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

STATS 220

R Markdown🧢

1 / 20

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
2 / 20
  • graphics for communication
  • keep learning communication
  • Rmd: a tool for integrating prose, code, and results
  • one md file for multiple documents

+

3 / 20

Rmd: glue 2 things together

Markdown .md

  • Created by John Gruber & Aaron Swartz in 2004
  • A lightweight markup language to add formatting elements to plain-text documents, contrasting to WYSIWYG
  • Portable, platform independent, everywhere (e.g. Piazza, but not Canvas 😠)

4 / 20
  • 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

Basic syntax

More on Markdown syntax

5 / 20
6 / 20

Create R Markdown .Rmd


---
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>.
7 / 20

YAML header

YAML is commonly used for configuration files, and starts and ends with ---

`r lubridate::today()`

⬆️ inline executable R code

  • one markdown file, many formats
    • pdf_document
    • xaringan::moon_reader

To compile to PDF, 

install.packages('tinytex')
tinytex::install_tinytex()
---
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>.
8 / 20

R chunk for global settings

```{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
---
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>.
9 / 20

Write in markdown


Weave together narrative text and code 

---
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>.
10 / 20

R chunk

  • mpg: unique chunk name
  • message: suppress message or not
library(tidyverse)
#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
#> βœ” ggplot2 3.3.3     βœ” purrr   0.3.4
#> βœ” tibble  3.1.1     βœ” dplyr   1.0.5
#> βœ” tidyr   1.1.3     βœ” stringr 1.4.0
#> βœ” readr   1.4.0     βœ” forcats 0.5.1
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> βœ– dplyr::filter() masks stats::filter()
#> βœ– dplyr::lag()    masks stats::lag()
---
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>.
11 / 20

Render



3 ways to render an .Rmd

  1. click
  2. shortcut: Ctrl/Cmd + Shift + K
  3. rmarkdown::render("demo.Rmd")

12 / 20
```{r scatterplot, fig.align = "center", fig.width = 4.5, fig.height = 4}
ggplot(gp, aes(gdpPercap, lifeExp)) +
  geom_point() + scale_x_log10()
```

13 / 20
```{r scatterplot, fig.align = "center", fig.width = 4.5, fig.height = 4}
ggplot(gp, aes(gdpPercap, lifeExp)) +
  geom_point() + scale_x_log10()
```

Chunk options

  • scatterplot gives the chunk a name.
  • fig.align: alignment of figures
  • fig.width/fig.height
  • other figure options

Good practice: naming every single chunk!

image credit: Maelle Salmon

14 / 20
```{r show-code, ref.label = "scatterplot", eval = FALSE}
```

Reuse chunks by reference

  • 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!

15 / 20
```{r lm, echo = FALSE, cache = TRUE}
fit <- lm(lifeExp ~ log10(gdpPercap), data = gp)
kable(coef(summary(fit)))
```

Chunk options

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

kable() generates a very simple HTML table. ➑️



Estimate Std. Error t value Pr(>|t|)
(Intercept) -9.100889 1.2276738 -7.413117 0
log10(gdpPercap) 19.353423 0.3425372 56.500206 0
16 / 20

Beyond : language engines

```{python hello}
# remotes::install_github("rstudio/reticulate")
x = "hello, python world!"
print(x.split(" "))
```
#> ['hello,', 'python', 'world!']
```{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
17 / 20

Beyond : language engines

```{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>
18 / 20

Beyond : language engines

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"
19 / 20

Reading

20 / 20

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
2 / 20
  • graphics for communication
  • keep learning communication
  • Rmd: a tool for integrating prose, code, and results
  • one md file for multiple documents
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