Reporting with R Markdown

.title[
# Reporting with R Markdown
]
.author[
### Meenakshi Kushwaha
]
.institute[
### ILK Labs
]
.date[
### 15th September 2022
]

---

![](img/rmd.jpeg)
.footnote[Artwork by Allison Horst]

---

# What is R Markdown?
### A place for your code, notes, and output to live together

- **.Rmd files** 
  - Develop code and ideas side by side
  - Run code in parts or as a whole
  
- **Dynamic Documents** 
  - Knit together plots, tables, and results with narrative text
  - Ouptut in variety of formats - HTML, PDF, word, ppt, etc.
  
- **Reprodcible Research**
  - Any can read or run your code

- **Collaboration**
  - Use for collaborating with other data scientists (including future you!)
  - Share your conclusions, and how you reached them (i.e. the code).

???
R Markdown provides an unified authoring framework for data science, combining your code, its results, and your prose commentary. R Markdown documents are fully reproducible and support dozens of output formats, like PDFs, Word files, slideshows, and more.

---
# Let's make a simple report
1. Click File -> New File --> R Markdown
2. Give a title to your document eg. Summary Project Report  
3. Knit your document 
4. Change the file name to something meaningful

--
![](img/demo.png)

---
class:middle, center
# Demo

---

---
# YAML
.left-column[
- Specifies document basics
  - title
  - date
  - author
  - output format

- Can also include
  - theme
  - toc
]
--
.right-column[
![](img/rmd_output.png)
]
---

# the `setup` chunk

- Specify universal rules for all other chunks
  - eg. show/hide code
  - can over-ride in invidual chunks
  
- Could be used to load libraries, datasets that you don't want to explicitly show in the report

---

# Caching

Useful when some chunks take long to compute
- set `cache = TRUE`

R will skip the execution of this code chunk if it has been executed before and nothing in the code chunk has changed since then.

!! Be careful, when using this option. R will not know if your original files have changed i.e. files or data on which the chunk depends. Learn about specifying dependincies [here] (https://bookdown.org/yihui/rmarkdown-cookbook/cache.html)

---
# Markdown text

## Header 2

### Header 3

* Item 1
* Item 2

]
.panel[.panel-name[Type this]

`*italic*`  
`**bold**`

`# Header 1`

`## Header 2`

`### Header 3`

`* Item 1`  
`* Item 2`

]
]

# Behind the scenes
![](img/rmd_work.png)
.footnote[Artwork by Allison Horst]
---

---
# theme
Following are built in themes
- "cerulean", "journal", "flatly", "readable", "spacelab", "united", and "cosmo"

Other packages for additional themes
 - Example - [`prettydoc`](https://www.datadreaming.org/post/r-markdown-theme-gallery/)
--

### YAML example

```r
---
title: "My First RMarkdown Report"
author: "Meenakshi Kushwaha"
date: "2022-09-13"
output: 
  html_document: 
*    theme: flatly
---
```

---
# table of contents

- `toc: true` to include a table of contents (TOC)
- `toc_depth: n` to specify that the lowest level of headings to add
- `toc_float: true` so the toc floats and is visible as you scroll through a long document

### YAML example

```r
---
title: "My First RMarkdown Report"
author: "Meenakshi Kushwaha"
date: "2022-09-13"
output: 
  html_document:
    toc: true
    toc_depth: 2
---  
```

---
# Code-chunk options
Customize your code chumk output
- show/hide code
- show/hide output
- show/hide warnings and messages

![](img/chunk-options.png)

---

# Figures

]
.panel[.panel-name[Type this]

`![](img/cute_kitten.jpeg)`

]
]

.footnote[Image by Sergey Semin on Unsplash]
---
# Tables
Tables can be included with the `kable()` function of the `knitr` package

```r
library(gapminder)
knitr::kable(head(gapminder), 
             align = "c",
             caption = "First few rows of Gapminder data set")
```

Table: First few rows of Gapminder data set

|   country   | continent | year | lifeExp |   pop    | gdpPercap |
|:-----------:|:---------:|:----:|:-------:|:--------:|:---------:|
| Afghanistan |   Asia    | 1952 | 28.801  | 8425333  | 779.4453  |
| Afghanistan |   Asia    | 1957 | 30.332  | 9240934  | 820.8530  |
| Afghanistan |   Asia    | 1962 | 31.997  | 10267083 | 853.1007  |
| Afghanistan |   Asia    | 1967 | 34.020  | 11537966 | 836.1971  |
| Afghanistan |   Asia    | 1972 | 36.088  | 13079460 | 739.9811  |
| Afghanistan |   Asia    | 1977 | 38.438  | 14880372 | 786.1134  |

---
# Mathematical Expressions

Type this
```
$$
E = mc^2  
$$
```
to get
$$
E = mc^2  
$$ 
Type this
```
$$
Y = X_1 + X_2
$$
```
to get
$$
Y = X_1 + X_2
$$
.footnote[See [source](https://rmd4sci.njtierney.com/math) for more notations]
---
# Hyperlinks
.panelset[
.panel[.panel-name[To get this]
Learn more [here](https://www.gapminder.org/data/documentation/)

]
.panel[.panel-name[Type this]

`Learn more [here](https://www.gapminder.org/data/documentation/)`

]
]

---
# In line text
.panelset[
.panel[.panel-name[To get this]
The dataset has 1704 rows and 6 columns.

]
.panel[.panel-name[Type this]

```r
The dataset has `r nrow(gapminder)` rows and `r ncol(gapminder)` columns.  
```

]
]

---
# Getting Help

- R Markdown Cheat Sheet
  - Help > Cheatsheets > R Markdown Cheat Sheet,

- R Markdown Reference Guide
   - Help > Cheatsheets > R Markdown Reference Guide.

---
class:middle, center
# Advanced RMarkdown options

---
# Using `glue` package
For more complex inline code

.panelset[
.panel[.panel-name[To get this]
-  Africa has 624 countries  
-  Americas has 300 countries  
-  Asia has 396 countries  
-  Europe has 360 countries  
-  Oceania has 24 countries

]
.panel[.panel-name[Type this]

```r
library(glue)
gapminder %>% 
  count(continent) %>% 
  glue_data("-  {continent} has {n} countries") %>% 
  glue_collapse(sep = " \ \n")
```

]
]

---
# Creating  multiple reports using parameters 
R Markdown documents can include one or more parameters whose values can be set when you render the report.

- Used to re-render the same report with distinct values for various key inputs, for example:

- Running a report specific to a department or geographic region.

- Running a report that covers a specific period in time.

- Parameters are declared using the `params` field within the YAML header

- You can also change the parameters using the `Knit` dropwdown button
  - Click on `Knit with Parameters` button

---
class: middle, center
# Demo

---

# Other output formats
![](img/rmd_more.png)
.footnote[Artwork by Allison Horst]
---

# What else can I do with R Markdown
- [Slides](https://rmarkdown.rstudio.com/lesson-11.html)
  - Using `xaringan` [package](https://bookdown.org/yihui/rmarkdown/xaringan.html)
- [Websites](https://rmarkdown.rstudio.com/lesson-13.html)
  - Example - our course website
- Interactive Dashboards
  - Using `shiny` [package](https://shiny.rstudio.com/)
  - See [examples](https://shiny.rstudio.com/gallery/)
- E-Books 
  - Using `bookdown` [package](https://bookdown.org/yihui/rmarkdown/)

---

# Resources
- [ReferenceR Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/)
- R for Data Science, [Chapters 27-30](https://r4ds.had.co.nz/)

---
#Thank You!