Introduction to RMarkdown

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## Introduction to RMarkdown
### Greg Rousell

---
class: left

## Introduction to R Markdown
### Agenda

- Introductions & Objectives
- Why RMarkdown?
- Basics
- PDF
- HTML
- Word
- Online Dashboards

---
## Introductions & Objectives

- Name and organization
- Experience with R, RStudio
- What do you hope to get out of today

---
## GitHub

- All the materials are hosted on my GitHub page:

https://github.com/grousell/Intro-RMarkdown

---

## Why RMarkdown?

- One language is translated to different languages (HTML, LaTex, Word)
- Provides environment for data anaysis and notes
- Creates high quality reports for distribution 
- Easily reproduce analyses and reports for different groups

---
## Getting Started

.center2[
<img src="images/start_document.png" width="90%" />
]

---
## Getting Started

.center2[
<img src="images/start_document_2.png" width="90%" />
]

---
## Basics

.pull-left[

`*Italics*`  
`**Bold**`  
`***Bold and Italics***`
`'Inline Code'`  
`# First Level Heading`  
`# Second Level Heading`  
`![](images/rstudio.png)` 
]

.pull-right[
*Italics*  
**Bold**  
***Bold and Italics***  
`Inline Code`  
### First Level Heading  
#### Second Level Heading  
![](images/rstudio.png)
]

---

## Lists

* Unordered lists are started with `*` or `-`  
* Ordered lists begin with a number  
* Sublists are created by indenting 4 spaces, or tab

.pull-left[
<img src = "images/list_1.png" width = 50%/>
]
.pull-right[
<img src = "images/list_2.png"/>
]

---
## Practice

* Open RStudio and a new RMarkdown file to create a PDF. 
* Click "Run" and knit the file
* Change some text and knit again
* Try different formats (HTML, Word, PowerPoint)

---
## Adding R Code

.pull-left[
<img src = "images/insert_r_chunk.png"/>
]

.pull-right[
<img src = "images/insert_r_chunk_2.png"/>
]

---

## Adding R Code

.center2[
<img src="images/insert_r_chunk_3.png" width="120%" />
]

---
## Charts

```r
chart <- df |> 
  count (session_useful) |> 
  mutate (perc = n / sum (n)) |> 
  ggplot (aes (session_useful, perc)) +
  geom_col() +
  scale_y_continuous(labels = scales::percent_format(accuracy = 1),
                     limits = c(0,0.5)) +
  geom_text (aes (label = scales::percent(perc)),
             vjust = -1) +
  labs (title = "I found the session useful", 
        x = "",
        y = "Percent")
```

---
## Charts

---
## Charts
.pull-left[
<img src = "images/chart_1.png" height=180px/>
]
.pull-right[
![](index_files/figure-html/unnamed-chunk-8-1.png)
]

---
class: left
## Charts

![](index_files/figure-html/unnamed-chunk-9-1.png)

---
## Practice

* In practice rmd file, add a new chuck of R code and read in some data
  * df <- read_csv ("https://t.ly/7hzC")
* Create quick plot and insert into document

---
## Tables

```r
table <- df |> 
  count (session_useful) |> 
  rename (`I found the session useful` = session_useful) |> 
  mutate (Percent = scales::percent (n / sum (n)) )

table
```

```
## # A tibble: 5 × 3
##   `I found the session useful`     n Percent
##   <fct>                        <int> <chr>  
## 1 1 - Not at All                   8 2.9%   
## 2 2                               25 9.1%   
## 3 3                               39 14.2%  
## 4 4                              119 43.3%  
## 5 5 - Significantly               84 30.5%
```

---
## Tables

```r
table |> 
  kable()
```

<table>
 <thead>
  <tr>
   <th style="text-align:left;"> I found the session useful </th>
   <th style="text-align:right;"> n </th>
   <th style="text-align:left;"> Percent </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> 1 - Not at All </td>
   <td style="text-align:right;"> 8 </td>
   <td style="text-align:left;"> 2.9% </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 2 </td>
   <td style="text-align:right;"> 25 </td>
   <td style="text-align:left;"> 9.1% </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 3 </td>
   <td style="text-align:right;"> 39 </td>
   <td style="text-align:left;"> 14.2% </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 4 </td>
   <td style="text-align:right;"> 119 </td>
   <td style="text-align:left;"> 43.3% </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 5 - Significantly </td>
   <td style="text-align:right;"> 84 </td>
   <td style="text-align:left;"> 30.5% </td>
  </tr>
</tbody>
</table>

---
## Tables: `kableExtra`

http://haozhu233.github.io/kableExtra/awesome_table_in_html.html

```r
table |> 
  kable() |> 
  kable_styling(position = "center", font_size = 25)
```

---
## Tables: `kableExtra`

```r
table |>
  kable(align = c ("lcc")) |> 
  kable_styling(font_size = 25) |> 
  column_spec(2:3, width = "8em")
```

---
## Tables: `kableExtra`

```r
table |>
  mutate (Percent = cell_spec (Percent, 
                               background = "#FA19C3"),
          n = ifelse (n > 40, 
                      cell_spec (n, color = "green"),
                      cell_spec (n, color = "red"))) |> 
  kable(escape = FALSE, 
        align = c ("lcc")) |> 
  kable_styling(font_size = 25) |> 
  column_spec(2:3, width = "8em")
```

---
## Tables: `kableExtra`

<table class="table" style="font-size: 25px; margin-left: auto; margin-right: auto;">
 <thead>
  <tr>
   <th style="text-align:left;"> I found the session useful </th>
   <th style="text-align:center;"> n </th>
   <th style="text-align:center;"> Percent </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> 1 - Not at All </td>
   <td style="text-align:center;width: 8em; "> <span style="     color: red !important;">8</span> </td>
   <td style="text-align:center;width: 8em; "> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #FA19C3 !important;">2.9%</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 2 </td>
   <td style="text-align:center;width: 8em; "> <span style="     color: red !important;">25</span> </td>
   <td style="text-align:center;width: 8em; "> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #FA19C3 !important;">9.1%</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 3 </td>
   <td style="text-align:center;width: 8em; "> <span style="     color: red !important;">39</span> </td>
   <td style="text-align:center;width: 8em; "> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #FA19C3 !important;">14.2%</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 4 </td>
   <td style="text-align:center;width: 8em; "> <span style="     color: green !important;">119</span> </td>
   <td style="text-align:center;width: 8em; "> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #FA19C3 !important;">43.3%</span> </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 5 - Significantly </td>
   <td style="text-align:center;width: 8em; "> <span style="     color: green !important;">84</span> </td>
   <td style="text-align:center;width: 8em; "> <span style="     border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #FA19C3 !important;">30.5%</span> </td>
  </tr>
</tbody>
</table>

---
## Tables

Other packages include:
- `flextable`
- `gt`
- `formattable`

---
## Practice

* In practice rmd file, add a new chuck of R code and insert table into document
* Add some custome formatting
  * https://bit.ly/kable_extra
  * https://bit.ly/flextable

---

## Split Columns

---

## Split Columns

---
## Split Columns

.pull-left[
The figure on the right shows Horsepower vs Miles per Gallon. 
]
.pull-right[
<img src = "images/plot.png"/>
]

---
## Multiple Reports - One File

```r
for (sch in unique(df$school)) {  
  rmarkdown::render("Advanced_PDF_Example.Rmd",  
                    output_file =  paste(sch, "_report.pdf", sep=''),   
                    output_dir = './reports/')  
}
```

---
## Practice

* Create custom report using multi-columns
* Try loop to create multiple reports

---
## Questions?