An R function library to create scientific figures and reports easily. Update v2.5.0

What is _MarkdownReports_?

MarkdownReports is a set of R functions that allows you to generate precise figures easily, and create clean reports about what you just discovered with your analysis script. It helps you to:

1. Create scientifically accurate figures and save them automatically as vector graphic (.pdf), that you can use from presentation to posters anywhere.
2. Note down your findings easily in a clear and nicely formatted way, parsed from your variables into english sentences.
3. Link & display your figures automatically inside your report, right there where they are needed.
4. Version your findings, annotating which parameters were used to reach certain results.
5. Share your report with others via email, Github or a personal website.

Why did I make it & why you might like it too?

I do exploratory data analysis as a daily routine, and I have constant interaction with all sorts of people: supervisors, collaborators, colleagues, etc.

I often have to...

1. ...write emails summarizing the results (text & figures) of the last few days.
2. ...find results from a couple of month back, with all tiny details (parameters used, etc).
3. ...assemble each step I did that day into a logical story line, that others can understand at first glimpse, e.g.: I observed X; I controlled for Y; Hypothesized explanation A; Falsified it; Came up with explanation B; Tested & proven it...

For all of the above, my solution is MarkdownReports. I think its better than other solutions I found. Many of those like to combine source code with results, and many are too complex to use. Most of people I interact with are not interested in the source code, but are very keen on seeing my results from all possible angles and are asking detailed questions about the analysis.

Where does _MarkdownReports_ stand out?

• Pure markdown output, simple and elegant layout.
• Handy integration of text with figures (linked to an external file & displayed: makes manual tailoring easy)
• Easy generation of precise figures (axis labels, etc) that are saved as a vector graphic (pdf), making it scalable for presentations, posters, etc
• The report file is automatically named after the R-script, so that it is linked to the source code that generated it.
• A timestamped subdirectory is created that you can backup once satisfied with your results.
• The generated report is easy to share on a GitHub wiki.
• It natively exports tables from R to Markdown
• It is all achieved in ~ 400 lines of well commented code.

Installation

Install directly from GitHub via devtools with one R command:

devtools::install_github(repo = "vertesy/MarkdownReports/MarkdownReports")

...then simply load the package:

require("MarkdownReports")

Alternatively, you simply source it from the web.
This way function help will not work, and you will have no local copy of the code on your hard drive.

source("https://raw.githubusercontent.com/vertesy/MarkdownReports/master/MarkdownReports/R/MarkdownReports.R")

Discover 4 Yourself!

• See it working: Check out a dummy R script
  and the MarkDown report
  it generates inside this GitHub Repo.
• Check out the wiki
  • See how easy it is to make customized figures
  • See the list of functions in the package.
• Browse the code of the functions.

Learn about the markdown format

• See the power and simplicity of markdown format explained on Github
• Checkout some cool markdown editors, like MOU, or markdownpad.
• See how these markdown reports are rendered:

Cite it via its Digital Object Identifier (DOI):

**MarkdownReports** is a project of @vertesy.