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POrpy2/Rmagic: can't read csv data file
 

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  1. POrpy2/Rmagic: can't read csv data file
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    <p>I have a pretty standard csv data set that I'm trying to read in IPython Notebook using rpy2/Rmagic:</p> <pre><code># R code %load_ext rmagic %R my.data &lt;- read.csv("/Users/xxx/Documents/data.csv") </code></pre> <p>I get this error:</p> <pre><code>--------------------------------------------------------------------------- TypeError Traceback (most recent call last) &lt;ipython-input-31-844400cf68c6&gt; in &lt;module&gt;() 25 ####Chunk 1: Inputting and checking the data ---&gt; 27 get_ipython().magic(u'R my.data &lt;- read.csv("/Users/xxx/Documents/data.csv")') 28 get_ipython().magic(u'R summary(my.data)') /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in magic(self, arg_s) 2162 magic_name, _, magic_arg_s = arg_s.partition(' ') 2163 magic_name = magic_name.lstrip(prefilter.ESC_MAGIC) -&gt; 2164 return self.run_line_magic(magic_name, magic_arg_s) 2165 2166 #------------------------------------------------------------------------- /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_line_magic(self, magic_name, line) 2088 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals 2089 with self.builtin_trap: -&gt; 2090 result = fn(*args,**kwargs) 2091 return result 2092 /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/IPython/extensions/rmagic.pyc in R(self, line, cell, local_ns) /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/IPython/core/magic.pyc in &lt;lambda&gt;(f, *a, **k) 189 # but it's overkill for just that one bit of state. 190 def magic_deco(arg): --&gt; 191 call = lambda f, *a, **k: f(*a, **k) 192 193 if callable(arg): /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/IPython/extensions/rmagic.pyc in R(self, line, cell, local_ns) 579 if return_output and not args.noreturn: 580 if result != ri.NULL: --&gt; 581 return self.Rconverter(result, dataframe=False) 582 583 __doc__ = __doc__.format( /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/IPython/extensions/rmagic.pyc in Rconverter(Robj, dataframe) 113 return np.asarray(Robj) 114 Robj = np.rec.fromarrays(Robj, names = names) --&gt; 115 return np.asarray(Robj) 116 117 @magics_class /Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/numpy/core/numeric.py in asarray(a, dtype, order) 233 234 """ --&gt; 235 return array(a, dtype, copy=False, order=order) 236 237 def asanyarray(a, dtype=None, order=None): TypeError: __float__ returned non-float (type rpy2.rinterface.NAIntegerType) </code></pre> <p>I'm guessing this has something to do with NA values in my csv data. I don't actually put a value there - just a blank entry (e.g. 1,,3,4).</p> <p>I tried replacing the blank entries with NA, a space, 0, etc. -- I always get the same error. What am I doing wrong?</p> <p><strong>Edit:</strong> I tried doing it with pure rpy2 (without making any changes to my data set):</p> <pre><code>import rpy2.robjects as robjects myData = robjects.r['read.csv']("/Users/xxx/Documents/data.csv") print robjects.r['summary'](myData) </code></pre> <p>and it works fine! So this must be something with IPython/Rmagic.</p>
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