RMarkdown documents

Writing documents in RMarkdown

🔗 Lets start with some of my favourite essential resources

• R Markdown: The Definitive Guide by Yihui Xie, J. J. Allaire, Garrett Grolemund.
• R Markdown Cookbook by Yihui Xie and Christophe Dervieux
• Pimp by RMD: a few tips for R Markdown by Yan Holtz.
• Reference Guide
• R Markdown Cheat Sheet
• R Markdown formats - R for data science
• RMarkdown overview/references
• pagedown
• Creating Dynamic Documents with RMarkdown and Knitr
• Creating Dynamic Documents with RMarkdown and Knitr
• Pandoc markdown
• BIMS8382 Reproducible reporting with Rmarkdown
• Ulrik Lyngs - RMarkdown workshop 2019 day 1 slide
  • Github repo for workshop
• From raw data to paper and presentation, by Eva Mae Rey
• Steven V. Miller
  • article example
  • course website
  • RMarkdown CV,
  • RMarkdown syllabus
• Lucy McGown
  • website
  • disseration toolkit
• RMarkdown Template that Manages Academic Affiliations, by Lab-R-torian
• Robert Mitchell, GitHub repo, website

If are a R Markdown newbie I suggest starting at the official lessons on R Markdown by R Studio.

Here is a presentation I have presented in the past to give you a give overview of using RMarkdown

INSTALL Just like the rest of R packages, get started with R Markdown by executing the following from the console

install.packages("rmarkdown")

Create a new RMarkdown document by selecting File > New File > R Markdown... > Document > HTML > Open This will open the default RMarkdown document that will knit to html, however you can change to PDF, word etc.

Templates

To get the most out of RMarkdown there are a number of various templates to suit whatever document and style you need. Below are some links to get you started.

🔗 General links on RMarkdown templates

• Document templates
• Pandoc
• RMarkdown overview/references

Check out these examples here:

• https://robertmitchellv.com/index.html
• https://ulriklyngs.com/
• https://github.com/svmiller?tab=repositories
• https://github.com/ulyngs

Bookdown

• Document Templates
• Bookdown
• Oxforddown
• R Markdown for Scientists
• Latex line breaks and blank space overleaf
• knitr::kable and kableExtra
• kableExtra
• RMarkdown cookbook
• bookdown: Authoring Books and Technical Documents with R Markdown
• R Bookdownplus textbook
• pagedown
• Bookdownplus gallery

CV

vitae, Nick Strayer package based on pagedown pagedown CVs another example from pagedown another example from pagedown

Articles

rticles

Thesis

Write your thesis with ease using Thesisdown and Oxforddown. Some extra links here and here.

Websites

• blogdown
• hugo academic
• hugo academic
• hugo themes

Other themes

EpuRate

• Blog post by Dr. Jianghao Wang
• Rob Hyndman

Posters

A new R package to make posters by Brent Thorne called posterdown

install.packages("posterdown")

Gnatt chart

Make gnatt chart into easy to read format by reading in csv.

library(ggplot2)

Attaching package: 'ggplot2'

The following object is masked from 'package:crayon':

    %+%

library(readr)
# Load data
gnatt <-
  read_csv("gnatt.csv", col_types = cols(
    end = col_date(format = "%d/%m/%Y"),
    start = col_date(format = "%d/%m/%Y")
  ))

## Set factor level to order the activities on the plot

gnatt$chapter <- factor(gnatt$chapter)

plot_gnatt <- qplot(
  ymin = start,
  ymax = end,
  x = chapter,
  colour = activity,
  geom = "linerange",
  data = gnatt,
  size = I(5)
) +
  scale_colour_manual(values = c("red", "grey", "purple", "orange", "blue")) +
  coord_flip() +
  theme_bw() +
  theme(panel.grid = element_blank()) +
  xlab("") +
  ylab("") +
  ggtitle("Project planning")
plot_gnatt