Writing Dynamic Reports with rmarkdown

class: bottom, left, title-slide

# Writing Dynamic Reports with <code style='color: white;'>rmarkdown</code>
### Garrick Aden-Buie
### October 8, 2018

---

class: middle left inverse

## Step 1: Markdown

## Step 2: **R** Markdown

## Step 3: ...

## Step 4: Profit!

---
class: big

## Why Use R Markdown?

1. Blend code and text.

2. Updating the code also updates the text.

3. Change the output format with _just one click_.*
 - Word Documents, PDF, HTML, Slides, Powerpoint, ...

.footnote.muted[Standard disclaimers apply.]

---
background-image: url(../images/kelly-sikkema-580858-unsplash_cropped.jpeg)
background-size: cover
class: center middle

## Markdown

### Plain Text Formatting

---

## Markdown

.pull-left[
#### Source

```markdown
With **markdown**, you write your text
in *plain text*, in a standard text
editor. To format your text, you use
standard characters that make sense
when you're reading the plain version.

You can use tools, like RStudio, to
render the plain text into a more
visually appealing format, like an
HTML page or Microsoft Word document.
```
]
--
.pull-right[
#### Output

With **markdown**, you write your text
in *plain text*, in a standard text
editor. To format your text, you use
standard characters that make sense
when you're reading the plain version.

You can use tools, like RStudio, to
render the plain text into a more
visually appealing format, like an
HTML page or Microsoft Word document.
]

---

## Markdown

.pull-left[
#### Source

```markdown
The `mutate()` function from the 
[dplyr](https://dplyr.tidyverse.org) 
package can be used 
to *mutate* your data frame.

Like all **dplyr** functions, it

1. Takes a data frame
2. Returns a data frame
```
]
--
.pull-right[
#### Output

The `mutate()` function from the [dplyr](https://dplyr.tidyverse.org) package can be used to *mutate* your data frame.

Like all **dplyr** functions, it

1. Takes a data frame
2. Returns a data frame
]

---

## Formatting

.pull-left[
```markdown
 *italics*

**bold**

> quoted text

~~strikethrough~~

equation: $e = mc^2$
```
]

.pull-right[
*italics*

**bold**

> quoted text

~~strikethrough~~

equation: `$e = mc^2$`

]

---
layout: true
## Code
---

.pull-left[
````markdown
Inline code: `x %>% group_by()`.

A code block:

```
View(x)
```

Another code block:

glimpse(x)
````
]

.pull-right[
Inline code: `x %>% group_by()`.

A code block:

```
View(x)
```

Another code block:

glimpse(x)
]

---

.pull-left[
````markdown
A code block with syntax highlighting

```r
x <- sample(letters, 10)
x <- paste(x, collapse = ", ")
print(x)
```

Many supported styles

```javascript
var i;
for (i=0; i<5; i++) {
 console.log(i);
}
```
````
]

.pull-right[
A code block with syntax highlighting

```r
x <- sample(letters, 10)
x <- paste(x, collapse = ", ")
print(x)
```

Many supported styles

```javascript
var i;
for (i=0; i<5; i++) {
 console.log(i);
}
```
]

---
layout: false
## Headers

.pull-left[
```markdown
# Section 1

## Section 2

### Section 3

#### Section 4

##### Section 5

***
```
]
--
.pull-right[
# Section 1

## Section 2

### Section 3

#### Section 4

##### Section 5

* * *
]

---

## Links

.pull-left[
```markdown
[RStudio](https://rstudio.com)

[gerkelab]: https://gerkelab.com

I develop software in R 
for [Dr. Gerke's Lab][gerkelab].

![Caption](https://bit.ly/2RwSDjL)

Jump to a [Section](#header-name).

Text with a note[^1].

[^1]: Footnote defined anywhere.
```
]

.pull-right[
[RStudio](https://rstudio.com)

[gerkelab]: https://gerkelab.com

I develop software in R 
for [Dr. Gerke's Lab][gerkelab].

![me](https://bit.ly/2RwSDjL)

Jump to a [Section](#16).

A footnote1.

.footnote.muted[1Footnote defined anywhere.]
]

---
layout: true
## Lists
---

.pull-left[
```markdown
* Fruit
* Apple
* Orange
* Banana
* Dairy
* Milk
* Cheese
```
]

.pull-right[
* Fruit
* Apple
* Orange
* Banana
* Dairy
* Milk
* Cheese
]

---

.pull-left[
```markdown
* Fruit
    * Apple
    * Orange
    * Banana
* Dairy
    * Milk
    * Cheese
```
]

.pull-right[
* Fruit
    * Apple
    * Orange
    * Banana
* Dairy
    * Milk
    * Cheese
]

---

.pull-left[
```markdown
* Fruit
    - Apple
    - Orange
    - Banana
* Dairy
    + Milk
    + Cheese
```

]

.pull-right[
* Fruit
    - Apple
    - Orange
    - Banana
* Dairy
    + Milk
    + Cheese
]

You can use `*`, `-`, or `+` for bullet points

---

.pull-left[
```markdown
* Fruit
    1. Apple
    2. Orange
    3. Banana
* Dairy
    1. Milk
    1. Cheese
```
]

.pull-right[
* Fruit
    1. Apple
    2. Orange
    3. Banana
* Dairy
    1. Milk
    1. Cheese
]

Use numbers like `1.` for ordered lists.

---

.pull-left[
```markdown
* Fruit
    1. Apple
    2. Orange
    3. Banana
    
* Dairy
    1. Milk
    1. Cheese
```
]

.pull-right[
* Fruit
    1. Apple
    2. Orange
    3. Banana
    
* Dairy
    1. Milk
    1. Cheese
]

Add empty lines between elements  
to increase line spacing

---

.pull-left[
```markdown
1. A short item
    * Has it's own things
    
1. A longer item with a few paragraphs.

Indent continuation by four spaces.
    
    * Still can have sub-items.
```
]

.pull-right[
1. A short item
    * Has it's own things
    
1. A longer item with a few paragraphs.

Indent continuation by four spaces.
    
    * Still can have sub-items.
]

---
layout: false

## Tables

.center[
<pre>
| height| mass|hair_color |skin_color |species |
|------:|----:|:----------|:-----------|:-------|
| 172| 77|blond |fair |Human |
| 167| 75| |gold |Droid |
| 96| 32| |white, blue |Droid |
| 202| 136|none |white |Human |
| 150| 49|brown |light |Human |
</pre>
]

| height| mass|hair_color |skin_color  |species |
|------:|----:|:----------|:-----------|:-------|
|    172|   77|blond      |fair        |Human   |
|    167|   75|           |gold        |Droid   |
|     96|   32|           |white, blue |Droid   |
|    202|  136|none       |white       |Human   |
|    150|   49|brown      |light       |Human   |

---
background-image: url(../images/ben-white-197668-unsplash.jpg)
background-size: cover
class: middle inverse big

.pull-right[
## Learn More

<a href="https://commonmark.org/help/" style="color: white;">commonmark.org/help/</a>
]

---
background-image: url(../images/scott-webb-199470-unsplash.jpg)
background-size: cover
class: center top

---
layout: true
## Write Code _Inside_ Your Markdown
---

.pull-left[
````markdown
Use a code block but use `{r}` 
where we previously used `r`.

```{r}
summary(cars)
```
````
]
--
.pull-right[
Use a code block but use `{r}` 
where we previously used `r`.

```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
```
]

---

.pull-left[
````markdown
The average speed of the cars
was `r mean(cars$speed)` mph
and the average distance
travelled was `r mean(cars$dist)`
meters (or another unit of distance).
````
]
--
.pull-right[
The average speed of the cars
was 15.4 mph
and the average distance
travelled was 42.98
meters (or another unit of distance).
]

---
layout: true
## Code Chunk Options
---

.pull-left[
````markdown
```{r cars}
head(cars)
```
````

]
.pull-right[

```r
head(cars)
```

```
##   speed dist
## 1     4    2
## 2     4   10
## 3     7    4
## 4     7   22
## 5     8   16
## 6     9   10
```
]

---

.pull-left[
````markdown
```{r cars, echo=FALSE}
head(cars)
```
````

Set `echo = FALSE` to hide the code.
]
.pull-right[

```
##   speed dist
## 1     4    2
## 2     4   10
## 3     7    4
## 4     7   22
## 5     8   16
## 6     9   10
```
]

---

.pull-left[
````markdown
```{r cars, include=FALSE}
head(cars)
```
````

Set `include = FALSE` to hide the code and the output, but still run the code.
]
.pull-right[

]

---

.pull-left[
````markdown
```{r cars, results='hide'}
head(cars)
```
````

Set `results = 'hide'` to hide the output.
]
.pull-right[

```r
head(cars)
```
]

---

.pull-left[
````markdown
```{r cars, results='asis'}
head(cars)
```
````

Set `results = 'asis'` to print the output exactly.
]
.pull-right[

```r
head(cars)
```

speed dist
1     4    2
2     4   10
3     7    4
4     7   22
5     8   16
6     9   10
]

---

.pull-left[
````markdown
```{r cars, results='asis'}
knitr::kable(head(cars))
```
````

Set `results = 'asis'` and use `kable()` from .pkg[knitr]  to print pretty tables.
]
.pull-right[
```r
knitr::kable(head(cars))
```

| speed| dist|
|-----:|----:|
|     4|    2|
|     4|   10|
|     7|    4|
|     7|   22|
|     8|   16|
|     9|   10|
]

---
background-image: url(../images/aaron-burden-60068-unsplash.jpg)
background-size: cover
layout: false
class: inverse right bottom

# Let's Try
## rmarkdown.rstudio.com