Rmarkdown: Difference between revisions
Line 331: | Line 331: | ||
* [https://experimentalbehaviour.wordpress.com/2019/03/28/using-rstudio-and-latex/ Using tikzdevice to insert R Graphs into LaTeX] | * [https://experimentalbehaviour.wordpress.com/2019/03/28/using-rstudio-and-latex/ Using tikzdevice to insert R Graphs into LaTeX] | ||
* [https://cran.r-project.org/web/packages/tikzDevice/index.html tikzDevice]: R Graphics Output in LaTeX Format | * [https://cran.r-project.org/web/packages/tikzDevice/index.html tikzDevice]: R Graphics Output in LaTeX Format | ||
== Landscape output == | |||
https://stackoverflow.com/questions/25849814/rstudio-rmarkdown-both-portrait-and-landscape-layout-in-a-single-pdf | |||
== Bibliographies == | == Bibliographies == |
Revision as of 09:47, 12 September 2019
Markdown language
According to wikipedia:
Markdown is a lightweight markup language, originally created by John Gruber with substantial contributions from Aaron Swartz, allowing people “to write using an easy-to-read, easy-to-write plain text format, then convert it to structurally valid XHTML (or HTML)”.
- Markup is a general term for content formatting - such as HTML - but markdown is a library that generates HTML markup.
- Nice summary from stackoverflow.com and more complete list from github.
- An example https://gist.github.com/jeromyanglim/2716336
- Convert mediawiki to markdown using online conversion tool from pandoc.
- R markdown file and use it in RStudio. Customizing Chunk Options can be found in knitr page and rpubs.com. For example, the following will hide the code and also hide any messages
{r eval=TRUE, echo=FALSE, message=FALSE}
Github markdown Readme.md
- https://help.github.com/en/categories/writing-on-github
- https://guides.github.com/features/mastering-markdown/
- https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet
- Online editor with preview https://jbt.github.io/markdown-editor/
- An example from pathwayHeatmap
How to nest code within a list using Markdown
https://meta.stackexchange.com/questions/3792/how-to-nest-code-within-a-list-using-markdown
Continuous publication
Open collaborative writing with Manubot Himmelstein et al 2019
Rmarkdown
- http://rmarkdown.rstudio.com/html_document_format.html
- R Markdown: Eight ways
- https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf
- https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf
- https://www.rstudio.com/wp-content/uploads/2016/03/rmarkdown-cheatsheet-2.0.pdf
- Chunk options http://kbroman.org/knitr_knutshell/pages/Rmarkdown.html
HTML5 slides examples
- http://yihui.name/slides/knitr-slides.html
- http://yihui.name/slides/2012-knitr-RStudio.html
- http://yihui.name/slides/2011-r-dev-lessons.html#slide1
- http://inundata.org/R_talks/BARUG/#intro
Software requirement
- Rstudio
- knitr, XML, RCurl (See omegahat or this internal link for installation on Ubuntu)
- pandoc package This is a command line tool. I am testing it on Windows 7.
Slide #22 gives an instruction to create
- regular html file by using RStudio -> Knit HTML button
- HTML5 slides by using pandoc from command line.
Files:
- Rcmd source: 009-slides.Rmd Note that IE 8 was not supported by github. For IE 9, be sure to turn off "Compatibility View".
- markdown output: 009-slides.md
- HTML output: 009-slides.html
We can create Rcmd source in Rstudio by File -> New -> R Markdown.
There are 4 ways to produce slides with pandoc
- S5
- DZSlides
- Slidy
- Slideous
Use the markdown file (md) and convert it with pandoc
pandoc -s -S -i -t dzslides --mathjax html5_slides.md -o html5_slides.html
If we are comfortable with HTML and CSS code, open the html file (generated by pandoc) and modify the CSS style at will.
Built-in examples from rmarkdown
# This is done on my ODroid xu4 running Ubuntu Mate 15.10 (Wily) # I used sudo apt-get install pandoc in shell # and install.packages("rmarkdown") in R 3.2.3 library(rmarkdown) rmarkdown::render("~/R/armv7l-unknown-linux-gnueabihf-library/3.2/rmarkdown/rmarkdown/templates/html_vignette/skeleton/skeleton.Rmd") # the output <skeleton.html> is located under the same dir as <skeleton.Rmd>
Note that the image files in the html are embedded Base64 images in the html file. See
- http://stackoverflow.com/questions/1207190/embedding-base64-images
- Data URI scheme
- http://www.r-bloggers.com/embed-images-in-rd-documents/
- How to not embed Base64 images in RMarkdown
- Upload plots as PNG file to your wordpress
Templates
- https://github.com/rstudio/rticles/tree/master/inst/rmarkdown/templates
- https://github.com/rstudio/rticles/blob/master/inst/rmarkdown/templates/jss_article/resources/template.tex
Knit button
- It calls rmarkdown::render()
- R Markdown = knitr + Pandoc
- rmarkdown::render () = knitr::knit() + a system() call to pandoc
Pandoc's Markdown
Originally Pandoc is for html.
Extensions
- YAML metadata
- Latex Math
- syntax highlight
- embed raw HTML/Latex (raw HTML only works for HTML output and raw Latex only for Latex/pdf output)
- tables
- footnotes
- citations
Types of output documents
- Latex/pdf, HTML, Word
- beamer, ioslides, Slidy, reval.js
- Ebooks
- ...
Some examples:
pandoc test.md -o test.html pandoc test.md -s --mathjax -o test.html pandoc test.md -o test.docx pandoc test.md -o test.pdf pandoc test.md --latex-engine=xlelatex -o test.pdf pandoc test.md -o test.epb
Check out ?rmarkdown::pandoc_convert()/
When you click the Knit button in RStudio, you will see the actual command that is executed.
Global options
Suppose I want to create a simple markdown only documentation without worrying about executing code, instead of adding eval = FALSE to each code chunks, I can insert the following between YAML header and the content. Even bash chunks will not be executed.
```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE, eval = FALSE) ```
Examples/gallery
Some examples of creating papers (with references) based on knitr can be found on the Papers and reports section of the knitr website.
- https://rmarkdown.rstudio.com/gallery.html
- https://github.com/EBI-predocs/knitr-example
- https://github.com/timchurches/meta-analyses
- http://www.gastonsanchez.com/depot/knitr-slides
- Reproducible Research: Write your Clinical Chemistry paper using R Markdown
Read the docs Sphinx theme and journal article formats
http://blog.rstudio.org/2016/03/21/r-markdown-custom-formats/
- rticles package
- rmdformats package
rmarkdown news
Useful tricks when including images in Rmarkdown documents
http://blog.revolutionanalytics.com/2017/06/rmarkdown-tricks.html
RMarkdown Template that Manages Academic Affiliations
RMarkdown Template that Manages Academic Affiliations
Converting Rmarkdown to F1000Research LaTeX Format
BiocWorkflowTools package and paper
Internal links
If my section header is written as "## my section Header". Then I can link to it by using "[linked phrase](#my-section-header)".
Note here
- Use one number sign (#) even it is a subsection
- Use the hyphen sign to connect the space character
- Use lower cases even the header contains capital letters
Colored text
Blue text . See How to apply color in Markdown?.
icons for rmarkdown
https://ropensci.org/technotes/2018/05/15/icon/
Reproducible data analysis
- http://blog.jom.link/implementation_basic_reproductible_workflow.html
- liftr package (John M. Chambers Statistical Software Award, 2018).
- Infrastructure and Tools for Teaching Computing Throughout the Statistical Curriculum Mine Çetinkaya-Rundel & Colin Rundel 2017
- R Markdown: 3 sources of reproducibility issues and options how to tackle them
Interactive document: Shiny
When I follow the direction to add the code to the end of this Rmd file, I see
- I can't run "Build" anymore. An error will come out: Error in numericInput("n", "How many cars?", 5) : could not find function "numericInput".
- After I click "Run Document", the Rmd file will be displayed in either RStudio or a regular browser using R's built-in web server (http://127.0.0.1:YYYY/XXX.Rmd).
Automatic document production with R
https://itsalocke.com/improving-automatic-document-production-with-r/
Documents with logos, watermarks, and corporate styles
http://ellisp.github.io/blog/2017/09/09/rmarkdown
rticles and pinp for articles
- https://cran.r-project.org/web/packages/rticles/index.html
- http://dirk.eddelbuettel.com/code/pinp.html
Gmisc: create Table 1 used in medical articles
https://cran.r-project.org/web/packages/Gmisc/index.html
Tips
- Create R Markdown reports and presentations even better with these 3 practical tips
- Live preview of R Markdown files with xaringan’s infinite_moon_reader(). The Ultimate Infinite Moon Reader for xaringan Slides.
- Creating beautiful, multi format reports directly from R scripts
- Advanced chunk options with useful effects
Cache
- Cache not work
- Examples
> system.time(rmarkdown::render("~/Downloads/tmp.Rmd")) # first time ... Output created: tmp.html user system elapsed 3.123 0.108 5.426 # It will create two directories: tmp_files, tmp_cache > system.time(rmarkdown::render("~/Downloads/tmp.Rmd")) # Second time ... Output created: tmp.html user system elapsed 0.239 0.019 0.317
RStudio
RStudio is the best editor.
Markdown has two drawbacks: 1. it does not support TOC natively. 2. RStudio cannot show headers in the editor.
Therefore, use rmarkdown format instead of markdown.
Writing a R book and self-publishing it in Amazon
Create professional reports from R scripts, with custom styles
How to create professional reports from R scripts, with custom styles
Publish R results
5 amazing free tools that can help with publishing R results and blogging
Scheduling R Markdown Reports via Email
http://www.analyticsforfun.com/2016/01/scheduling-r-markdown-reports-via-email.html
Create presentation file (beamer)
- http://rmarkdown.rstudio.com/beamer_presentation_format.html
- http://www.theresearchkitchen.com/archives/1017 (markdown and presentation files)
- http://rmarkdown.rstudio.com/
- Create Rmd file first in Rstudio by File -> R markdown. Select Presentation > choose pdf (beamer) as output format.
- Edit the template created by RStudio.
- Click 'Knit pdf' button (Ctrl+Shift+k) to create/display the pdf file.
An example of Rmd is
--- title: "My Example" author: You Know Me date: Dec 32, 2014 output: beamer_presentation --- ## R Markdown This is an R Markdown presentation. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>. When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. ## Slide with Bullets - Bullet 1 - Bullet 2 - Bullet 3. Mean is $\frac{1}{n} \sum_{i=1}^n x_i$. $$ \mu = \frac{1}{n} \sum_{i=1}^n x_i $$ ## New slide ![picture of BDGE](/home/brb/Pictures/BDGEFinished.png) ## Slide with R Code and Output ```{r} summary(cars) ``` ## Slide with Plot ```{r, echo=FALSE} plot(cars) ```
R notebook vs R markdown in RStudio
Difference between R MarkDown and R NoteBook
There is no coding difference. The difference is in the rendering. The file extension is the same.
R notebook
- It adds html_notebook in the output option in the header.
- You can then preview the rendering quickly without having to knit it (does not execute any of your R code chunks). If you manually 'Run' the chunks, the result will be shown up in preview.
- It also refreshes the preview every time you save.
- However in that preview you don't have the code output (no figures, no tables..)
- You can mix several output options in your header so that you can keep the preview and keep your knit options for export
- R Notebook is everything and above what R MarkDown is
Table creating packages
stargazer: Produces LaTeX code, HTML/CSS code and ASCII text for well-formatted tables that hold regression analysis results from several models side-by-side, as well as summary statistics
Graphics Output in LaTeX Format
- Using tikzdevice to insert R Graphs into LaTeX
- tikzDevice: R Graphics Output in LaTeX Format
Landscape output
Bibliographies
Bibliographies in RStudio Markdown are difficult – here’s how to make it easy
bookdown.org
The website is full of open-source books written with R markdown.
- Announce bookdown
- bookdown package: Authoring Books and Technical Documents with R Markdown. We can download bookdown-demo to write our book.
- Compile R for Data Science to a PDF
It is easy to download the book. Check the download icon on top (Toggle Sidebar, Search, Font settings, Edit, Download, Info).
To build the book, either use the "Build" button on the top right panel or use the command line
bookdown::render_book("index.Rmd", "bookdown::gitbook") bookdown::render_book("index.Rmd", "bookdown::pdf_book")
Figures in a bookdown are handled different from regular R markdown files. The full file path does not work. The "~/" or "../" symbol does not work. The symbolic link directories or files do not work. The only way it works is by creating a subdirectory under the bookdown index.Rmd file.
Also the way of including figures is different in R markdown and bookdown. In bookdown, we should follow this way. That is including knitr::include_graphics("images/myfile.png") in an R block. Recall that in R markdown file, we use ![](figures/myfile.png).
TexLive
TexLive can be installed by 2 ways
- sudo apt install texlive It includes tlmgr utility for package manager.
- Official website
texlive-latex-extra
https://packages.debian.org/sid/texlive-latex-extra
For example, framed and titling packages are included.
tlmgr - TeX Live package manager
https://www.tug.org/texlive/tlmgr.html
TinyTex
https://github.com/yihui/tinytex
Examples
- Tidy Text Mining with R by Julia Silge and David Robinson (one of many books hosted on BOOKDOWN website).
- Build 'R for Data Science by Garrett Grolemund, Hadley Wickham' 2019-0808
- Build gitbook is OK.
- Book will not compile for PDF. It shows an error about always_allow_html: yes.
- Run sudo apt install texlive-xetex on Ubuntu (See _output.yaml file). We need to use xelatex. If we change to use pdflatex, we will get an error Rendering of unicode characters fails.
- The pdf output _main.pdf is under _book/.
pkgdown: create a website for your package
- Creating websites in R Emily C. Zabor
- Tip: After creating an R project with <_site.yml> and <index.Rmd> files, we need to quit and open the R project again in order to see the "Build" tab. This can be confirmed by clicking Tools -> Project Options -> Build Tools. The 'Project build tools' should show "Website" (other choices are "(None)", "Package", "Makefile", "Custom"). See also the RStudio IDE section from blogdown: Creating Websites with R Markdown.
- R Markdown Websites
- Building a website with pkgdown: a short guide
- Integrating 'pkgdown' with Your Personal Website
- Introduction to pkgdown. The source code is an Rmd file.
Blogdown
- https://github.com/rstudio/blogdown
- https://bookdown.org/yihui/blogdown/
- BLOGDOWN TUTORIAL Peter's blog
- Customizing Hugo / Blogdown RSS Templates
- Setting up our blog with RStudio and blogdown I: Creating the blog
Posterdown
posterdown: Use RMarkdown to generate PDF Conference Posters via HTML or LaTeX
Latex tools
Mathpix Snip Take a screenshot of math and paste the LaTeX into your editor