Bug in networkTMLE/example_usage.py

[milechin]

There seems to be a bug in the follow example script:
networkTMLE/example_usage.py

I get the following error when running the script:

Traceback (most recent call last):
  File "./networkTMLE/example_usage.py", line 79, in <module>
    tmle.define_threshold(variable='diet', threshold=3,
TypeError: define_threshold() got an unexpected keyword argument 'definition'

The error message indicates the issue is with line 79. It indicates the argument 'definition' is not defined for define_threshold function.

publications-code/networkTMLE/example_usage.py

Lines 79 to 80 in 4ef67e7

	tmle.define_threshold(variable='diet', threshold=3,
	definition='sum') # Defining threshold measure of at least 3 contacts with a diet

The define_threshold function seems to be part of the mossspider package and I found the code block linked below associated with that function and it is indeed missing the "definition" argument.

https://github.com/pzivich/MossSpider/blob/62e6bd20364c7ef01b6964fd79f21be84e5ac579/mossspider/estimators/tmle.py#L753-L762

[pzivich]

Yes, I updated how define_threshold operates when switching from the internal amonhen library to mossspider. The function call should instead be

 tmle.define_threshold(variable='diet_sum', threshold=3)

This is described here: https://mossspider.readthedocs.io/en/latest/Summary%20Measures.html#threshold

I will update the example_usage.py file. Thanks for catching