at the end of a line.

I can make a separating line by using ---

# If you know html we can make extra spaces using <br> or   Note: this does not work for LaTeX

Comments

Comments in the general text work differently than in R code.

I commented a line out, but you could not see it in the .html file, here is how I did it.

<!-- This has been commented out and will not show up in the rendered document. -->

Boldface, Italics, Strikthrough & Quotations

Code that needs italicized can be made using a single set of underscores or asterisks.

Code that needs to be bold uses two underscores or asterisks instead.

I’ve never used strikethrough personally, but it’s nice to know you can.

The > symbol makes a quote paragraph block.

Quoting verbatim computer code inline is done by surrounding with left-single-quotes (a.k.a. “back-ticks”) (next to the 1 key). If you want to display multiple lines like this, start them with three back ticks in a row on a line by themselves, and end them the same way:

Ordered and Unordered Lists

Math Equations

There are times when you need to write some math, this is handles using LaTeX notation.

Inline equations such as \(A = \pi * r^2\) are surrounded by a set of $ signs. Sometimes entire equation blocks are needed with more extensive math. In this case, surround your math by a set of $$. \[ \int_{a}^{b} f(x) dx \]

You can even do linear algebra

$$
\mathbf{A} = \begin{bmatrix}
1 & 2 & 3 \\
4 & 5 & 6 \\
7 & 8 & 9 \\
10 & 11 & 12
\end{bmatrix}
$$

\[ \mathbf{A} = \begin{bmatrix} 1 & 2 & 3 \\ 4 & 5 & 6 \\ 7 & 8 & 9 \\ 10 & 11 & 12 \end{bmatrix} \]

Tables

| Tables        | Are           | Cool  |
| :------------ |:-------------:| -----:|
| col 1 is      | left-aligned  |   -$5 |
| col 2 is      | centered      |   $12 |
| col 3 is      | right-aligned | $1600 |
| zebra stripes | are neat      |    $1 |

# The original console output
head(mtcars)

                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1

# A table using kable()
library(kableExtra)
kable( head(mtcars), caption = "Table using kable()") %>%
  kable_styling(font_size = 10)

# A table using pander()
library(pander)
pander( head(mtcars) )

# A table using DT::datatable()
library(DT)
datatable( head(mtcars) )

Images

# Usage
![alternative text](location of image)
# If the image is on your computer
![A local image](/folder1/subfolder/local-picture.jpg)
# If the image in the internet somewhere
![A remote image](https://upload.wikimedia.org/wikipedia/en/8/80/Wikipedia-logo-v2.svg)

A remote image

The problem with the above method, is that using R Markdown to render directly to HTML, there is no easy way to resize the image.

One good alternative is to use knitr::include_graphics() which you can read about on your own.

Hyperlinks

Hyperlinks anchored by URLs are easy: Simply type the URL, e.g., https://www.stat.vt.edu/academics/graduate/daas-nva.html

Hyperlinks anchored to text have the [anchor in square brackets, then the link in parentheses](https://www.stat.vt.edu/academics/graduate/daas-nva.html)

Hyperlinks anchored by URLs are easy: Simply type the URL, e.g., https://www.stat.vt.edu/academics/graduate/daas-nva.html

Hyperlinks anchored to text have the anchor in square brackets, then the link in parentheses

Code Chunks

# This chunk will echo the code AND run it.
# Here is some comments, below is the code
x <- runif(5, min = -5, max = 10)
print(x)

[1]  0.1109415  7.9101084  7.9611550  7.2324957 -4.3394611

Most of your write-up should be regular text, not comments within chunks. Everyone once in a while you can include the output from a chunk where the code is not necessarily important to be seen (as long as the context is clear), like the example below which has 5 uniform random numbers between -5 and 10.

[1]  3.3524274  1.7768364 -0.8009476 -2.6978338  5.4420078

# eval=FALSE
# This chunk will echo the code BUT NOT run it.
# Here is some comments, below is the code
x <- runif(5, min = -5, max = 10)
print(x)

# You are unlikely to use this for class reports, but it's useful for your later career.
# z was made in a chunk that had include=FALSE, tt's now showing the result
print(z)

[1] "This is message"

# Notice that it doesn't use the full width of the page when I look at this
describe(cars)

      vars  n  mean    sd median trimmed   mad min max range  skew
speed    1 50 15.40  5.29     15   15.47  5.93   4  25    21 -0.11
dist     2 50 42.98 25.77     36   40.88 23.72   2 120   118  0.76
      kurtosis   se
speed    -0.67 0.75
dist      0.12 3.64

# You can make R output use more width by changing
#  R.options=list(width=130) # 130 is character length
#   in the R chunk options.
describe(cars)

      vars  n  mean    sd median trimmed   mad min max range  skew kurtosis   se
speed    1 50 15.40  5.29     15   15.47  5.93   4  25    21 -0.11    -0.67 0.75
dist     2 50 42.98 25.77     36   40.88 23.72   2 120   118  0.76     0.12 3.64

# You can call R scripts from R Chunks if you specify the path
source("/home/username/.../Lecture_03/my_scripts/awesome_script.R")

# If you have set the current working directory to be in Lecture_03
#  then you can specify the relative path
source("my_scripts/awesome_script.R")

Customizing Plot Output

In the setup chunk I specified a folder where all figures will be stored. This is helpful if you want to use those plots for some other purpose. Keep in mind, the plots will only have names if you give your chunks names like what I show below.

# The default is based upon what you set in the setup chunk
#  In this case, plots are 7 x 7 inches and aligned in the center.
plot(cars)

# fig.width and fig.height can be used to specify dimensions
#  In this case I used {r fig.width=5, fig.height=5}
plot(cars)

# fig.width and fig.height can be used to specify dimensions
#  In this case I used {r fig.width=8, fig.height=5}
plot(cars)

# However there are times when out.width and out.height is a better looking option
#  In th is case I used {r, out.width="50%"} we let it figure out the height on it's own.
plot(cars)

#  In this case I used {r, out.width="65%", fig.align='left', fig.cap="This is a plot"}
plot(cars)

Figure 1: This is a plot