[R] Run a Python code from R

[Nelly Reduan]

Hello,



Thanks a lot for your answers. Finally, I'm using the function system2() to run the python script. However, I don't know how to define a list of numeric values in the character vector of arguments for the function system2 (i.e., in “args” of the function system2() ) ?



In the Python script, the list of numeric values is defined as follows:

import sys

import nlmpy



weights = sys.argv[1] ## where weights = [0.5, 0.5]



outputNLM = nlmpy.classifyArray(…, weights)



print outputNLM



In the script R, how can I specify the argument weights = [0.5, 0.5] to run the Python script ?



Thanks a lot for your time.

Have a nice day

Nell


________________________________
De : Robert Baer <rbaer at atsu.edu>
Envoyé : samedi 19 novembre 2016 16:05:13
À : David Winsemius; Nelly Reduan
Cc : r-help at r-project.org
Objet : Re: [R] Run a Python code from R


>From https://www.r-bloggers.com/rpithon-vs-rpython/

<https://www.r-bloggers.com/rpithon-vs-rpython/>"Similar to rPython, the rPithon package (http://rpithon.r-forge.r-project.org) allows users to execute Python code from R and exchange the data between Python and R. However, the underlying mechanisms between these two packages are fundamentally different. Wihle rPithon communicates with Python from R through pipes, rPython accomplishes the same task with json. A major advantage of rPithon over rPython is that multiple Python processes can be started within a R session. However, rPithon is not very robust while exchanging large data objects between R and Python."

On 11/16/2016 7:10 PM, David Winsemius wrote:




On Nov 16, 2016, at 4:53 PM, Nelly Reduan <nell.redu at hotmail.fr><mailto:nell.redu at hotmail.fr> wrote:

[[elided Hotmail spam]]


I 'm trying to use the package "rPithon" but I obtain this error message:



Are you sure you are not just misspelling rPython? If that's not the issue than you need to say where you got rPithon,


>From https://www.r-bloggers.com/rpithon-vs-rpython/

"Similar to rPython, the rPithon package (http://rpithon.r-forge.r-project.org) allows users to execute Python code from R and exchange the data between Python and R. However, the underlying mechanisms between these two packages are fundamentally different. While rPithon communicates with Python from R through pipes, rPython accomplishes the same task with json. A major advantage of rPithon over rPython is that multiple Python processes can be started within a R session. However, rPithon is not very robust while exchanging large data objects between R and Python."


On Wed, Nov 16, 2016 at 4:53 PM, Nelly Reduan <nell.redu at hotmail.fr><mailto:nell.redu at hotmail.fr> wrote:


Hello,


How can I run this Python code from R ?




import nlmpy
nlm = nlmpy.mpd(nRow=50, nCol=50, h=0.75)
nlmpy.exportASCIIGrid("raster.asc", nlm)




Nlmpy is a Python package to build neutral landscape models

https://pypi.python.org/pypi/nlmpy . The example comes from this website. I tried to use the function system2 but I don't know how to use it.


path_script_python <- "C:/Users/Anaconda2/Lib/site-packages/nlmpy/nlmpy.py"

test <- system2("python", args = c(path_script_python, as.character(nRow), as.character(nCol), as.character(h)))

Thanks a lot for your help.
Nell


nlmpy 0.1.3 : Python Package Index<https://pypi.python.org/pypi/nlmpy><https://pypi.python.org/pypi/nlmpy>
pypi.python.org
NLMpy. NLMpy is a Python package for the creation of neutral landscape models that are widely used in the modelling of ecological patterns and processes across ...



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David Winsemius
Alameda, CA, USA

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