Daily lab notebook with R


(This tutorial and the associated R project are only the first drafts that will be implemented in the future)

Using the R package bookdown I built a small project compiling daily logs of my work together with description and schedule of my projects. The lab book was built using the bookdown R package (Xie, 2021) to easily integrate daily notes, figures and code chunks. Using blogdown allows for a high flexibility in the format, and working with several collaborators once the notebook is uploaded on GitHub (or GitLab).

Here how it looks like: example of output


I. Initiate your notebook

i. Clone the full repository on your local machine

Code available on GitHub

ii. Open notebook.RProj in RStudio

The general information of the notebook can be defined in index.Rmd, for instance, the cover page, the output format …

iii. Start your Notebook

  1. Write the introduction for your Notebook in 00_intro.Rmd
  2. Describe your projects in 01_Project.Rmd
  3. Plan your year in Planning.csv
  4. Prepare your ToDo list in 02_ToDo.Rmd

Now your Notebook is ready to be used

II. Add daily records

i. Open notebook.RProj in RStudio

ii. Start a new log using the Terminal

In the Terminal write ./start.sh and return. A new log will be created and will open in your RStudio script panel.

iii. Fill the log

The logs are coded in Markdown language, remove the comments and start filling your log

  • ## are header levels for the months

  • ### are headers for the days

  • #### can be used for any desired subsection

  • Use “@” to insert bibliographical references (tutorial)

All possible options can be found in the R Markdown Cookbook (Xie and Dervieux 2020)

iv. Correct previous log

Use ./open.sh in the Terminal to open and correct previous logs

v. Compiling your Lab Book

In the Terminal write ./stop.sh , your notebook will be compiler and saved in the _book folder


  • RStudio implemented a visual editor for Rmarkdown which allows you to write your logs like a Word document (tutorial)

  • I would recommend to start the Notebook every year as the number of logs and figures in the folder can increase quite quickly.

  • Label your figures like “yyyy-mm-dd-title.png” if you want to have a chance to find them again later.

  • Details and additional bookdown options on bookdown.org.


Yihui Xie (2020). bookdown: Authoring Books and Technical Documents with R Markdown. R package version 0.21.

Yihui Xie and Christophe Dervieux and Emily Riederer (2020). R Markdown Cookbook. Chapman and Hall/CRC. ISBN 9780367563837. URL: https://bookdown.org/yihui/rmarkdown-cookbook

Rémy Beugnon
Rémy Beugnon

I am a PosDoc between iDiv, the CEFE and LIM working vegetation diversity effects on soil microclimate.