m-jahn / lab-notebook

Digital Laboratory Notebook with R markdown

lab-notebook

Digital Laboratory Notebook with R markdown

Overview

This repository contains a laboratory notebook in form of an R markdown document (*.Rmd).

All care was taken to guarantee scientific accuracy and adhere to good scientific practice in terms of statistics, reproducibility and code documentation. Please report any errors by filing a github issue for this repository, or contact [e-mail].

How to view notebooks

Data and notebook(s) collected in this repository are self-contained and executable. The code and the documentation are part of one and the same R markdown document for each notebook. The notebook(s) can be downloaded and executed from the /notebook sub-folder. To simply view the rendered notebook follow the links to the *.html reports under Notebooks.

To download the repository on your local drive use git clone in a (linux) terminal:

cd /your-target-folder
git clone https://github.com/m-jahn/lab-notebook

Open a notebook with Rstudio and execute code (chunks) with the Run button. Alternatively, open an interactive R session and render the R markdown document:

require(rmarkdown)
rmarkdown::render("lab-notebook.Rmd")

Data

• data/lab-notebook.RData - data used in the notebook in RData format

Libraries

• lattice
• latticeExtra
• latticetools from github
• tidyverse (metapackage)

Notebooks

• Rendered lab notebook as HTML web page