R Markdown

What is
R Markdown?

Gallery

RPubs

Formatted Templates

Research Computing Workshop Files

Why?

Reproducible Workflows

video

Version Control

Multiple Versions

Easy for you and your Audience

Multiple Audiences

Kindness to Future Self

How does it work?

R Markdown

---
output:
  html_document:
    keep_md: true
---

# Header 1

Markdown text, **bold**, *italics*, 
[a link](http://google.com).

```{r}
summary(cars)
```

Markdown

# Header 1

Markdown text, **bold**, *italics*, 
[a link](http://google.com).

```r
summary(cars)
```

```
##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00
```

HTML Code

<h1>Header 1</h1>

<p>Markdown text, <strong>bold</strong>, 
<em>italics</em>, 
<a href="http://google.com">a link</a>.</p>

<pre class="r"><code>summary(cars)</code></pre>

<pre><code>##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00</code></pre>
</div>

Header 1

Markdown text, bold, italics, a link.

summary(cars)

##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

Compilation Options

RStudio Knit Button

rmarkdown::render()

YAML Header

Spacing matters

Look up the options: R Markdown Formats

Text Chunks: Markdown

# Header 1
## Header 2
### Header 3

*Italics*
**Bold**

[link text](http://google.com)
![caption][images/image.png]

- List Item 1
- List Item 2
  - Item 2a
  - Item 2b
  
1. Numbered list item 1
1. Numbered list item 2

Options chunk

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

R chunks

```{r chunkname}
a<-2
a + 1
a<-3
a + 2
```

a<-2
a + 1

## [1] 3

a<-3
a + 2

## [1] 5

Plot

```{r, fig.width=8, echo=FALSE}
plot(cars)
```

Pretty Output with knitr::kable

head(mtcars)

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

```{r, results='asis'}
library(knitr)
kable(head(cars))
```

summary(lm(mpg ~ hp + disp, data=mtcars))

## 
## Call:
## lm(formula = mpg ~ hp + disp, data = mtcars)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.7945 -2.3036 -0.8246  1.8582  6.9363 
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)
## (Intercept) 30.735904   1.331566  23.083  < 2e-16
## hp          -0.024840   0.013385  -1.856 0.073679
## disp        -0.030346   0.007405  -4.098 0.000306
##                
## (Intercept) ***
## hp          .  
## disp        ***
## ---
## Signif. codes:  
## 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 3.127 on 29 degrees of freedom
## Multiple R-squared:  0.7482, Adjusted R-squared:  0.7309 
## F-statistic: 43.09 on 2 and 29 DF,  p-value: 2.062e-09

```{r, results='asis'}
reg1 <- lm(mpg ~ hp + disp, data=mtcars)
kable(summary(reg1)$coef, digits=2)
```

Interactive Output
DT::datatable

```{r, echo=FALSE}
library(DT)
datatable(mtcars, rownames = FALSE)
```

When not to use R Markdown

Long data processing and import scripts

Long-running or complex calculations

Precise formatting required

R Notebooks

Link