STATS 220

# STATS 220
## R Markdown🧶

---

.pull-left[
.center[
[<img src="https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/rmarkdown.png" width="26%">](https://rmarkdown.rstudio.com)
[<img src="https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/blogdown.png" width="26%">](https://bookdown.org/yihui/blogdown/)

[<img src="https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/bookdown.png" width="26%">](http://bookdown.org)
[<img src="https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/xaringan.png" width="26%">](http://slides.yihui.org/xaringan/)
]
]
.pull-right[
## .center[Dynamic documents]

* Combine code, rendered output (such as figures), and prose
* Reproduce your analyses
* Collaborate and share code with others
* Communicate your results with others
]

???

* graphics for communication
* keep learning communication
* Rmd: a tool for integrating prose, code, and results
* one md file for multiple documents

---

# .large[.large[.large[]]] + .large[.large[.large[.blue[]]]]

???

Rmd: glue 2 things together

---

## Markdown .blue[] `.md`

* Created by [John Gruber](https://daringfireball.net/projects/markdown/) & [Aaron Swartz](http://www.aaronsw.com) in 2004
* A lightweight .brown[markup language] to add formatting elements to plain-text documents, contrasting to WYSIWYG
* Portable, platform independent, everywhere (e.g. Piazza, but not Canvas 😠)

???

* md originated back to 2004, but emerged around 2010
* aaron, reddit, a loss
* The course website: write in md, and render in html by hugo
* commonmark: it's one of markdown flavours, richer features. e.g. github
* learned it in 5 mins, unlike R

---

## .blue[] Basic syntax

More on [Markdown syntax](https://www.markdownguide.org/basic-syntax/)

---

background-image: url(https://raw.githubusercontent.com/allisonhorst/stats-illustrations/master/rstats-blanks/rmarkdown_wizards_blank.png)
background-size: 100% 100%

---

.pull-left[
## Create R Markdown `.Rmd`
 
.center[
<img src="img/click-rmd.png" width="20%">
<img src="img/new-rmd.png" width="60%">]
]
.pull-right[
````markdown
---
title: "STATS220 R Markdown demo"
author: "Earo Wang"
date: "`r lubridate::today()`"
output: html_document
---

```{r setup, include = FALSE}
library(knitr)
opts_knit$set(root.dir = here::here())
opts_chunk$set(echo = TRUE)
```

## R Markdown

You can embed an R code chunk like this:

```{r gapminder, message = FALSE}
library(tidyverse)
gp <- read_rds("data/gapminder.rds")
gp
```

See <http://rmarkdown.rstudio.com>.
````
]

---

.pull-left[
## YAML header
YAML is commonly used for configuration files, and starts and ends with
`---`

````markdown
`r lubridate::today()`
````
⬆️ inline executable R code
* one markdown file, many formats
  + `pdf_document`
  + `xaringan::moon_reader`

.small[
To compile to PDF, 
```r
install.packages('tinytex')
tinytex::install_tinytex()
```
]
]
.pull-right[
````markdown
*---
*title: "STATS220 R Markdown demo"
*author: "Earo Wang"
*date: "`r lubridate::today()`"
*output: html_document
*---

```{r setup, include = FALSE}
library(knitr)
opts_knit$set(root.dir = here::here())
opts_chunk$set(echo = TRUE)
```

## R Markdown

You can embed an R code chunk like this:

```{r gapminder, message = FALSE}
library(tidyverse)
gp <- read_rds("data/gapminder.rds")
gp
```

See <http://rmarkdown.rstudio.com>.
````
]

---

.pull-left[
## R chunk for global settings
````markdown
```{r setup, include = FALSE}
library(knitr)
opts_knit$set(root.dir = here::here())
opts_chunk$set(echo = TRUE)
```
````
⬆️ executable R chunk
* `r`: language engine
* `setup`: unique chunk name
* `include`: include chunk output or not
* `echo`: display source code or not
]
.pull-right[
````markdown
---
title: "STATS220 R Markdown demo"
author: "Earo Wang"
date: "`r lubridate::today()`"
output: html_document
---

*```{r setup, include = FALSE}
*library(knitr)
*opts_knit$set(root.dir = here::here())
*opts_chunk$set(echo = TRUE)
*```

## R Markdown

You can embed an R code chunk like this:

```{r gapminder, message = FALSE}
library(tidyverse)
gp <- read_rds("data/gapminder.rds")
gp
```

See <http://rmarkdown.rstudio.com>.
````
]

---

.pull-left[
## Write in markdown
 
.center[Weave together narrative text and code]
 
 
.center[<img src="https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/knitr.png" width="240px">]
]
.pull-right[
````markdown
---
title: "STATS220 R Markdown demo"
author: "Earo Wang"
date: "`r lubridate::today()`"
output: html_document
---

```{r setup, include = FALSE}
library(knitr)
opts_knit$set(root.dir = here::here())
opts_chunk$set(echo = TRUE)
```

*## R Markdown

*You can embed an R code chunk like this:

```{r gapminder, message = FALSE}
library(tidyverse)
gp <- read_rds("data/gapminder.rds")
gp
```

*See <http://rmarkdown.rstudio.com>.
````
]

---

```r
library(tidyverse)
```

```
#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
```

```
#> ✔ ggplot2 3.3.3     ✔ purrr   0.3.4
#> ✔ tibble  3.1.1     ✔ dplyr   1.0.5
#> ✔ tidyr   1.1.3     ✔ stringr 1.4.0
#> ✔ readr   1.4.0     ✔ forcats 0.5.1
```

```
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> ✖ dplyr::filter() masks stats::filter()
#> ✖ dplyr::lag()    masks stats::lag()
```
]
.pull-right[
````markdown
---
title: "STATS220 R Markdown demo"
author: "Earo Wang"
date: "`r lubridate::today()`"
output: html_document
---

```{r setup, include = FALSE}
library(knitr)
opts_knit$set(root.dir = here::here())
opts_chunk$set(echo = TRUE)
```

## R Markdown

You can embed an R code chunk like this:

*```{r gapminder, message = FALSE}
*library(tidyverse)
*gp <- read_rds("data/gapminder.rds")
*gp
*```

See <http://rmarkdown.rstudio.com>.
````
]

---

1. click <img src="img/knit.png" width="20%">
2. shortcut: Ctrl/Cmd + Shift + K
3. `rmarkdown::render("demo.Rmd")`
]
.pull-right[
<img src="img/demo-rmd-render.png", style = "box-shadow: 3px 5px 3px 1px #00000080;", width="100%">
]

---

````r
```{r scatterplot, fig.align = "center", fig.width = 4.5, fig.height = 4}
ggplot(gp, aes(gdpPercap, lifeExp)) +
  geom_point() + scale_x_log10()
```
````

---

````r
```{r scatterplot, fig.align = "center", fig.width = 4.5, fig.height = 4}
ggplot(gp, aes(gdpPercap, lifeExp)) +
  geom_point() + scale_x_log10()
```
````

* `scatterplot` gives the chunk a name.
* `fig.align`: alignment of figures
* `fig.width`/`fig.height`
* [other figure options](https://yihui.org/knitr/options/#plots)

**Good practice**: naming every single chunk!
]
.pull-right[
<img src="https://itsalocke.com/blog/img/namer-oh-no.png" width="100%">
<img src="https://itsalocke.com/blog/img/namer-yaaasss.png" width="100%">

---

````r
```{r show-code, ref.label = "scatterplot", eval = FALSE}
```
````

* `ref.label`: labels of the chunks from which the code of the current chunk is inherited
* `eval`: evaluate the code chunk

**Good practice**: naming every single chunk!
]
.pull-right[
<img src="figure/right-plot-1.png" width="480" style="display: block; margin: auto;" />
]

---

````r
```{r lm, echo = FALSE, cache = TRUE}
fit <- lm(lifeExp ~ log10(gdpPercap), data = gp)
kable(coef(summary(fit)))
```
````

* `echo`: overwrites the global setting
* `cache`: evaluate once and skip for the future

`kable()` generates a very simple HTML table. ➡️
]
.pull-right[

|                 |  Estimate| Std. Error|   t value| Pr(>&#124;t&#124;)|
|:----------------|---------:|----------:|---------:|------------------:|
|(Intercept)      | -9.100889|  1.2276738| -7.413117|                  0|
|log10(gdpPercap) | 19.353423|  0.3425372| 56.500206|                  0|
]

---

## Beyond : language engines

````py
*```{python hello}
# remotes::install_github("rstudio/reticulate")
x = "hello, python world!"
print(x.split(" "))
```
````

```
#> ['hello,', 'python', 'world!']
```

<hr>

````sh
*```{sh head}
head -4 data/pisa/pisa-student.csv
```
````

```
#> year,country,school_id,student_id,mother_educ,father_educ,gender,computer,internet,math,read,science,stu_wgt,desk,room,dishwasher,television,computer_n,car,book,wealth,escs
#> 2000,ALB,1001,1,NA,NA,female,NA,no,324.35,397.87,345.66,2.16,yes,no,no,1,3+,1,11-50,-0.6,0.10575582991490981
#> 2000,ALB,1001,3,NA,NA,female,NA,no,NA,368.41,385.83,2.16,yes,yes,no,2,0,0,1-10,-1.84,-1.424044581128788
#> 2000,ALB,1001,6,NA,NA,male,NA,no,NA,294.17,327.94,2.16,yes,yes,no,2,0,0,1-10,-1.46,-1.306683855365612
```

---

## Beyond : language engines

````r
```{r db}
library(RSQLite)
db <- dbConnect(SQLite(), dbname = "data/pisa/pisa-student.db")
```

*```{sql query, connection = db, output.var = "pisa18"}
SELECT * FROM pisa WHERE year = 2018
```
````

```
#> # A tibble: 612,004 x 22
#> year country school_id student_id mother_educ father_educ
#> <dbl> <chr> <chr> <chr> <chr> <chr> 
#> 1 2018 ALB 800002 800251 ISCED 3A ISCED 3A 
#> 2 2018 ALB 800002 800402 ISCED 2 ISCED 2 
#> 3 2018 ALB 800002 801902 ISCED 2 ISCED 2 
#> 4 2018 ALB 800002 803546 ISCED 2 ISCED 2 
#> 5 2018 ALB 800002 804776 ISCED 2 ISCED 3A 
#> 6 2018 ALB 800002 804825 ISCED 2 ISCED 2 
#> # … with 611,998 more rows, and 16 more variables:
#> # gender <chr>, computer <chr>, internet <chr>,
#> # math <dbl>, read <dbl>, science <dbl>, stu_wgt <dbl>,
#> # desk <chr>, room <chr>, dishwasher <chr>,
#> # television <chr>, computer_n <chr>, car <chr>,
#> # book <chr>, wealth <dbl>, escs <dbl>
```

---

## Beyond : language engines

```r
names(knitr::knit_engines$get())
```

```
#>  [1] "awk"       "bash"      "coffee"    "gawk"      "groovy"    "haskell"  
#>  [7] "lein"      "mysql"     "node"      "octave"    "perl"      "psql"     
#> [13] "Rscript"   "ruby"      "sas"       "scala"     "sed"       "sh"       
#> [19] "stata"     "zsh"       "highlight" "Rcpp"      "tikz"      "dot"      
#> [25] "c"         "cc"        "fortran"   "fortran95" "asy"       "cat"      
#> [31] "asis"      "stan"      "block"     "block2"    "js"        "css"      
#> [37] "sql"       "go"        "python"    "julia"     "sass"      "scss"     
#> [43] "R"         "bslib"
```

---

## Reading

.pull-left[
.center[[<img src="https://d33wubrfki0l68.cloudfront.net/b88ef926a004b0fce72b2526b0b5c4413666a4cb/24a30/cover.png" height="520px">](https://r4ds.had.co.nz)]
]
.pull-right[
* [R Markdown](https://r4ds.had.co.nz/r-markdown.html)
* [R Markdown formats](https://r4ds.had.co.nz/r-markdown-formats.html)
* [R Markdown cheat sheet](https://www.rstudio.com/wp-content/uploads/2016/03/rmarkdown-cheatsheet-2.0.pdf?_ga=2.253787336.159731575.1620189500-118347454.1620189500)
* [R Markdown reference guide](https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf?_ga=2.253787336.159731575.1620189500-118347454.1620189500)
]