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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>MAT381E-Week 1: Introduction to Data Science</title>
<meta charset="utf-8" />
<meta name="author" content="Gül İnan" />
<meta name="date" content="2021-10-11" />
<script src="intro_rmarkdown_files/header-attrs-2.11/header-attrs.js"></script>
<link href="intro_rmarkdown_files/remark-css-0.0.1/default.css" rel="stylesheet" />
<link rel="stylesheet" href="xaringan-themer.css" type="text/css" />
</head>
<body>
<textarea id="source">
class: left, middle, my-title, title-slide
# MAT381E-Week 1: Introduction to Data Science
### Gül İnan
### Department of Mathematics<br/>Istanbul Technical University
### October 11, 2021
---
class: center, middle
# Introduction to R Markdown
<img src="https://bookdown.org/yihui/rmarkdown/images/hex-rmarkdown.png" width="30%" style="display: block; margin: auto;" />
---
# What is R Markdown?
- In the world of **reproducible research**, we want other researchers to easily reproduce what we did in our analysis so that they can be certain that we analyzed our data properly.
- `R Markdown` allows us to **create documents** that serve as a neat record of our analysis and it presents `R` code alongside its output (graphs, tables, etc.) with external text, equations, data tables, links, and images to explain it.
- `R Markdown` is **a reproducible and dynamic notebook**.
---
class: center, middle
<iframe width="669" height="502" src="https://player.vimeo.com/video/178485416" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen data-external="1"></iframe>
[R Markdown video](https://player.vimeo.com/video/178485416).
---
- `R Markdown` actually uses [Markdown](https://daringfireball.net/projects/markdown/) syntax.
- [Markdown](https://daringfireball.net/projects/markdown/) is a very simple **`markup` language** which provides methods for creating documents with headers, texts, images, links etc. from plain text files, while keeping the original plain text file easy to read.
- `Markdown` documents can be **converted to many other file types** like .html or .pdf to display the headers, texts, images etc..
- In a similar fashion, `R Markdown` is a language that allows you to embed `R` code directly into a document to present its outputs (graphs, tables, etc.) accompanied by text, equations, data tables, figures, links, and images via [Markdown](https://daringfireball.net/projects/markdown/) syntax.
- An `R Markdown` file has the `.Rmd` file suffix. Once it is created, an `.Rmd` file can then be **rendered into** a PDF (.pdf), Microsoft Word (.doc), HTML (html), or GitHub (.md) documents, and a range of other formats.
---
# Download R Markdown
- We first need the `rmarkdown package` on [CRAN](https://cran.r-project.org/web/packages/rmarkdown/index.html)
to get `R Markdown` be working in `RStudio`.
--
- Wee need to run the following commands in `RStudio`:
```r
install.packages("rmarkdown")
library(rmarkdown)
```
---
# Create an R Markdown file
.pull-left[
- To **create a new R Markdown file** (`.Rmd`) in `RStudio`, go to menu bar across the top of the screen
and select `File -> New File -> R Markdown`.
]
--
.pull-right[
<img src="images/rmarkdown1.png" width="80%" style="display: block; margin: auto;" />
]
---
<style type="text/css">
.pull-left {
float: left;
width: 35%;
}
.pull-right {
float: right;
width: 65%;
}
</style>
.pull-left[
.left[ - Select the document type you need.
- For now we **will focus on** a `.html` document, which can be easily converted to other file types later.]
]
--
.pull-right[
<img src="images/rmarkdown2.png" width="85%" style="display: block; margin: auto;" />
]
--
- Give it an **informative title** such as "Deneme" for this trial.
- Accept the default Author or edit if you wish.
---
<style type="text/css">
.pull-left {
float: left;
width: 25%;
}
.pull-right {
float: right;
width: 75%;
}
</style>
.pull-left[
- Go to menu bar across the top of the screen
and select `File -> Save as` and **save this document as deneme** to a reasonable filename and location.
- Click on “Knit HTML” button at the top of `RStudio` script pane or click `File > Knit Document` at menu bar.
See what appears:
]
--
.pull-right[
<img src="images/rmarkdown4.png" width="200%" style="display: block; margin: auto;" />
]
--
- Also look at the file browser. You should see the `R Markdown` document, i.e. `deneme.Rmd` and the resulting HTML `deneme.html`.
---
# Content structure
<style type="text/css">
.pull-left {
float: left;
width: 25%;
}
.pull-right {
float: right;
width: 75%;
}
</style>
.pull-left[
- The newly created `.Rmd` file can have **three** types of text in general:
- YAML metadata
- Text
- `R` Code chunks
]
--
.pull-right[
<img src="images/rmarkdown3.png" width="150%" style="display: block; margin: auto;" />
]
---
# YAML metadata
- The first is the **YAML section** containing configurations for the file.
- This section looks like this:
```
---
title: "Deneme"
author: "Gul Inan"
date: "10/9/2021"
output: html_document
---
```
- Feel free to change the title and author names and see what results in your rendered report.
---
- You can stamp the **current time** on your report by doing so:
```r
---
title: "Deneme"
author: "Gül İnan"
*date: "`r format(Sys.Date(), '%B %e, %Y')`"
output: html_document
---
#more at https://statistics.berkeley.edu/computing/faqs/dates-and-times-r
```
--
<img src="images/rmarkdown5.png" width="70%" style="display: block; margin: auto;" />
---
<style type="text/css">
.pull-left {
float: left;
width: 70%;
}
.pull-right {
float: right;
width: 30%;
}
</style>
# Text
- Here we present a few commonly used features in `R Markdown`.
- Feel free to try them out yourself.
.pull-left[
- Code:
```markdown
Plain text.
End a line with two spaces to start a new paragraph.
*italics* and _italics_
**bold** and __bold__
$R^2$
~~strikethrough~~
inline equation: $A = \pi*r^{2}$
End a line with two spaces to start a new paragraph.
```
]
--
.pull-right[
- Output:
Plain text.
End a line with two spaces to start a new paragraph.
*italics* and _italics_
**bold** and __bold__
`\(R^2\)`
~~strikethrough~~
inline equation: `\(A = \pi*r^{2}\)`
]
--
---
<style type="text/css">
.pull-left {
float: left;
width: 50%;
}
.pull-right {
float: right;
width: 50%;
}
</style>
# Headers
.pull-left[
- Code:
```{markdown
# Header 1
## Header 2
### Header 3
#### Header 4
```
]
--
.pull-right[
- Output:
# Header 1
## Header 2
### Header 3
#### Header 4
]
--
- Note that head sizes and colors will be default ones in your document.
---
<style type="text/css">
.pull-left {
float: left;
width: 50%;
}
.pull-right {
float: right;
width: 50%;
}
</style>
# Unordered Lists
.pull-left[
- Code:
```{markdown
- Fruits
- apples
- bananas
- grapes
- Vegetables
- carrots
- broccoli
```
]
--
.pull-right[
Output:
- Fruits
- apples
- bananas
- Vegetables
- carrots
- broccoli
]
---
<style type="text/css">
.pull-left {
float: left;
width: 50%;
}
.pull-right {
float: right;
width: 50%;
}
</style>
# Ordered Lists
.pull-left[
- Code:
```{markdown
scary (ordered list)
1. ocelots
1. bears
1. tigers
Not scary (ordered list)
1. elephants
2. monkeys
3. rabbits
```
]
--
.pull-right[
Output:
scary
1. ocelots
1. bears
1. tigers
not scary
1. elephants
2. monkeys
3. rabbits
]
---
# Link
- Code:
```markdown
This is a link to [GitHub](https://github.com/).
```
--
- Output:
This is a link to [GitHub](https://github.com/).
---
# Image
- Code:
```markdown
```
--
- Output:
---
# R Code
- `R` code can be **directly embedded into** an `.Rmd` file and will be executed during rendering.
- The **result of the code** would be **printed** into resulting report.
## Inline R code in a sentence
- Surround code with back ticks and r such as ` `r ` and end it with ` ` `.
- `R` replaces inline code with its results.
- Code:
```markdown
Two plus two equals `r 2 + 2`.
```
--
- Output:
Two plus two equals 4.
---
## R code chunks
- Start a `R` code chunk with ` ```{r} ` and end it with ` ``` `.
- Code:
```{markdown
```r
x <- mean(rnorm(100))
x
```
```
--
- Output:
```r
x <- mean(rnorm(100))
x
```
```
#> [1] 0.1034298
```
--
- It prints both `R` code and result.
---
## Display options for R code chunks
- There are a large number of chunk options in **knitr** documented at https://yihui.name/knitr/options.
- Most common two of them are below:
- `eval`: Whether to evaluate a code chunk (if you do not want to evaluate the R code then ` ```{r, eval=FALSE} ` and end it with ` ``` `).
- `echo`: Whether to echo (print) the source code in the output document (if you do not want to print the output then` ```{r, echo=FALSE} ` and end it with ` ``` `).
---
# Figures
- Code:
`````{markdown
```r
plot(cars)
```
`````
---
- Output:
```r
plot(cars)
```
<!-- -->
---
# Figures
- **Figures** that is not generated from R code can be imported by the `knitr::include_graphics()` function, which provides more control over the attributes of the image than the Markdown syntax of `` (e.g., you can specify the image width via out.width).
- Code:
`````{markdown
```r
knitr::include_graphics("https://cdnuploads.aa.com.tr/uploads/Contents/2019/04/25/thumbs_b_c_fcbe8545d3b85ab8d3ad9f6adff42d49.jpg")
```
`````
---
- Output:
```r
knitr::include_graphics("https://cdnuploads.aa.com.tr/uploads/Contents/2019/04/25/thumbs_b_c_fcbe8545d3b85ab8d3ad9f6adff42d49.jpg")
```
<img src="https://cdnuploads.aa.com.tr/uploads/Contents/2019/04/25/thumbs_b_c_fcbe8545d3b85ab8d3ad9f6adff42d49.jpg" width="50%" style="display: block; margin: auto;" />
---
# A short summary to `knitr options`
- [Default-knitr-options](https://www.r-bloggers.com/2021/03/default-knitr-options-and-hooks/).
---
# Creating .pdf files in R Markdown
- `R Studio` uses `LaTeX` to make `.pdf` documents.
- If you are using `Windows`, go to the [MikTeX](https://miktex.org/download) and download the appropriate “Complete MikTeX Installer” for your system, either 32-bit or 64-bit.
- If you are using a `Mac`, go to the [MacTeX](https://tug.org/mactex/mactex-download.html) and download the “MacTeX.pkg”.
- Running these installers will install a version of `LaTeX` onto your system, which `R` will then be able to call on to compile the `.pdf`.
- To compile a `.pdf` document instead of a `.html` document, change `output: from html_document` to `pdf_document`.
---
# Final remarks
- In a nutshell:
<img src="images/rmarkdown6.png" width="80%" style="display: block; margin: auto;" />
--
- More on `Markdown syntax`:
- [Markdown](https://www.markdownguide.org/basic-syntax/).
- More on `R Markdown`:
- [Djnavarro](https://slides.djnavarro.net/starting-rmarkdown/#95),
- [Garrick](https://www.garrickadenbuie.com/talk/toronto-data-workshop/),
- [The R Markdown Cheat Sheet](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf), and
- [The R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/).
---
# Attributions
- All images used in this slide are taken from the web.
- Some part of this lecture note is developed through following sources:
- [The R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/),
- [STAT540](https://github.com/STAT540-UBC/STAT540-UBC.github.io/blob/master//seminars/seminars_winter_2021/seminar2a/sm2a_intro_to_markdown.Rmd), and
- [Our Coding Club](https://ourcodingclub.github.io/tutorials/rmarkdown/).
</textarea>
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