Getting Started with R Markdown

class: center, middle, inverse, title-slide

.title[
# Getting Started with R Markdown
]
.subtitle[
## Beginner to intermediate level tutorial for R Markdown
]
.author[
### Dave Bosworth<br>EMRR Branch<br>Collaborative Science and Innovation Section
]
.date[
### Part 1: October 17, 2022<br>Part 2: December 6, 2022
]

---

# Introduction

- A little about me

- About you
  - Most of you have used R before
  - Some of you have used R Markdown before 
  - All of you want to learn about using R Markdown to help with communicating your scientific work

---

# Tutorial Outline

R Markdown basics: What is it, and why should I use it?  
**Activity 1:** Open test file, load data, and run code

Basic syntax and structure  
**Activity 2:** Create new document, practice using some syntax options, knit file to html

Code chunks and inline code  
**Activity 3:** Inserting and running code

Code chunk options  
**Activity 4:** Modify code chunk options

Basic Pandoc-header options  
**Activity 5:** Modify YAML options

---

# Tutorial Outline - continued

Adding and formatting tables  
**Activity 6:** Tables

Adding interactive elements: plotly, leaflet, datatable (DT)  
**Activity 7:** Interactive elements

Adding tabs  
**Activity 8:** Tabs

Open Questions

GitHub Introduction

---

# What is R Markdown?

- R-specific file type (.Rmd) that provides a platform for science communication

- Used to save and execute code just like an R script, but in a notebook format

- Allows for code and text narrative in the same document

---

# How is R Markdown different than an R script?

- Results from code and narrative text can be stitched ("knitted") together in the output

- Allows for many output options including: 
  - HTML, PDF, and Microsoft Word 
  - presentation slides
  - books and scientific articles
  - dashboards and shiny applications
  - websites

---

# Why use R Markdown?

- Organize your code into "chunks" that can be run individually (notebook format)

- Save code and narrative text together in one document

- Share code and results with others - reproducible, transparent, clearly communicated

- Can be used to create automated reports

---
class: inverse, middle

# Activity 1

### Basic Setup

- Create new R Project for tutorial
- Add files to new R Project:
  - markdown_format_examples.Rmd
  - Monthly_Catch_CPUE.csv
  - rmarkdown_activities_code.R
  - test_rmarkdown.Rmd
  - DWR_Logo.png
- Open test_rmarkdown.Rmd file
- Knit test_rmarkdown.Rmd to make sure it renders correctly

---

# R Markdown Document Structure

## Metadata (YAML header)

Optional section for rendering options (pandoc) as key: value pairs

```r
---
title: "Testing R Markdown"
author: "Dave Bosworth"
date: '`r format(Sys.Date(), "%B %d, %Y")`'
output: html_document
---
```

---

# R Markdown Document Structure

## Narrative Text

Narration formatted with markdown -

- Plain text
- Headers
- Text formatting (bold, italic)
- Links
- Images
- Numbered and unordered lists
- Code
- Equations

[R Markdown Reference Guide](https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf)

---

# R Markdown Document Structure

## Code chunks

- Sections of embedded R code within the document
- Code is run when R Markdown file is "knitted" with results displayed in the output document

```r
plot(pressure)
```

![](RMarkdown_tutorial_slides_files/figure-html/code chunk example-1.png)

---
class: inverse, middle

# Activity 2

### Basic Usage

- Create new Rmd document
- Practice using some markdown syntax options - see markdown_format_examples.Rmd file for examples
- "Knit" Rmd file to html

---

# Code within R Markdown

### Code chunks

```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
```

***

### Inline code

```r
# Today's date is `r Sys.Date()`
```

Today's date is 2022-12-06

---

# File paths and working directories in R Markdown

This can be a source of confusion, so its worthwhile taking a moment to cover this:

- The default working directory when an .Rmd file is knitted is the .Rmd document directory

- The default working directory of an R project is the root directory of the R project

- So it's possible to have different working directories when you are running code from code blocks in an .Rmd file versus when you knit the .Rmd file

- A useful R package to help with working directories and file paths is the [`here` R package](https://here.r-lib.org/)

- The `here::here()` function points to the root directory of an R project regardless of what the current working directory is

---
class: inverse, middle

# Activity 3

### Inserting and running code

- Add code chunks to Rmd document:
  - Load R packages
  - Import Monthly CPUE data
  - Plot monthly CPUE data
- Practice using inline code

---

# Code Chunk Options

### message, warning

`message = TRUE`

```r
library(tidyverse)
```

```
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.3.6      ✔ purrr   0.3.5 
## ✔ tibble  3.1.8      ✔ dplyr   1.0.10
## ✔ tidyr   1.2.1      ✔ stringr 1.4.1 
## ✔ readr   2.1.3      ✔ forcats 0.5.2 
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
```

***

`message = FALSE`

```r
library(tidyverse)
```

---

# Code Chunk Options

### eval, include, echo

- `eval` - default is `eval = TRUE`
  - if `eval = FALSE`, the code will not run in the code block when "knitted", but the code appears in the output file
  
--

- `include` - default is `include = TRUE`
  - if `include = FALSE`, the code and results won't appear in output file, but the code is still executed and results can be used by other code chunks

- `echo` - default is `echo = TRUE`
  - if `echo = FALSE`, the code won't appear in the output file, but the results are still displayed

---

# Code Chunk Options

### Figure output options

- `fig.height`, `fig.width` - the height and width in inches for figures created by the code chunk
  - Default figure dimensions are `fig.width = 7` and `fig.height = 5`

- `fig.align` - allows for custom alignment of figures in the output file. Can be "left", "right", or "center"
  - Default alignment is left

- `fig.cap` - figure caption

- `fig.alt` - alt text for a figure

---
class: inverse, middle

# Activity 4

### Modify code chunk options

- message TRUE vs FALSE
- eval = FALSE
- include = FALSE
- echo = FALSE
- Figure output options

---

# Basic Pandoc-header options

Standard options: title, author, date, output type

```r
---
title: "Testing R Markdown"
author: "Dave Bosworth"
date: "October 17, 2022"
output: html_document
---
```

Make the date dynamic by using R code in the YAML header:

```r
---
title: "Testing R Markdown"
author: "Dave Bosworth"
date: "`r Sys.Date()`"
output: html_document
---
```

---

# Basic Pandoc-header options

## HTML Output Options - Table of Contents

.pull-left[
#### Header

***

```r
---
output: 
  html_document: 
    toc: true
    toc_float:
      collapsed: false
---
```
]

.pull-right[
#### Output

***

<img src="images/YAML_TOC.png" width="80%" />
]

---

# Basic Pandoc-header options

## HTML Output Options - Code Folding and Download

.pull-left[
#### Header

***

```r
---
output: 
  html_document: 
    code_folding: show
    code_download: true
---
```
]

.pull-right[
#### Output

***

<img src="images/YAML_code_folding_download.png" width="40%" />
]

---

# Basic Pandoc-header options

## HTML Output Options - Bootswatch Themes

.pull-left[
#### Header

***

```r
---
output: 
  html_document: 
    theme:
      bootswatch: solar
---
```
]

.pull-right[
#### Output

***

<img src="images/YAML_solar_theme.png" width="90%" />
]

Use `bslib::bootswatch_themes()` to list available themes

---
class: inverse, middle

# Activity 5

### Modify YAML options

- Dynamic date
- Table of contents
- Code folding and download
- bootswatch themes

---

# Adding and formatting tables

### Basic printing

```r
df <- head(mtcars)
df
```

```
##                    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
```

---

# Adding and formatting tables

### Kable

```r
library(knitr)
kable(df)
```

|                  |  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|

---

# Adding and formatting tables

### Kable styling

```r
library(kableExtra)
kable(df, format = "html") %>% kable_styling(font_size = 10)
```

<table class="table" style="font-size: 10px; margin-left: auto; margin-right: auto;">
 <thead>
  <tr>
   <th style="text-align:left;">   </th>
   <th style="text-align:right;"> mpg </th>
   <th style="text-align:right;"> cyl </th>
   <th style="text-align:right;"> disp </th>
   <th style="text-align:right;"> hp </th>
   <th style="text-align:right;"> drat </th>
   <th style="text-align:right;"> wt </th>
   <th style="text-align:right;"> qsec </th>
   <th style="text-align:right;"> vs </th>
   <th style="text-align:right;"> am </th>
   <th style="text-align:right;"> gear </th>
   <th style="text-align:right;"> carb </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> Mazda RX4 </td>
   <td style="text-align:right;"> 21.0 </td>
   <td style="text-align:right;"> 6 </td>
   <td style="text-align:right;"> 160 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;"> 3.90 </td>
   <td style="text-align:right;"> 2.620 </td>
   <td style="text-align:right;"> 16.46 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Mazda RX4 Wag </td>
   <td style="text-align:right;"> 21.0 </td>
   <td style="text-align:right;"> 6 </td>
   <td style="text-align:right;"> 160 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;"> 3.90 </td>
   <td style="text-align:right;"> 2.875 </td>
   <td style="text-align:right;"> 17.02 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 4 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Datsun 710 </td>
   <td style="text-align:right;"> 22.8 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 108 </td>
   <td style="text-align:right;"> 93 </td>
   <td style="text-align:right;"> 3.85 </td>
   <td style="text-align:right;"> 2.320 </td>
   <td style="text-align:right;"> 18.61 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 4 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Hornet 4 Drive </td>
   <td style="text-align:right;"> 21.4 </td>
   <td style="text-align:right;"> 6 </td>
   <td style="text-align:right;"> 258 </td>
   <td style="text-align:right;"> 110 </td>
   <td style="text-align:right;"> 3.08 </td>
   <td style="text-align:right;"> 3.215 </td>
   <td style="text-align:right;"> 19.44 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Hornet Sportabout </td>
   <td style="text-align:right;"> 18.7 </td>
   <td style="text-align:right;"> 8 </td>
   <td style="text-align:right;"> 360 </td>
   <td style="text-align:right;"> 175 </td>
   <td style="text-align:right;"> 3.15 </td>
   <td style="text-align:right;"> 3.440 </td>
   <td style="text-align:right;"> 17.02 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 2 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Valiant </td>
   <td style="text-align:right;"> 18.1 </td>
   <td style="text-align:right;"> 6 </td>
   <td style="text-align:right;"> 225 </td>
   <td style="text-align:right;"> 105 </td>
   <td style="text-align:right;"> 2.76 </td>
   <td style="text-align:right;"> 3.460 </td>
   <td style="text-align:right;"> 20.22 </td>
   <td style="text-align:right;"> 1 </td>
   <td style="text-align:right;"> 0 </td>
   <td style="text-align:right;"> 3 </td>
   <td style="text-align:right;"> 1 </td>
  </tr>
</tbody>
</table>

---
class: inverse, middle

# Activity 6

### Tables

- Basic table printing
- Kables
- Basic kable options
- kableExtra

---

# Adding interactive elements

## datatable (DT)

```r
library(DT)
datatable(mtcars, options = list(pageLength = 5))
```

<div id="htmlwidget-aa78aebd93e6f317eeb0" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-aa78aebd93e6f317eeb0">{"x":{"filter":"none","vertical":false,"data":[["Mazda RX4","Mazda RX4 Wag","Datsun 710","Hornet 4 Drive","Hornet Sportabout","Valiant","Duster 360","Merc 240D","Merc 230","Merc 280","Merc 280C","Merc 450SE","Merc 450SL","Merc 450SLC","Cadillac Fleetwood","Lincoln Continental","Chrysler Imperial","Fiat 128","Honda Civic","Toyota Corolla","Toyota Corona","Dodge Challenger","AMC Javelin","Camaro Z28","Pontiac Firebird","Fiat X1-9","Porsche 914-2","Lotus Europa","Ford Pantera L","Ferrari Dino","Maserati Bora","Volvo 142E"],[21,21,22.8,21.4,18.7,18.1,14.3,24.4,22.8,19.2,17.8,16.4,17.3,15.2,10.4,10.4,14.7,32.4,30.4,33.9,21.5,15.5,15.2,13.3,19.2,27.3,26,30.4,15.8,19.7,15,21.4],[6,6,4,6,8,6,8,4,4,6,6,8,8,8,8,8,8,4,4,4,4,8,8,8,8,4,4,4,8,6,8,4],[160,160,108,258,360,225,360,146.7,140.8,167.6,167.6,275.8,275.8,275.8,472,460,440,78.7,75.7,71.1,120.1,318,304,350,400,79,120.3,95.1,351,145,301,121],[110,110,93,110,175,105,245,62,95,123,123,180,180,180,205,215,230,66,52,65,97,150,150,245,175,66,91,113,264,175,335,109],[3.9,3.9,3.85,3.08,3.15,2.76,3.21,3.69,3.92,3.92,3.92,3.07,3.07,3.07,2.93,3,3.23,4.08,4.93,4.22,3.7,2.76,3.15,3.73,3.08,4.08,4.43,3.77,4.22,3.62,3.54,4.11],[2.62,2.875,2.32,3.215,3.44,3.46,3.57,3.19,3.15,3.44,3.44,4.07,3.73,3.78,5.25,5.424,5.345,2.2,1.615,1.835,2.465,3.52,3.435,3.84,3.845,1.935,2.14,1.513,3.17,2.77,3.57,2.78],[16.46,17.02,18.61,19.44,17.02,20.22,15.84,20,22.9,18.3,18.9,17.4,17.6,18,17.98,17.82,17.42,19.47,18.52,19.9,20.01,16.87,17.3,15.41,17.05,18.9,16.7,16.9,14.5,15.5,14.6,18.6],[0,0,1,1,0,1,0,1,1,1,1,0,0,0,0,0,0,1,1,1,1,0,0,0,0,1,0,1,0,0,0,1],[1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1,1,1],[4,4,4,3,3,3,3,4,4,4,4,3,3,3,3,3,3,4,4,4,3,3,3,3,3,4,5,5,5,5,5,4],[4,4,1,1,2,1,4,2,2,4,4,3,3,3,4,4,4,1,2,1,1,2,2,4,2,1,2,2,4,6,8,2]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>mpg<\/th>\n      <th>cyl<\/th>\n      <th>disp<\/th>\n      <th>hp<\/th>\n      <th>drat<\/th>\n      <th>wt<\/th>\n      <th>qsec<\/th>\n      <th>vs<\/th>\n      <th>am<\/th>\n      <th>gear<\/th>\n      <th>carb<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":5,"columnDefs":[{"className":"dt-right","targets":[1,2,3,4,5,6,7,8,9,10,11]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false,"lengthMenu":[5,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>

---

# Adding interactive elements

## plotly

.pull-left[

```r
library(plotly)
plt <- 
  ggplot(
    data = mtcars, 
    aes(x = wt, y= mpg, color = cyl)
  ) +
  geom_point()

ggplotly(plt, width = 500, height = 400)
```
]

.pull-right[
<div id="htmlwidget-eb13373984bc41db67da" style="width:500px;height:400px;" class="plotly html-widget"></div>
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]

---

# Adding interactive elements

## leaflet

.pull-left[

```r
library(leaflet)
leaflet(width = 400, height = 400) %>%
  addTiles() %>%
  addMarkers(
    lng = 174.768, 
    lat = -36.852, 
    popup = "The birthplace of R"
  )
```
]

.pull-right[
<div id="htmlwidget-8b70c18931451b48c982" style="width:400px;height:400px;" class="leaflet html-widget"></div>
<script type="application/json" data-for="htmlwidget-8b70c18931451b48c982">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"calls":[{"method":"addTiles","args":["https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,null,{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a href=\"https://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a href=\"https://creativecommons.org/licenses/by-sa/2.0/\">CC-BY-SA<\/a>"}]},{"method":"addMarkers","args":[-36.852,174.768,null,null,null,{"interactive":true,"draggable":false,"keyboard":true,"title":"","alt":"","zIndexOffset":0,"opacity":1,"riseOnHover":false,"riseOffset":250},"The birthplace of R",null,null,null,null,{"interactive":false,"permanent":false,"direction":"auto","opacity":1,"offset":[0,0],"textsize":"10px","textOnly":false,"className":"","sticky":true},null]}],"limits":{"lat":[-36.852,-36.852],"lng":[174.768,174.768]}},"evals":[],"jsHooks":[]}</script>
]

---
class: inverse, middle

# Activity 7

### Interactive elements

- Datatables 
- Datatable options
- Plotly
- Leaflet maps
- Leaflet map options

---

# Adding tabs

---
class: inverse, middle

# Activity 8

### Tabs

- Adding tabs
- Format appearance and behavior of tabs

---

# Open Questions???

---

# GitHub Introduction

- Participants poll

- Tutorial will be held through MS Teams - **Date and Time to be Announced**