I wrote some R scripts in ipython notebook followed by tutorial
Here is one example of R script in .ipynb
In python, we can simply run .ipynb script in the terminal by runipy
Is any way I could also run R .ipynb scripts in the terminal as well?
Eg: runipy_R R_script.ipynb in terminal
Related
I am using Pycharm 2021.2.3 pro.
Is it possible to open a .py file as a jupyter notebook from within pycharm?
In the classical jupyter notebook, it is possible to open a .py file as a notebook and work with it like with a classical .ipynb (adding markdown etc.).
This allows to work on the full notebook without worrying about cells ordering like with a classical python script. When the script is ready, it is then possible to switch to the notebook view with its nice presentation features.
we did this when creating dash apps, you make the .py file upload and refer to it by way of importing as we do with regular python libraries
Let's say that you have two windows open in VS Code, one is a Jupyter notebook, and the other is the Python interactive window. Both are running the same kernel. Is there a way to link these two windows, so when cells are run in the notebook, the interactive window will know about the resulting variables?
I'm aware that VS Code has a Python code format that can be linked to the interactive window, and that Jupyter notebooks can be converted into this format. Is it possible to directly link a Jupyter notebook to the interactive window without first doing this conversion?
With JupyterLab the is accomplished with the New Console for Notebook command.
I'm trying to use the terminal to run a jupyter notebook (kernel: Julia v1.6.2), which contains generated using Plots.jl, before uploading the notebook to github for viewing on nbviewer.com.
Following this question:
How to run an .ipynb Jupyter Notebook from terminal?
I have been using nbconvert as follows:
jupyter nbconvert --execute --to notebook --inplace
This runs the notebook (if you tweak the timeout limits), however, it does not display plots when using Plots.jl, even when I explicitly call display(plot()) at the end of a cell.
Does anyone have any idea how notebooks can be run remotely in such a manner that plots will be generated and displayed, particularly when using Julia?
I managed to generate Plots.jl plots by getting from IJulia the same configuration it uses to run notebooks (this is probably the most sure way when you have many Pyhtons etc.).
using Conda, IJulia
Conda.add("nbconvert") # I made sure nbconvert is installed
mycmd = IJulia.find_jupyter_subcommand("nbconvert")
append!(mycmd.exec, ["--ExecutePreprocessor.timeout=600","--to", "notebook" ,"--execute", "note1.ipynb"])
Now mycmd has exactly the same environment as seen by IJulia so we can do run(mycmd):
julia> run(mycmd)
[NbConvertApp] Converting notebook note1.ipynb to notebook
Starting kernel event loops.
[NbConvertApp] Writing 23722 bytes to note1.nbconvert.ipynb
The outcome got saved to note1.nbconvert.ipynb, I open it with nteract to show that graphs actually got generated:
Launch notebook with using IJulia and notebook() in the REPL
I have some R code to update a database stored in update_db.ipynb. When I try to %run update_db.ipynb from a jupyter notebook with a python kernel, I get an error
File "<ipython-input-8-815efb9473c5>", line 14
city_weather <- function(start,end,airports){
^
SyntaxError: invalid syntax
Looks like it thinks that update_db.ipynb is written in python. Can I specify which kernel to use when I use %run?
Your error is not due to the kernel selected. Your command %run is made to run python only, but it has to be a script, not a notebook. You can check in details the ipython magic commands
For your use case I would suggest to install both python and R kernel in jupyter. Then you can use the magic cell command %%R to select to run R kernel for a cell inside the python notebook. Source :this great article on jupyter - tip 19
Other solution is to put your R code in an R script, and then execute it from a jupyter notebook. For this you can run a bash command from a jupyter notebook that will execute the script
!R path/to/script.r
Using putty, I installed the terminal environment. Here I want to run an R program which may produce some graph or plots. What are the commands to run such a R program? What are the commands to create the directory and see the output of such a R program?
You can run your R script in batch mode.
R CMD BATCH your_script.R your_scripts_output.txt
I'm not sure that you can view plots in terminal mode. However you can save the plots to an image (png, pdf, ...)