Error in running Python code for PLSR modelling

Question

I am trying to develop model using PLSR (Partial Least Squares Regression) in Python3 using code provided https://github.com/pgbrodrick/ensemblePLSR. Sample data is also provided.

When I try to run code, it gives me error

>>> python3 ensemble_plsr.py example_settings.txt

I am using Python (3.7.3), python modules scikit-learn (0.20.2) and pandas (0.23.3).

/usr/lib/python3/dist-packages/sklearn/externals/joblib.py:1: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
  import imp
n bad bands 57
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 3078, in get_loc
    return self._engine.get_loc(key)
  File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: -1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "ensemble_plsr.py", line 173, in <module>
    df.pop(col)
  File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 760, in pop
    result = self[item]
  File "/usr/lib/python3/dist-packages/pandas/core/frame.py", line 2688, in __getitem__
    return self._getitem_column(key)
  File "/usr/lib/python3/dist-packages/pandas/core/frame.py", line 2695, in _getitem_column
    return self._get_item_cache(key)
  File "/usr/lib/python3/dist-packages/pandas/core/generic.py", line 2491, in _get_item_cache
    values = self._data.get(item)
  File "/usr/lib/python3/dist-packages/pandas/core/internals.py", line 4115, in get
    loc = self.items.get_loc(item)
  File "/usr/lib/python3/dist-packages/pandas/core/indexes/base.py", line 3080, in get_loc
    return self._engine.get_loc(self._maybe_cast_indexer(key))
  File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: -1

benfarr · Accepted Answer · 2020-03-11 20:51:26Z

0

In short, you're attempting to remove columns for which there is no reference at row 173 of ensemble_plsr.py, hence the KeyError during execution. What's happening under the hood is that when Python attempts to execute the pop method on the DataFrame for the unspecified/non-existent column, it raises that error. There are different ways to resolve this but this solution will resolve the error you are seeing:

Replace rows 172 & 173 in ensemble_plsr.py with the following:

for col in sf.get_setting('ignore columns'):
    if col != 'nothing_here':
      df.pop(col)

Replace row 16 in example_settings.txt with the following:

ignore columns(any other columns to remove) = nothing_here

Good news, you're done with this issue. Bad news, you're going to hit the next error down the line but you're on your way!

answered Mar 11, 2020 at 20:51

benfarr

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1 Comment

MGD Over a year ago

This solution worked and yes stuck at new error. I'm not a programming guy, it would require much time to correct errors.

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