I followed the post, Installing an R kernel for IPython/jupyter notebook 3 on OSX, to install jupyter with python3 and R kernels in my iMac.

I have elementaryOS on my Macbook Pro and also want to have jupyter on it. The installation process is quite similar.

Install Jupyter

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sudo apt-get install python3-pip
sudo pip3 install jupyter

Then we can use the following command to start jupyter:

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ipython notebook

Install IRkernel

To compile IRkernel, we should firstly have zmq lib installed.

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sudo apt-get install libzmq3-dev python-zmq

In R, run the following command to install IRkernel:

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install.packages(c('rzmq','repr','IRkernel','IRdisplay'),
                  repos = c('http://irkernel.github.io/',     
                  getOption('repos')),
                  type = 'source')
IRkernel::installspec()

Now we can use R in jupyter. Inline image is a great feature especially for demonstration.

With many phylogenetic packages available in R and my package ggtree, R in jupyter can be a great environment for phylogenetics.

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