python - pandas and rpy2: Why does ezANOVA work via robjects.r but not robjects.packages.importr? -


like many, i'm hoping stop straddling r , python worlds , work in python using pandas, pyr2, numpy, etc. i'm using r package ez ezanova facility. it works if things hard way, why doesn't work when them easy way? don't understand resulting error:

file "/users/malcomreynolds/analysis/r_with_pandas.py", line 38, in <module>     res = ez.ezanova(data=testdata, dv='score', wid='subjectid', between='block', detailed=true)   file "/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 178, in __call__     return super(signaturetranslatedfunction, self).__call__(*args, **kwargs)   file "/usr/local/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 106, in __call__     res = super(function, self).__call__(*new_args, **new_kwargs) rpy2.rinterface.rruntimeerror: error in table(temp[, names(temp) == wid]) :    attempt set attribute on null

see below full reproducible code (requires python packages: pyr2, pandas, numpy):

import pandas pd rpy2 import robjects rpy2.robjects import pandas2ri pandas2ri.activate()  # make pyr2 accept , auto-convert pandas dataframes rpy2.robjects.packages import importr base = importr('base') ez = importr('ez') robjects.r['options'](warn=-1)  # ??? import numpy np  """make pandas data from scratch"""  score = np.random.normal(loc=10, scale=20, size=10) subjectid = range(10) block = ["sugar"] * 5 + ["salt"] * 5 testdata = pd.dataframe({'score':score, 'block':block, 'subjectid': subjectid}) # looks dataframe r print testdata  """hard way: use ezanova thorugh pyr2 *** works ***""" anova1 = robjects.r(""" library(ez) function(df) {     # df gets passed in     ezanova(         data=df,         dv=score,         wid=subjectid,         between=block,         detailed=true) } """) print anova1(testdata)   # command shows ez instance setup print ez.ezprecis(data=testdata)  # successful  """easy way: import ez directly , use """ # *** approach not work *** # yet, trying use ez.ezanova yields excpetion aboutthe wid value # res = ez.ezanova(data=testdata, dv='score', wid='subjectid', between='block', detailed=true) # print res  # *** approach works (and uses options change) *** res = ez.ezanova(data=testdata, dv=base.as_symbol('score'), wid=base.as_symbol('subjectid'), between=base.as_symbol('block')) print res

in easy version passing symbol names strings. not same symbol.

check use of as_symbol in minimal example of rpy2 regression using pandas data frame


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