R kernel in Jupyter notebook 3
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
sudo apt-get install python3-pip
sudo pip3 install jupyter
Then we can use the following command to start jupyter:
ipython notebook
Install IRkernel
To compile IRkernel, we should firstly have zmq lib installed.
sudo apt-get install libzmq3-dev python-zmq
In R, run the following command to install IRkernel:
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.