---
title: R Markdown
author: Abhijit Dasgupta
date: "BIOF 339"
---
```{r setup, include=FALSE, message = F, warning = F}
knitr::opts_chunk$set(echo = FALSE, message = F, warning = F, comment="",
cache = T)
library(tidyverse)
library(here)
library(fs)
library(readxl)
library(magick)
library(xaringanExtra)
use_extra_styles(hover_code_line=TRUE, mute_unhighlighted_code = TRUE)
use_tile_view()
use_share_again()
style_share_again(share_buttons = 'none')
imgdir <- here('slides','lectures','img')
datadir <- here('slides/lectures/data')
source(here('lib/R/update_header.R'))
```
```{r, echo=FALSE, results='asis'}
update_header()
```
---
class: inverse, center, middle
# R Markdown basics
---
```{r, echo=FALSE, results='asis'}
update_header('## A mashup of Markdown and R')
```
---
- Markdown is a text markup format that was meant to make writing HTML easier
- Convert Markdown to HTML, with simple text markup being converted to HTML code
```{r}
plt <- image_read('../img/md.png')
plt
```
---
.pull-left[
Add pieces of R code
Fence it inside a *code chunk*
]
.pull-right[
````markdown
Looking at the *penguins* data.
`r ''```{r}
library(tidyverse)
library(palmerpenguins)
penguins %>% group_by(species) %>%
summarise(across(bill_length_mm:body_mass_g,
~mean(., na.rm=T)))
```
````
]
---
.pull-left[
Add pieces of R code
Fence it inside a *code chunk*
Add options
]
.pull-right[
````markdown
Looking at the *penguins* data.
`r ''```{r, echo=FALSE, message=FALSE, warning=FALSE}
library(tidyverse)
library(palmerpenguins)
penguins %>% group_by(species) %>%
summarise(across(bill_length_mm:body_mass_g,
~mean(., na.rm=T)))
```
````
]
---
.pull-left[
Add pieces of R code
Fence it inside a *code chunk*
Add options
Name the chunk
]
.pull-right[
````markdown
Looking at the *penguins* data.
`r ''```{r means, echo=FALSE, message=FALSE, warning=FALSE}
library(tidyverse)
library(palmerpenguins)
penguins %>% group_by(species) %>%
summarise(across(bill_length_mm:body_mass_g,
~mean(., na.rm=T)))
```
````
]
---
You can set the chunk options for the entire document at the beginning of the document.
````markdown
`r ''```{r setup, include=FALSE}
knitr::opts_chunk()$set(echo = FALSE, eval = TRUE,
message=FALSE, warning=FALSE, comment = "")
```
````
The option `include=FALSE` is equivalent to .acidinline[`echo = FALSE, eval = TRUE, results = 'hide'`]
.footnote[Details of these options are [here](https://yihui.org/knitr/options/#chunk-options)]
---
.pull-left[
The **rmarkdown** package leverages the [pandoc](https://pandoc.org) universal document converter
to allow a R Markdown document to be converted to several different formats, as we'll see later.
To specify this, and some metadata, R Markdown uses a YAML header at the very beginning
of the R Markdown document
The YAML section begins and ends with three dashes
.footnote[YAML is another kind of structured text format.]
]
.pull-right[
```markdown
---
title: "My report"
author: "Abhijit"
date: '`r format(Sys.Date(), "%B %d, %Y")`'
output: html_document
---
```
]
---
```{r, echo=FALSE, results='asis'}
update_header()
```
---
---
class: inverse, center, middle
# Rich R Markdown Documents
---
```{r, echo=FALSE, results='asis'}
update_header('## What can you create from R Markdown?')
```
---
+ Documents
- HTML
- Microsoft Word
- PDF (requires [LaTeX](http://www.latex-project.org))
+ Presentations
- HTML (`ioslides`, `revealjs`, `xaringan`)
- PDF (`beamer`)
- PowerPoint
---
+ Interactive documents
- The [`htmlwidgets`](https://www.htmlwidgets.org/) meta-package
+ Dashboards
- The [`flexdashboard`](https://rmarkdown.rstudio.com/flexdashboard/) package
+ Books
- The [`bookdown`](https://bookdown.org/) package
+ Websites & Blogs
- [R Markdown](https://rmarkdown.rstudio.com/lesson-13.html)
- [`blogdown`](https://bookdown.org/yihui/blogdown/) package
---
+ Resumes/CVs
- The [`vitae`](https://pkg.mitchelloharawild.com/vitae/) package
+ Research papers
- include citations
- include appropriate formatting
- probably need [LaTeX](http://www.latex-project.org)
--
### See the [RMarkdown gallery](https://rmarkdown.rstudio.com/gallery.html)
---
```{r, echo=FALSE, results='asis'}
update_header()
```
---
The basic differences are in the front-matter at the top of your RMarkdown
document
### HTML document
```
---
title: "Lectures"
date: "Fall 2018"
output: html_document
---
```
--
### Word document
```
---
title: "Lectures"
date: "Fall 2018"
output: word_document
---
```
---
## Presentations
.pull-left[
### ioslides
```
---
title: "Lecture 2: \nData Frame, Matrix, List"
author: "Abhijit Dasgupta"
date: "September 19, 2018"
output: ioslides_presentation
---
```
### revealjs
```
---
title: "Lecture 2: \nData Frame, Matrix, List"
author: "Abhijit Dasgupta"
date: "September 19, 2018"
output:
revealjs::revealjs_presentation:
theme: default
highlight: default
transition: fade
slide_level: 1
---
```
]
.pull-right[
### Slides delimited by markdown sections
```
# Slide 1
This is my first slide
# Slide 2
This is my second slide
```
]
---
## Presentations
.pull-left[
### Powerpoint
```
---
title: "Lecture 2: \nData Frame, Matrix, List"
author: "Abhijit Dasgupta"
date: "September 19, 2018"
output: powerpoint_presentation
---
```
]
.pull-right[
### Slides delimited by markdown sections
```
# Slide 1
This is my first slide
# Slide 2
This is my second slide
```
]
---
## Presentations
.pull-left[
### xaringan
```
---
title: "Lecture 2: \nData Frame, Matrix, List"
author: "Abhijit Dasgupta"
date: "September 19, 2018"
output:
xaringan::moon_reader:
css: [default, './robot.css', './robot-fonts.css']
#css: [default, metropolis, metropolis-fonts]
nature:
ratio: '16:9'
highlightLanguage: R
countIncrementalSlides: false
highlightStyle: zenburn
highlightLines: true
---
```
]
.pull-right[
### Slides delimited by `---`
```
---
# Slide 1
This is my first slide
---
# Slide 2
This is my second slide
```
]
---
## R Markdown Templates
.pull-left[
- Several packages provide RMarkdown templates
- You can include citations
- EndNote, MEDLINE, RIS, BibTeX formats for references
- See https://rmarkdown.rstudio.com/
authoring_bibliographies_and_citations.html
]
.pull-right[
```{r 10-BestPractice-24}
knitr::include_graphics('../img/templates.png')
```
]
---
## You can even use other coding languages in R Markdown!!
The **knitr** package allows for [many](https://bookdown.org/yihui/rmarkdown/language-engines.html) other computer languages to be run within a R Markdown document.
Of particular note are Python and Julia, which can be interfaced from R using the **reticulate** and **JuliaCall** packages, respectively
.left-column30[
This is an example of a Python manual written using R Markdown
]
.right-column30[
```{r}
plt <- image_read('../img/biof085.png')
plt
```
]
---
class: middle, center, inverse
# Creating documents from R scripts
---
```{r, echo=FALSE, results='asis'}
update_header('## Creating documents from R scripts')
```
---
A typical R workflow is to do your analyses using R scripts (`.R`) and then,
at the end, copy-and-paste code to create a R Markdown file for reporting.
.acidinline[This is actually not necessary]
You can actually create R Markdown-based documents .heatinline[directly from R scripts]
This is done using `rmarkdown::render` applied to a R script formatted in a particular way, as we will see.
This can also be done in RStudio using the shortcut Ctrl/Cmd-Shift-K or the small binder icon.
---
.pull-left[
```{r purl1, echo=T, eval=F}
library(palmerpenguins)
library(tidyverse)
library(janitor)
tabyl(penguins, species)
```
]
.pull-right[
```{r, ref.label='purl1', echo=F, eval=T }
```
]
---
.pull-left[
```{r, echo=T, eval=F}
#' # Exploring the penguins dataset
#'
#' The following is relative frequencies of the different species of penguins
library(palmerpenguins)
library(tidyverse)
library(janitor)
tabyl(penguins, species)
```
You write lines starting with `#'`, i.e, hash and then single-quote
These are interpreted as Markdown lines
]
.pull-right[
```{r, echo=FALSE}
plt <- image_read('../img/spin1.png')
image_scale(plt, '400')
```
]
---
.pull-left[
```{r, eval=F, echo=T}
#' # Exploring the penguins dataset
#'
#' The following is relative frequencies of the different species of penguins
#+ message=FALSE, warning=FALSE #<<
library(palmerpenguins)
library(tidyverse)
library(janitor)
tabyl(penguins, species)
```
You can then add code chunk options by starting a line with `#+`.
]
.pull-right[
```{r}
plt <- image_read('../img/spin2.png')
image_scale(plt, '400')
```
]
---
.pull-left[
```{r, eval=F, echo=T}
#' # Exploring the penguins dataset
#'
#' The following is relative frequencies of the different species of penguins
#+ message=FALSE, warning=FALSE
library(palmerpenguins)
library(tidyverse)
library(janitor)
tabyl(penguins, species) %>%
adorn_pct_formatting() %>%
knitr::kable() #<<
```
Format the output for HTML
]
.pull-right[
```{r}
plt <- image_read('../img/spin4.png')
image_scale(plt, '400')
```
]
---
.pull-left[
```{r, eval=F, echo=T}
#' ---
#' title: Exploring penguins
#' author: Abhijit
#' date: "`r format(Sys.Date(), '%B %d, %Y')`"
#' output:
#' html_document:
#' theme: cerulean
#' ---
#'
#' # Exploring the penguins dataset
#'
#' The following is relative frequencies of the different species of penguins
#+ message=FALSE, warning=FALSE
library(palmerpenguins)
library(tidyverse)
library(janitor)
tabyl(penguins, species) %>%
adorn_pct_formatting() %>%
knitr::kable()
```
Add header information, starting lines with `#'`, since these lines need to be text in the corresponding Rmd file
]
.pull-right[
```{r}
plt <- image_read('../img/spin5.png')
image_scale(plt, '400')
```
]
---
.pull-left[
```{r, eval=F, echo=T}
#' ---
#' title: Exploring penguins
#' author: Abhijit
#' date: "`r format(Sys.Date(), '%B %d, %Y')`"
#' output:
#' html_document:
#' theme: cerulean
#' ---
#'
#' # Exploring the penguins dataset
#'
#' The following is relative frequencies of the different species of penguins
#+ message=FALSE, warning=FALSE, echo=FALSE #<<
library(palmerpenguins)
library(tidyverse)
library(janitor)
tabyl(penguins, species) %>%
adorn_pct_formatting() %>%
knitr::kable()
```
Remove code to clean up HTML
]
.pull-right[
```{r}
plt <- image_read('../img/spin6.png')
image_scale(plt, '400')
```
]
---
## Resources