1.1 R Packages for Basic R Installation or Update

For new installation, here is a list of most-used packages to install:

install.packages('xlsx')
install.packages('rmarkdown')
install.packages("tinytex")
# install TinyTeX (must-do-this-step)
tinytex::install_tinytex()  
install.packages('tidyverse')
install.packages('ggplot2')
#table creation with specific formatting
install.packages('kableExtra')
#for writing reproducible research paper in R Markdown
install.packages(c("stargazer","plotly","knitr","bookdown"))
#To import the SAS files
install.packages('haven')
install.packages('sas7bdat')
install.packages('HSAUR3')
# Activate the `sas7bdat` library
library(sas7bdat)
library(haven)
# Read in the SAS data
#mySASData <- read.sas7bdat("example.sas7bdat")
#data <- read_sas("C:/temp/yoursasdataset.sas7bdat")

Once in a while, update all the packages by calling update.packages().

1.2 Read SAS sas7bdat data into R

library(sas7bdat)
data <-read.sas7bdat("psu97ai.sas7bdat")
view(data)

library(haven)
data <- read_sas("C:/temp/yoursasdataset.sas7bdat")
View(data)

2.1 RMarkdown, Hugo, Netlify

You can easily create beautiful static website powered by RMarkdown developed by Yihui Xie, Hugo, Academic theme, and Netlify.

The first step is to install blogdown and Hugo. Open RStudio , installing the Blogdown and Hugo dependencies:

 install.packages("blogdown")
 blogdown::install_hugo(version = "0.60.1", force = TRUE)

The contents are created using RMarkdown with guidance from the Step-by-Step Instruction provided by ALISON PRESMANES HILL, “Blogdown: Creating Websites with R Markdown” and R Markdown: The Definitive Guide

Hugo has a variety of theme that you can choose from. For instance, Hugo-Academic is a very rich theme for the academics. A few advantages include:

• Latex math rendering via simply enabling it in config toml file.

  # In config\_default\param.toml
  # Enable global LaTeX math rendering?
  #   If false, you can enable it locally on a per page basis.
  math = true

• rich widget system for customization.

If you prefer a simple/minimal style, you can choose from the minimalist themes. This website is created and powered by Ezhil theme and hugo-xmin theme, both themes were minimal/simple styles.

Yihui Xie provided a step-by-step guide for the hugo-xmin theme in the book blogdown: Creating Websites with R Markdown. It is very useful to finish the Hugo chapter to get a better understanding of its structure, rules of overriding, tips to add functionalities to your website (e.g., add math, add highlight.js, add custom.css for codes).

Two most important folders related to website design are

• layouts
  • partials: header.html, footer.html
  • _default: list.html,single.html,terms.html
• static
  • css:custom.css, fonts.css, styles.css

Modify the folders above in your own website folder but not the exampleSite, as they will override the same folder/files in the theme folder. This also will make it easy to maintain, migrate, and upgrade.

Reference

• Yihui Xie, J. J. Allaire, Garrett Grolemund (2018). R Markdown: The Definitive Guide. Chapman & Hall/CRC. ISBN 9781138359338.
  
• Yihui Xie, Amber Thomas, Alison Presmanes Hill (2017). blogdown: Creating Websites with R Markdown. Chapman & Hall/CRC. ISBN 9780815363729.
• Yihui Xie (2016). bookdown: Authoring Books and Technical Documents with R Markdown. Chapman and Hall/CRC. ISBN 9781138700109

2.2 Blogdown & Hugo - Fix ToC (with Rmd)

The solution to fix Table of Contents (TOC) came from both Create Websites with RMarkdown and Fubits@GIT . In the yaml header of your Rmd file, specific the following:

-----
output: 
 blogdown::html_page:
  number_sections: true
  toc: true
  toc_depth: 3
  css: "/css/custom.css"
-----

Create and save the custom.css under the \static\css in the root directory. Using the css formating in link, Your custom.css should look like:

/* Add some Heading / Title before the TOC */
#TOC:before{
    content: "Table of Content";
    font-family: 'Lato', sans-serif!important;
    font-weight:400;
    font-size: 26px;
}

/* Numbering suffix in TOC */
.toc-section-number:after{
    content: ". "
}
/* Numbering suffix in Body/Content */
.header-section-number:after{
    content: ". "
}

3.1 Templates

3.2 YAML options

There are a lot of advanced setting in the YAML header. An example is provided below with some highlighted options:

• tex packages: header-includes:
• use bookdown::pdf_document2: keep_tex: true for pdf output creation.
  
• documentclass can be the built-in article or your own customized cls file (e.g., uofsthesis-cs.cls).
• page setup: geometry, fontsize, and linestretch
• bibliography: put your .bib file in the same directory with your article.
• citation style: csl. You can search and download/create one(e.g., ACM or IEEE) from zotero or Mendeley. Save it in the same directory with your article.
  • nocite: |@Lander14 to include references currently not cited in the article.

---
title: |
  | \vspace{1cm}\pagenumbering{gobble}This is my topic
  | A Literature Review \vspace{0.5cm}
author:  |
  | My Name
  | Department of Computer Science
date: |
  | 28 February, 2020
  |
abstract: this is my abstract
colorlinks: true
output: 
  bookdown::pdf_document2:
    toc: no
    keep_tex: true
geometry: [top=0.85in,left=1in,right=1in, footskip=0.40in]
fontsize: [10pt,letterpaper]
linestretch: 1.1
documentclass: article
header-includes:
   - \usepackage{dcolumn}
   - \usepackage{color}
   - \usepackage{floatrow}
   - \floatsetup[figure]{capposition=top}
   - \floatsetup[table]{capposition=top}
   - \floatplacement{figure}{H}
   - \floatplacement{table}{H}
   - \usepackage{booktabs}
   - \usepackage{longtable}
   - \usepackage{array}
   - \usepackage{multirow}
   - \usepackage{wrapfig}
   - \usepackage{float}
   - \usepackage{colortbl}
   - \usepackage{pdflscape}
   - \usepackage{tabu}
   - \usepackage{threeparttable}
   - \usepackage{threeparttablex}
   - \usepackage[normalem]{ulem}
   - \usepackage{makecell}
   - \usepackage[usenames,dvipsnames]{xcolor}
   - \usepackage[hang]{footmisc}
   - \renewcommand{\footnotesize}{\normalsize}
bibliography: references.bib
csl: transactions-on-management-information-systems.csl
suppress-bibliography: FALSE
always_allow_html: yes
link-citations: true
---

3.3 Tricks - citations in a table

Cross-referencing tables or figures in a Rmarkdown article are straightforward and can be found in Paul’s article and template. However, citations within a table is very tricky in the PDF/TEX environment. It is easy to get it working in the HTML environment, but not with pdf, pandoc, and latex.

• Pandoc Markdown supports a citation extension to the basic markup, like [@krycho].

• For citation in a table in a pdf output file. Rachael Lappan offered a working solution for it.

I had success with the bookdown text references - I’m not sure if you need to be making a bookdown book or if it will work with the bookdown package loaded. In my case, I defined the references first outside of a code block, e.g.

(ref:studies-table-ref1) Bogaert *et al.* (2011) [@BogaertVariabilityDiversityNasopharyngeal2011]

then added them to the table

studies.table$Reference <- c("(ref:studies-table-ref1)", "(ref:studies-table-ref2)", # etc

And kable interpreted them correctly.

4.1 save() and load() datasets in R

For big datasets, importing the data and doing manipulaiton, aggregation and selection could take several minutes (or even longer), you might not want to start from scrach everytime you are working with the data.

So, you hope you can save your dataset at a stage (e.g. pre-analyses). You can do that using the save() and load() functions in base-R.

• How to save and load datasets in R: an overview

4.2 How to knit a document without rerunnning code

Dynamic Documents with and knitr: knitr::options give you multiple options which allow you to knit a document without re-running or displaying the code.

Chunk options and package options can be found https://yihui.org/knitr/options/

A few highlights from the document:

• echo: (TRUE; logical or numeric) whether to include R source code in the output file
• eval: (TRUE; logical) whether to evaluate the code chunk
• collapse: (FALSE; logical) collapse all the source and output blocks from one code chunk into a single block
• include: (TRUE; logical) whether to include the chunk output in the final output document; if include=FALSE, nothing will be written into the output document, but the code is still evaluated and plot files are generated.