Cox_time_varying_fitter can't be estimated

[chenzijin2018]

Hi. I am trying to build a cox model. But failed. here attached the log. It looks like some death_only variables has low variance, Then later, there is some non-None axis issue. Can anyone help how should I fix this problem? I know this might be the data issue. I guess I want to ask how can I fix this data issue?

Thank you very much.

ValueError Traceback (most recent call last)
/tmp/ipykernel_196/3504620182.py in
1 final_data=final_data[final_data['dl_size']!=0]
2 cx_md = CoxTimeVaryingFitter()
----> 3 cx_md.fit(final_data, id_col="ID", event_col="Event", start_col="start", stop_col="stop", show_progress=True, formula=f"dl_size + lag_s1 + lag_s2 + lag_s3 + lag_s4 + lag_s5 + lag_s6 + lag_s7 + lag_s8 + lag_s9 + {varlist}")
4
5 parm=cx_md.params_

/opt/oss/conda3/lib/python3.7/site-packages/lifelines/fitters/cox_time_varying_fitter.py in fit(self, df, event_col, start_col, stop_col, weights_col, id_col, show_progress, step_size, robust, strata, initial_point, formula)
204 X = self.regressors.transform_df(df)["beta_"]
205
--> 206 self._check_values(X, events, start, stop)
207
208 self._norm_mean = X.mean(0)

/opt/oss/conda3/lib/python3.7/site-packages/lifelines/fitters/cox_time_varying_fitter.py in _check_values(self, df, events, start, stop)
240 check_nans_or_infs(df)
241 check_low_var(df)
--> 242 check_complete_separation_low_variance(df, events, self.event_col)
243 check_for_numeric_dtypes_or_raise(df)
244 check_for_nonnegative_intervals(start, stop)

/opt/oss/conda3/lib/python3.7/site-packages/lifelines/utils/init.py in check_complete_separation_low_variance(df, events, event_col)
1107
1108 events = events.astype(bool)
-> 1109 deaths_only = df.columns[_low_var(df.loc[events])]
1110 censors_only = df.columns[_low_var(df.loc[~events])]
1111 total = df.columns[_low_var(df)]

/opt/oss/conda3/lib/python3.7/site-packages/pandas/core/indexing.py in getitem(self, key)
929
930 maybe_callable = com.apply_if_callable(key, self.obj)
--> 931 return self._getitem_axis(maybe_callable, axis=axis)
932
933 def _is_scalar_access(self, key: tuple):

/opt/oss/conda3/lib/python3.7/site-packages/pandas/core/indexing.py in _getitem_axis(self, key, axis)
1142 return self._get_slice_axis(key, axis=axis)
1143 elif com.is_bool_indexer(key):
-> 1144 return self._getbool_axis(key, axis=axis)
1145 elif is_list_like_indexer(key):
1146

/opt/oss/conda3/lib/python3.7/site-packages/pandas/core/indexing.py in _getbool_axis(self, key, axis)
946 # caller is responsible for ensuring non-None axis
947 labels = self.obj._get_axis(axis)
--> 948 key = check_bool_indexer(labels, key)
949 inds = key.nonzero()[0]
950 return self.obj._take_with_is_copy(inds, axis=axis)

/opt/oss/conda3/lib/python3.7/site-packages/pandas/core/indexing.py in check_bool_indexer(index, key)
2383 result = key
2384 if isinstance(key, ABCSeries) and not key.index.equals(index):
-> 2385 result = result.reindex(index)
2386 mask = isna(result._values)
2387 if mask.any():

/opt/oss/conda3/lib/python3.7/site-packages/pandas/core/series.py in reindex(self, index, **kwargs)
4578 )
4579 def reindex(self, index=None, **kwargs):
-> 4580 return super().reindex(index=index, **kwargs)
4581
4582 @deprecate_nonkeyword_arguments(version=None, allowed_args=["self", "labels"])

/opt/oss/conda3/lib/python3.7/site-packages/pandas/core/generic.py in reindex(self, *args, **kwargs)
4817 # perform the reindex on the axes
4818 return self._reindex_axes(
-> 4819 axes, level, limit, tolerance, method, fill_value, copy
4820 ).finalize(self, method="reindex")
4821

/opt/oss/conda3/lib/python3.7/site-packages/pandas/core/generic.py in _reindex_axes(self, axes, level, limit, tolerance, method, fill_value, copy)
4841 fill_value=fill_value,
4842 copy=copy,
-> 4843 allow_dups=False,
4844 )
4845

/opt/oss/conda3/lib/python3.7/site-packages/pandas/core/generic.py in _reindex_with_indexers(self, reindexers, fill_value, copy, allow_dups)
4887 fill_value=fill_value,
4888 allow_dups=allow_dups,
-> 4889 copy=copy,
4890 )
4891 # If we've made a copy once, no need to make another one

/opt/oss/conda3/lib/python3.7/site-packages/pandas/core/internals/managers.py in reindex_indexer(self, new_axis, indexer, axis, fill_value, allow_dups, copy, consolidate, only_slice)
668 # some axes don't allow reindexing with dups
669 if not allow_dups:
--> 670 self.axes[axis]._validate_can_reindex(indexer)
671
672 if axis >= self.ndim:

/opt/oss/conda3/lib/python3.7/site-packages/pandas/core/indexes/base.py in _validate_can_reindex(self, indexer)
3783 # trying to reindex on an axis with duplicates
3784 if not self._index_as_unique and len(indexer):
-> 3785 raise ValueError("cannot reindex from a duplicate axis")
3786
3787 def reindex(

ValueError: cannot reindex from a duplicate axis