Re: [R] Run a Python code from R
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 <rb...@atsu.edu>
Envoy� : samedi 19 novembre 2016 16:05:13
� : David Winsemius; Nelly Reduan
Cc : r-help@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.r...@hotmail.fr><mailto:nell.r...@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.r...@hotmail.fr><mailto:nell.r...@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 ...
[[alternative HTML version deleted]]
David Winsemius
Alameda, CA, USA
__
R-help@r-project.org<mailto:R-help@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@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.
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.r...@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.r...@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@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@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.
Re: [R] Run a Python code from R
> On Nov 16, 2016, at 4:53 PM, Nelly Reduan <nell.r...@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
>
>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 <liuwen...@gmail.com>
> Envoy� : mercredi 16 novembre 2016 16:00:03
> � : Nelly Reduan
> Cc : r-help@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.r...@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@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@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
__
R-help@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.
Re: [R] Run a Python code from R
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
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 <liuwen...@gmail.com>
Envoy� : mercredi 16 novembre 2016 16:00:03
� : Nelly Reduan
Cc : r-help@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.r...@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@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@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.
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.r...@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@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.
__
R-help@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.
[R] Run a Python code from R
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@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.
