Simple plot

Here is a basic plot using base graphics:

plot(x)

Note that unlike traditional Sweave, there is no need to write fig=TRUE.

Multiple plots

Also, unlike traditional Sweave, you can include multiple plots in one code chunk:

boxplot(1:10~rep(1:2,5))

plot(x, y)

ggplot2 plot

ggplot2 plots work well:

qplot(x, y, data=df)

lattice plot

As do lattice plots:

xyplot(y~x)

Note that unlike traditional Sweave, there is no need to print lattice plots directly.

Create Markdown code from R

The following code hides the command input (i.e., echo=FALSE), and outputs the content directly as code (i.e., results=asis, which is similar to results=tex in Sweave).

Here are some dot points

* The value of y[1] is 0.52
* The value of y[2] is 1
* The value of y[3] is 2.22

Here are some dot points

• The value of y[1] is 0.52
• The value of y[2] is 1
• The value of y[3] is 2.22

Create Markdown table code from R

x | y
--- | ---
1 | 0.52
2 | 1
3 | 2.22
4 | 4.06
5 | 5.96
6 | 5.89
7 | 6.49
8 | 7.09
9 | 8.16
10 | 12.42

Control output display

The folllowing code supresses display of R input commands (i.e., echo=FALSE) and removes any preceding text from console output (comment=""; the default is comment="##").

```
  x    y
1 1 0.52
2 2 1.00
3 3 2.22
4 4 4.06
5 5 5.96
6 6 5.89
```

  x    y
1 1 0.52
2 2 1.00
3 3 2.22
4 4 4.06
5 5 5.96
6 6 5.89

Control figure size

The following is an example of a smaller figure using fig.width and fig.height options.

```r
plot(x)
```

<img src="2019-02-07-rmd-example_files/figure-html/unnamed-chunk-7-1.png" width="288" />

plot(x)

Cache analysis

Caching analyses is straightforward. Here’s example code. On the first run on my computer, this took about 10 seconds. On subsequent runs, this code was not run.

If you want to rerun cached code chunks, just delete the contents of the cache folder

```r
for (i in 1:5000) {
    lm((i+1)~i)
}
```

Dot Points

Simple dot points:

• Point 1
• Point 2
• Point 3

and numeric dot points:

1. Number 1
2. Number 2
3. Number 3

and nested dot points:

• A
  • A.1
  • A.2
• B
  • B.1
  • B.2

Equations

Equations are included by using LaTeX notation and including them either between single dollar signs (inline equations) or double dollar signs (displayed equations). If you hang around the Q&A site CrossValidated you’ll be familiar with this idea.

There are inline equations such as \(y_i = \alpha + \beta x_i + \varepsilon_i\).

And displayed formulas:

\[\frac{1}{1+\exp(-x)}\]

knitr provides self-contained HTML code that calls a Mathjax script to display formulas. However, in order to include the script in my blog posts I took the script and incorporated it into my blogger template. If you are viewing this post through syndication or an RSS reader, this may not work. You may need to view this post on my website.

Tables

Tables can be included using the following notation

Hyperlinks

• If you like this post, you may wish to subscribe to my RSS feed.

Images

Here’s an example image:

Code

Here is Markdown R code chunk displayed as code:

```r
x <- 1:10
x
```

```
##  [1]  1  2  3  4  5  6  7  8  9 10
```

And then there’s inline code such as x <- 1:10.

Quote

Let’s quote some stuff:

To be, or not to be, that is the question: Whether ’tis nobler in the mind to suffer The slings and arrows of outrageous fortune,

Temporarily disable caching

Question: I asked on StackOverflow about How to set cache=FALSE for a knitr markdown document and override code chunk settings?

Answer: Delete the cache folder. But there are other possible workflows.

Equivalent of Sexpr

Question: I asked on Stack Overvlow about whether there an R Markdown equivalent to Sexpr in Sweave?.

Answer: Include the code between brackets of “backick r space” and “backtick”. E.g., in the source code I have calculated 2 + 2 = 4 .