Research reporting systems

class: center, middle, inverse, title-slide

# Research reporting systems
### Jinliang Yang
### Feb. 27th, 2020

---

# How to present your results?

### Rmarkdown report

### Research presentation

### Research poster and paper

### Personal website

---

# How to present your results?

### Rmarkdown report
  - R Notebook

### Research presentation

### Research poster and paper

### Personal website

---

# R Markdown

R Markdown is a format for writing __reproducible__, __dynamic__ reports with R.
- We can use it to embed R (or python, bash, etc.) code and results into _slideshows_, _pdfs_, _html_ documents, _Word_ files and more.

### Workflow

1. __Open__: Open a file that uses the `.Rmd` extension. 
  - For example, `R Notebook`

2. __Write__: Write content with the easy to use R __Markdown syntax__.

3. __Embed__: Embed code that creates output to include in the report.

4. __Render__: Replace code with its output and transform the report into a slideshow, pdf, html or ms Word file.

---

#	Markdown Syntax

See here to find [Extended Markdown systax](https://www.markdownguide.org/cheat-sheet/)

---

# Example: selection

`\begin{align*}
q_1 & = \frac{pq(1-s_{12}) + q^2(1-s_{22})}{T} \\
 & = \frac{q(p -ps_{12} + q -qs_{22})}{1 - (p^2s_{11} + 2pqs_{12} + q^2s_{22})} \\
 & = \frac{q(1 -ps_{12} -qs_{22})}{1 - (p^2s_{11} + 2pqs_{12} + q^2s_{22})} \\
\end{align*}`

```r
Dq <- function(q, s11=0, s12=0, s22=0, n=10){
  
  out <- data.frame(n=0, q=q)
  # loop through n generations
  for (i in 1:n){
    p = 1 - q
    q <- (q*(1-p*s12 - q*s22))/(1- (p^2*s11 + 2*p*q*s12 + q^2*s22))
    tem <- data.frame(n=i, q= q)
    out <- rbind(out, tem)
  }
  return(out)
}
```

- We completely select against the __heterozygote `\(A_1A_2\)` with `\(s_{12}=1\)`__
- Selection coeffecients are `\(s_{11} = s_{22} =0\)` for `\(A_1A_1\)` and `\(A_2A_2\)` genotypes.

---

# About the YAML header

```
---
title: "Hello R Markdown"
author: "Awesome Me"
date: "2018-02-14"
output: html_document
---
```

YAML (YAML Ain’t Markup Language, https://en.wikipedia.org/wiki/YAML)
  - sometimes it is also called the YAML metadata or the YAML frontmatter.

### Warning!

__Indentation matters in YAML__, so do not forget to indent the sub-fields of a top field properly

---

# Embed Code

Use `knitr` syntax to embed R code into your report. 
- R will run the code and include the results when you render your report.

For more details visit [yihui's website](yihui.name/knitr/)

---

# How to present your results?

### Rmarkdown report

### Research presentation
 - xaringan Presentations

### Research poster and paper

### Personal website

---

# Get started with Xaringan presentations

First of all, you need to install the R package:

```r
# install from CRAN
install.packages('xaringan')

# or GitHub
devtools::install_github('yihui/xaringan')
```

If you use RStudio, it is easy to get started from the menu 
- `File -> New File -> R Markdown -> From Template -> Ninja Presentation`. 
- Press the Knit button to compile it, or use the RStudio addin `Infinite Moon Reader` to live preview the slides: 
  - every time you update and save the Rmd document, the slides will be automatically reloaded.

---

# How to present your results?

### Rmarkdown report
  - R Notebook

### Research presentation
 - xaringan Presentations

### Research poster and paper
  - LaTeX editor

### Personal website
  - Blogdown
  
---

# `Blogdown` for personal website

With `blogdown`, you can write a blog post or a general page in an Rmd document.

Because the website is generated from R Markdown, the content is more likely to be reproducible, and also easier to maintain.

### Get started

```r
# from CRAN
install.packages("blogdown")

# or the development version from GitHub
devtools::install_github("rstudio/blogdown")
```

The easiest way to get started with a blogdown-based website is to create a website project from RStudio: 
- `File -> New Project`

---

# Website

The first time when you create a new website, `blogdown` will do a series of things behind the scenes: 
- it downloads __[Hugo](https://gohugo.io/)__ (the default static site generator)
- creates a website skeleton, 
- installs a theme, 
- adds some example posts, 
- builds the site, 
- and serves it 
so that you can see the website in your browser (or RStudio Viewer if you are in RStudio).

It will not go through all these steps again the next time when you work on this website. All you need in the future is `blogdown::serve_site()`, or equivalently, the RStudio addin `Serve Site`.