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444 add clustering methods for npi data #883

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Changes and Information

Please briefly list the changes made, additional Information and what the Reviewer should look out for:

  • Add clustering for NPI data set

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Closes #444

@mknaranja mknaranja linked an issue Jan 5, 2024 that may be closed by this pull request
Add clustering methods for NPI data #444
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mknaranja
mknaranja commented Jan 8, 2024
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pycode/memilio-epidata/memilio/epidata/assessNPIEffects.py
Comment on lines +116 to +118
# NOTE: if changing method, pay attention to linkage methods;
# 'centroid', 'median', and 'ward' are correctly defined only if
# Euclidean pairwise metric is used in distance matrix that we used as input.
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Does this "still" hold? For ward, I don't see this at all directly, for the others, (only) the meaning changes

mknaranja
mknaranja commented Jan 15, 2024
View reviewed changes
pycode/memilio-epidata/memilio/epidata/assessNPIEffects.py
all_subcodes = [x for x in npis.NPI_code if len(x) <=8]
if not npi_codes_considered:
npi_codes_considered = [
x for x in npis[dd.EngEng['npiCode']] if len(x.split('_')) == 2]
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len == 3?

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I think 2 is the right option here

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codecov bot commented Mar 28, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.34%. Comparing base (8ddb863) to head (d3d1d5c).
Report is 27 commits behind head on main.

❗ Current head d3d1d5c differs from pull request most recent head 3eaf31c

Please upload reports for the commit 3eaf31c to get more accurate results.

Additional details and impacted files 
@@           Coverage Diff           @@
##             main     #883   +/-   ##
=======================================
  Coverage   96.34%   96.34%           
=======================================
  Files         129      129           
  Lines       10056    10056           
=======================================
  Hits         9688     9688           
  Misses        368      368

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mknaranja and others added 16 commits April 4, 2024 10:51
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Add clustering methods for NPI data
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@mknaranja @patricklnz @annawendler