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# -*- coding: utf-8 -*-
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"""
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======
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Rmagic
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======
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Magic command interface for interactive work with R via rpy2
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Usage
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=====
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``%R``
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{R_DOC}
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``%Rpush``
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{RPUSH_DOC}
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``%Rpull``
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{RPULL_DOC}
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"""
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#-----------------------------------------------------------------------------
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# Copyright (C) 2012 The IPython Development Team
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#
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# Distributed under the terms of the BSD License. The full license is in
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# the file COPYING, distributed as part of this software.
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#-----------------------------------------------------------------------------
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import sys
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import tempfile
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from glob import glob
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from shutil import rmtree
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from getopt import getopt
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# numpy and rpy2 imports
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import numpy as np
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import rpy2.rinterface as ri
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import rpy2.robjects as ro
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from rpy2.robjects.numpy2ri import numpy2ri
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ro.conversion.py2ri = numpy2ri
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# IPython imports
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from IPython.core.displaypub import publish_display_data
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from IPython.core.magic import (Magics, magics_class, cell_magic, line_magic,
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line_cell_magic)
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from IPython.testing.skipdoctest import skip_doctest
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from IPython.core.magic_arguments import (
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argument, magic_arguments, parse_argstring
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)
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from IPython.utils.py3compat import str_to_unicode, unicode_to_str
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class RMagicError(ri.RRuntimeError):
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pass
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@magics_class
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class RMagics(Magics):
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"""A set of magics useful for interactive work with R via rpy2.
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"""
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def __init__(self, shell, Rconverter=np.asarray,
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pyconverter=np.asarray,
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cache_display_data=False):
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"""
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Parameters
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----------
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shell : IPython shell
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Rconverter : callable
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To be called on return values from R before returning
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to ipython.
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pyconverter : callable
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To be called on values in ipython namespace before
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assigning to variables in rpy2.
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cache_display_data : bool
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If True, the published results of the final call to R are
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cached in the variable 'display_cache'.
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"""
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super(RMagics, self).__init__(shell)
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self.cache_display_data = cache_display_data
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self.r = ro.R()
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self.Rstdout_cache = []
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self.Rconverter = Rconverter
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self.pyconverter = pyconverter
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def eval(self, line):
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'''
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Parse and evaluate a line with rpy2.
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Returns the output to R's stdout() connection
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and the value of eval(parse(line)).
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'''
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old_writeconsole = ri.get_writeconsole()
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ri.set_writeconsole(self.write_console)
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try:
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value = ri.baseenv['eval'](ri.parse(line))
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except (ri.RRuntimeError, ValueError) as exception:
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raise RMagicError(unicode_to_str('parsing and evaluating line "%s". R traceback: "%s"\n' %
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(line, str_to_unicode(exception.message, 'utf-8'))))
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text_output = self.flush()
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ri.set_writeconsole(old_writeconsole)
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return text_output, value
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def write_console(self, output):
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'''
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A hook to capture R's stdout in a cache.
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'''
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self.Rstdout_cache.append(output)
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def flush(self):
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'''
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Flush R's stdout cache to a string, returning the string.
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'''
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value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache])
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self.Rstdout_cache = []
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return value
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@skip_doctest
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@line_magic
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def Rpush(self, line):
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'''
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A line-level magic for R that pushes
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variables from python to rpy2. The line should be made up
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of whitespace separated variable names in the IPython
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namespace::
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In [7]: import numpy as np
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In [8]: X = np.array([4.5,6.3,7.9])
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In [9]: X.mean()
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Out[9]: 6.2333333333333343
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In [10]: %Rpush X
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In [11]: %R mean(X)
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Out[11]: array([ 6.23333333])
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'''
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inputs = line.split(' ')
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for input in inputs:
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self.r.assign(input, self.pyconverter(self.shell.user_ns[input]))
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@skip_doctest
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@line_magic
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def Rpull(self, line):
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'''
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A line-level magic for R that pulls
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variables from python to rpy2::
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In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4)
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In [19]: %Rpull x y z
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In [20]: x
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Out[20]: array([ 3. , 4. , 6.7])
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In [21]: y
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Out[21]: array([ 4., 6., 7.])
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In [22]: z
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Out[22]:
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array(['a', '3', '4'],
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dtype='|S1')
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Notes
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-----
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Beware that R names can have '.' so this is not fool proof.
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To avoid this, don't name your R objects with '.'s...
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'''
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outputs = line.split(' ')
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for output in outputs:
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self.shell.push({output:self.Rconverter(self.r(output))})
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@skip_doctest
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@magic_arguments()
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@argument(
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'-i', '--input', action='append',
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help='Names of input variable from shell.user_ns to be assigned to R variables of the same names after calling self.pyconverter. Multiple names can be passed separated only by commas with no whitespace.'
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)
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@argument(
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'-o', '--output', action='append',
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help='Names of variables to be pushed from rpy2 to shell.user_ns after executing cell body and applying self.Rconverter. Multiple names can be passed separated only by commas with no whitespace.'
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)
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@argument(
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'-w', '--width', type=int,
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help='Width of png plotting device sent as an argument to *png* in R.'
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)
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@argument(
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'-h', '--height', type=int,
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help='Height of png plotting device sent as an argument to *png* in R.'
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)
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@argument(
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'-u', '--units', type=int,
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help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].'
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)
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@argument(
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'-p', '--pointsize', type=int,
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help='Pointsize of png plotting device sent as an argument to *png* in R.'
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)
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@argument(
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'-b', '--bg',
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help='Background of png plotting device sent as an argument to *png* in R.'
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)
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@argument(
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'-n', '--noreturn',
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help='Force the magic to not return anything.',
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action='store_true',
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default=False
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)
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@argument(
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'code',
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nargs='*',
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)
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@line_cell_magic
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def R(self, line, cell=None):
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'''
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Execute code in R, and pull some of the results back into the Python namespace.
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In line mode, this will evaluate an expression and convert the returned value to a Python object.
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The return value is determined by rpy2's behaviour of returning the result of evaluating the
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final line. Multiple R lines can be executed by joining them with semicolons::
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In [9]: %R X=c(1,4,5,7); sd(X); mean(X)
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Out[9]: array([ 4.25])
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As a cell, this will run a block of R code, without bringing anything back by default::
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In [10]: %%R
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....: Y = c(2,4,3,9)
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....: print(summary(lm(Y~X)))
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....:
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Call:
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lm(formula = Y ~ X)
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Residuals:
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1 2 3 4
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0.88 -0.24 -2.28 1.64
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Coefficients:
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Estimate Std. Error t value Pr(>|t|)
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(Intercept) 0.0800 2.3000 0.035 0.975
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X 1.0400 0.4822 2.157 0.164
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Residual standard error: 2.088 on 2 degrees of freedom
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Multiple R-squared: 0.6993,Adjusted R-squared: 0.549
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F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638
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In the notebook, plots are published as the output of the cell.
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%R plot(X, Y)
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will create a scatter plot of X bs Y.
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If cell is not None and line has some R code, it is prepended to
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the R code in cell.
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Objects can be passed back and forth between rpy2 and python via the -i -o flags in line::
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In [14]: Z = np.array([1,4,5,10])
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In [15]: %R -i Z mean(Z)
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Out[15]: array([ 5.])
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In [16]: %R -o W W=Z*mean(Z)
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Out[16]: array([ 5., 20., 25., 50.])
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In [17]: W
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Out[17]: array([ 5., 20., 25., 50.])
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The return value is determined by these rules:
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* If the cell is not None, the magic returns None.
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* If the cell evaluates as False, the resulting value is returned
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unless the final line prints something to the console, in
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which case None is returned.
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* If the final line results in a NULL value when evaluated
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by rpy2, then None is returned.
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'''
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args = parse_argstring(self.R, line)
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# arguments 'code' in line are prepended to
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# the cell lines
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if not cell:
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code = ''
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return_output = True
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line_mode = True
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else:
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code = cell
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return_output = False
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line_mode = False
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code = ' '.join(args.code) + code
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if args.input:
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for input in ','.join(args.input).split(','):
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self.r.assign(input, self.pyconverter(self.shell.user_ns[input]))
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png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'height', 'width', 'bg', 'pointsize']])
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png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None])
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# execute the R code in a temporary directory
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tmpd = tempfile.mkdtemp()
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self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd, png_args))
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text_output = ''
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if line_mode:
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for line in code.split(';'):
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text_result, result = self.eval(line)
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text_output += text_result
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if text_result:
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# the last line printed something to the console so we won't return it
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return_output = False
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else:
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text_result, result = self.eval(code)
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text_output += text_result
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self.r('dev.off()')
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# read out all the saved .png files
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images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)]
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# now publish the images
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# mimicking IPython/zmq/pylab/backend_inline.py
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fmt = 'png'
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mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' }
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mime = mimetypes[fmt]
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# publish the printed R objects, if any
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display_data = []
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if text_output:
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display_data.append(('RMagic.R', {'text/plain':text_output}))
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# flush text streams before sending figures, helps a little with output
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for image in images:
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# synchronization in the console (though it's a bandaid, not a real sln)
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sys.stdout.flush(); sys.stderr.flush()
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display_data.append(('RMagic.R', {mime: image}))
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# kill the temporary directory
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rmtree(tmpd)
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# try to turn every output into a numpy array
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# this means that output are assumed to be castable
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# as numpy arrays
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if args.output:
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for output in ','.join(args.output).split(','):
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# with self.shell, we assign the values to variables in the shell
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self.shell.push({output:self.Rconverter(self.r(output))})
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for tag, disp_d in display_data:
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publish_display_data(tag, disp_d)
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# this will keep a reference to the display_data
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# which might be useful to other objects who happen to use
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# this method
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if self.cache_display_data:
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self.display_cache = display_data
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# if in line mode and return_output, return the result as an ndarray
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if return_output and not args.noreturn:
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if result != ri.NULL:
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return self.Rconverter(result)
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__doc__ = __doc__.format(
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R_DOC = ' '*8 + RMagics.R.__doc__,
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RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__,
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RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__
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)
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_loaded = False
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def load_ipython_extension(ip):
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"""Load the extension in IPython."""
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global _loaded
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if not _loaded:
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ip.register_magics(RMagics)
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_loaded = True
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