Thank you very much for your help ! I 'm trying to use the package "rPithon" but I obtain this error message:> 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]]
> 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
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> 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,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> 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]] >>> >>> >>> David Winsemius >>> Alameda, CA, USA >>> >>> ______________________________________________ >>> 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]]