[R] Run a Python code from R

[David Winsemius]

> On Nov 16, 2016, at 4:53 PM, Nelly Reduan <nell.redu at hotmail.fr> wrote:
> 
> Thank you very much for your help !
> 
> 
> 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,


> 
> 
>> if (pithon.available())
> 
> + {
> 
> +   nRow <-50
> 
> +   nCol <-50
> 
> +   h <- 0.75
> 
> +
> 
> +   # this file contains the definition of function concat
> 
> +   pithon.load("C:/Users/Anaconda2/Lib/site-packages/nlmpy/nlmpy.py")
> 
> +   pithon.call( "mpd", nRow, nCol, h)
> 
> +
> 
> + } else {
> 
> +   print("Unable to execute python")
> 
> + }
> 
> Show Traceback
> 
> 
> 
> Rerun with Debug
> 
> 
> 
> Error in pithon.get("_r_call_return", instance.name = instname) :
> 
>  Couldn't retrieve variable: Traceback (most recent call last):
> 
>  File "C:/Users/Documents/R/win-library/3.3/rPithon/pythonwrapperscript.py", line 110, in <module>
> 
>    reallyReallyLongAndUnnecessaryPrefix.data = json.dumps([eval(reallyReallyLongAndUnnecessaryPrefix.argData)])
> 
>  File "C:\Users\ANACON~1\lib\json\__init__.py", line 244, in dumps
> 
>    return _default_encoder.encode(obj)
> 
>  File "C:\Users\ANACON~1\lib\json\encoder.py", line 207, in encode
> 
>    chunks = self.iterencode(o, _one_shot=True)
> 
>  File "C:\Users\ANACON~1\lib\json\encoder.py", line 270, in iterencode
> 
>    return _iterencode(o, 0)
> 
>  File "C:\Users\ANACON~1\lib\json\encoder.py", line 184, in default
> 
>    raise TypeError(repr(o) + " is not JSON serializable")
> 
> TypeError: array([[ 0.36534654,  0.31962481,  0.44229946, ...,  0.11513079,
> 
>         0.07156331,  0.00286971],
> 
>       [ 0.41534291,  0.41333479,  0.48118995, ...,  0.19203674,
> 
>         0.04192771,  0.03679473],
> 
>       [ 0.5188
> 
> 
> 
> 
> 
> Nell
> 
> 
> ________________________________
> De : Wensui Liu <liuwensui at gmail.com>
> Envoy� : mercredi 16 novembre 2016 16:00:03
> � : Nelly Reduan
> Cc : r-help at r-project.org
> Objet : Re: [R] Run a Python code from R
> 
> take a look at rpython or rPithon package
> 
> On Wed, Nov 16, 2016 at 4:53 PM, Nelly Reduan <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>
>> 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 ...
>> 
>> 
>> 
>>        [[alternative HTML version deleted]]
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA