Practical R: R Markdown

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# Practical R: R Markdown
### Abhijit Dasgupta
### BIOF 339

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layout: true

---
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# RMarkdown

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![](../img/rmd1.png)
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## R Markdown

.left-column30[
+ There are some choices you might need to make
  + Document is like a paper
  + Presentation is like PowerPoint
  + Shiny is an interactive web app developed in R. May talk about it towards the end
  + Various packages also provide templates for RMarkdown documents

]
.right-column30[
![](../img/rmd2.png)
]

---

.left-column30[
+ Elements on the right are output formats
  - Documents produce Word, PDF or HTML
  - Presentations produce PowerPoint, PDF, or HTML
]
.right-column30[
![](../img/rmd2.png)
]

---

```
---
title: "Untitled"
author: "Abhijit Dasgupta"
date: "9/11/2019"
output: html_document
---
```

This determines the title and author, and the output type. Typically don't modify the 
entry in `output` for now

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

This is a code chunk. RMarkdown evaluates this chunk of code and replaces the code 
with the results. This code chunk happens to be named "cars". The naming is optional but useful.

---

.pull-left[
### RMarkdown

````markdown
```{r cars}
summary(cars)
```
````
]
.pull-right[
### Results

```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[
### RMarkdown

````markdown
```{r}
library(tableone) # Use a package
kableone(CreateTableOne(data=airquality), 
         format='html')
```
````
]
.pull-right[
### Results

```r
library(tableone) # Use a package
kableone(CreateTableOne(data=airquality), 
         format='html')
```

<table>
 <thead>
  <tr>
   <th style="text-align:left;">   </th>
   <th style="text-align:left;"> Overall </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> n </td>
   <td style="text-align:left;"> 153 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Ozone (mean (SD)) </td>
   <td style="text-align:left;"> 42.13 (32.99) </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Solar.R (mean (SD)) </td>
   <td style="text-align:left;"> 185.93 (90.06) </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Wind (mean (SD)) </td>
   <td style="text-align:left;"> 9.96 (3.52) </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Temp (mean (SD)) </td>
   <td style="text-align:left;"> 77.88 (9.47) </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Month (mean (SD)) </td>
   <td style="text-align:left;"> 6.99 (1.42) </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Day (mean (SD)) </td>
   <td style="text-align:left;"> 15.80 (8.86) </td>
  </tr>
</tbody>
</table>

]

<br>
<br>
The code chunk on the left gets **replaced** by the table on the right in your document

---

![](../img/rmd5.png)

---

## Inline code evaluation

.pull-left[

### RMarkdown
The airquality data set has   
`` `r
nrow(airquality)` `` observations

The average ozone level is `` `r
mean(airquality$Ozone)` `` parts per billion
]
.pull-right[

### Results

The airquality data set has 153 observations

The average ozone level is   
42.1293103 `` parts per billion

]