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2012-09-21T00:48:59.713
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2012-09-21T00:48:59.713
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The error is because <code>%R</code> in IPython is attempting to turn the entire csv file into a single array of dtype float. The NA value in the integer column cannot be converted to a float, so an exception is raised. For example: <pre><code>>>> import rpy2.robjects as ro >>> import numpy as np >>> myData = ro.r['read.csv']('data.csv') >>> np.asarray(myData) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 235, in asarray return array(a, dtype, copy=False, order=order) TypeError: __float__ returned non-float (type rpy2.rinterface.NAIntegerType) </code></pre> A simple fix is to use the <code>--dataframe</code> / <code>-d</code> flag in <code>%R</code>. Note that we'll need to use the <code>--noreturn</code> / <code>-n</code> flag so ensure that we don't try to convert the return value into an array (which would again trigger the error). [Alternatively we could have put a semicolon at the end of the command.] For example: <pre><code>In [1]: %load_ext rmagic In [2]: %R -n -d myData myData <- read.csv('data.csv') In [3]: myData Out[3]: array([(1, 1, 1, 25, 0.590334, 0.4991572, 0.2189781, 9), (1, 1, 1, 25, 0.5504164, 0.5007439, 0.2136691, 13), (1, 1, 1, 25, 0.588486, 0.4879058, 0.2105431, 11), (1, 1, 1, 25, 0.5882244, 0.5148501, 0.2105431, -2147483648), (1, 2, 1, 25, nan, 0.489045, 0.2025757, 12)], dtype=[('replicate', '<i4'), ('line', '<i4'), ('genotype', '<i4'), ('temp', '<i4'), ('femur', '<f8'), ('tibia', '<f8'), ('tarsus', '<f8'), ('SCT', '<i4')]) </code></pre> Beware that the <code>NAInteger</code> value was converted to <code>-2147483648</code> (which is equal to <code>numpy.iinfo('<i4').min</code>).
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1. POrpy2/Rmagic: can't read csv data file
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1. USbfroehle
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1. COThe assumption that a csv file is homogeneous in type is looking a bit bold. May be it would be more intuitive to make what is currently the *--dataframe* option the default, and create a new option, e.g., "--homogeneous" ?
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