jupyter R magics to python script

Question

How can I convert the jupyter R magics like %%R or %Rpush or %Rpull or the execution of an R function into a regular python script?

Do you want an automatic conversion? One possibility is to put all the %%R cells into a script and then use subprocess to call the script. This question suggests using rpy2 with r.source("script.R") — cd98
– cd98, Commented Oct 24, 2016 at 22:13
You mean like: stackoverflow.com/questions/6434569/… process = subprocess.Popen(['R', '--vanilla', '--args', '\\%s_DM_Instances_R.csv\\' % output_filename, '<', '/home/kevin/AV-labels/Results/R/hierarchical_clustering.R'], stdout=subprocess.PIPE, stdin=subprocess.PIPE, shell=True) process.communicate()#[0] is stdout but how whould %Rpush / %Rpull work? — Georg Heiler
– Georg Heiler, Commented Oct 25, 2016 at 5:48
In Jupyter I already have a single %%R function which takes the arguments via %Rpush and I get the result via %Rpull I just would like to put it into a "normal" python script without the jupyter magics dependencies. — Georg Heiler
– Georg Heiler, Commented Oct 25, 2016 at 5:49
And here r-bloggers.com/… system2 is used for the subprocess. Is this "required"? — Georg Heiler
– Georg Heiler, Commented Oct 25, 2016 at 5:53

Georg Heiler · Accepted Answer · 2016-10-27 12:16:08Z

0

The answer is partly in the comments above: http://rpy2.readthedocs.io/en/version_2.8.x/introduction.html#creating-rpy2-vectors here is a nice and longer explanation This is the solution to the last mentioned problem of implementing a %Rpush robjects.IntVector([1, 2, 3])

answered Oct 27, 2016 at 12:16

Georg Heiler

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