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def test_dataframe_to_numpy(self):
df = robjects.vectors.DataFrame(dict((('a', 1), ('b', 2))))
rec = conversion.rpy2py(df)
assert numpy.recarray == type(rec)
assert rec.a[0] == 1
assert rec.b[0] == 2
# check value
if isinstance(object_, int):
assert object_ == rebuilt
elif isinstance(object_, float):
assert object_ == rebuilt
elif isinstance(object_, str):
assert object_ == rebuilt
elif isinstance(object_, np.ndarray):
assert (object_ == rebuilt).all()
elif isinstance(object_, pd.DataFrame):
assert (object_ == rebuilt).all().all()
elif isinstance(object_, pd.Series):
assert (object_.to_frame() == rebuilt).all().all()
elif isinstance(object_, robjects.DataFrame):
with localconverter(pandas2ri.converter):
assert (robjects.conversion.rpy2py(object_) == rebuilt) \
.all().all()
else:
raise Exception("Could not compare")
def test_factor2Category(self):
factor = robjects.vectors.FactorVector(('a', 'b', 'a'))
with localconverter(default_converter + rpyp.converter) as cv:
rp_c = robjects.conversion.rpy2py(factor)
assert isinstance(rp_c, pandas.Categorical)
'''
function(object, data) {
rout_ = predict(object, data, prob=TRUE, debug=FALSE)
rout = list(rout_, attributes(rout_)$prob)
rout
}
''')
r_df_in = pydf_to_factorrdf(X)
r_out = rpredictwithprobfn(self.rfit, r_df_in)
r_df_out = r_out[0]
r_proba_out = r_out[1]
with rpy2.robjects.conversion.localconverter(ro.default_converter + rpy2.robjects.pandas2ri.converter):
y = ro.conversion.rpy2py(r_df_out).astype(cdt)
proba = pd.DataFrame(ro.conversion.rpy2py(r_proba_out).T, columns=list(r_proba_out.dimnames[0]), index=X.index)
return proba
# print(dims)
coords = {}
dim_names = []
if len(dims) == 1:
dname = node
dim_names += [dname]
levels = list(dims[0])
coords.update({dname: levels})
else:
for dname in dims.names:
dim_names += [dname]
levels = list(dims.rx(dname)[0])
coords.update({dname: levels})
with rpy2.robjects.conversion.localconverter(ro.default_converter + rpy2.robjects.pandas2ri.converter):
values = ro.conversion.rpy2py(prob)
ar = xr.DataArray(values, dims = dim_names, coords= coords)
ds['cpt' + node] = ar
lpd = convert_xarray_dataset_to_pandas_dtcpm_dict(ds)
did_adapt_ds_p = False
for df_name in lpd.keys():
ldf = lpd[df_name]
null_index_combinations = ldf[pd.isnull(ldf['p'])][ldf.columns[:-2]]
if len(null_index_combinations) == 0:
continue
null_index_combinations = null_index_combinations.drop_duplicates()
did_adapt_ds_p = True
lar = ds[df_name]
python_name, as_property, \
docstring in accessors:
if where is None:
where = rinterface.globalenv
else:
where = StrSexpVector(('package:%s' % where, ))
if python_name is None:
python_name = rname
signature = StrSexpVector((cls_rname, ))
r_meth = getmethod(StrSexpVector((rname, )),
signature=signature,
where=where)
r_meth = conversion.rpy2py(r_meth)
if as_property:
cls_dict[python_name] = property(r_meth, None, None,
doc=docstring)
else:
cls_dict[python_name] = lambda self: r_meth(self)
return type.__new__(mcs, name, bases, cls_dict)
def __truediv__(self, x):
res = globalenv_ri.find('/')(self._parent, conversion.py2rpy(x))
return conversion.rpy2py(res)
def _get_rownames(self):
res = baseenv_ri["rownames"](self)
return conversion.rpy2py(res)
def head(self, *args, **kwargs):
""" Call the R generic 'head()'. """
res = utils_ri['head'](self, *args, **kwargs)
return conversion.rpy2py(res)
def transpose(self):
""" transpose the matrix """
res = self._transpose(self)
return conversion.rpy2py(res)