Jupyter Lab:

nb-py-quarcs: Python computational notebooks to explore and learn

Online Analysis Environment

The notebooks can be executed online at GESIS Notebooks. Just copy the URL of this repository and paste it on the BINDER form

• To open a virtual Jupyter lab session, make sure you change you click on File and change it to URL. Then, write lab in the field URL to open (optional). Finally, click on launch. Alternatively, you could just click on this Binder badge:

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Terms of Use

Materials are licensed under CC BY-SA 4.0.

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Conda environment with environment.yml

A Binder-compatible repo with an environment.yml file.

Access this Binder by clicking the blue badge above or at the following URL:

http://mybinder.org/v2/gh/binder-examples/conda_environment/master?filepath=index.ipynb

Notes

The environment.yml file should list all Python libraries on which your notebooks depend, specified as though they were created using the following conda commands:

conda activate example-environment
conda env export --from-history -f environment.yml

Note that the only libraries available to you will be the ones specified in the environment.yml, so be sure to include everything that you need!

Also note that if you skip the --from-history, conda may include OS-specific packages in environment.yml, which you would have to manually prune from environment.yml. For example, confirmed macOS-specific packages that should be removed are:

• libcxxabi=4.0.1
• appnope=0.1.0
• libgfortran=3.0.1
• libcxx=4.0.1

R environment with a runtime.txt file

Jupyter+R:

RStudio:

RShiny:

Binder supports using R and RStudio, with libraries pinned to a specific snapshot on MRAN.

Note: We recommend to follow r-conda instead. Especially if you want to use a specific version of R or need faster build times.

Note: Another alternative is to use the holepunch package for R.

Requirements and suggestions

You need to have a runtime.txt file that is formatted like:

r-<YYYY>-<MM>-<DD>

where YYYY-MM-DD is a snapshot at MRAN that will be used for installing libraries. In this line, you can request a specific version of R. To do this list the version between the 'r' and the year, as in r-3.6-2019-09-24. Right now the default version of R is 3.6.

We recommend using https://github.com/binder-examples/r-conda for faster installs than using a install.R

To install R libraries (or packages) you can add an install.R file that specifies one library to install per line.

Both RStudio and IRKernel are installed by default, so you can use either the Jupyter notebook interface or the RStudio interface.

This repository also contains an example of a Shiny app.

URL addresses for RStudio and Shiny environments

The Binder repository can be used to allow anyone to access an RStudio environment containing our code and data right in their web browser. It also allows hosting a Shiny app. For those purposes, we have to append a bit of text to the URL of our Binder repository, which we can find out at mybinder.org when we enter the URL of our original repository from GitHub or Figshare, etc.

• For the RStudio environment, we must add the following at the end of the URL: ?urlpath=rstudio

  • Example: http://mybinder.org/v2/gh/binder-examples/r/master?urlpath=rstudio

• For the Shiny app environment, we must add the following at the end of the URL: ?urlpath=shiny. In this case, we also have to note that if the Shiny app files are located in a folder, this folder should be specified in the URL, after a slash. We would then also have to put in a trailing slash at the end of the URL, and to avoid spaces in the name of the repository, placing instead a hyphen (the reason is that spaces are converted to %20).

  • Example: http://mybinder.org/v2/gh/binder-examples/r/master?urlpath=shiny/bus-dashboard/