Fix ICD codes mapping to multiple comorbidities

[Copilot]

Dictionary-based reverse mapping prevented ICD codes from mapping to multiple comorbidities. Code I426 (alcoholic cardiomyopathy) should map to both CHF and alcohol abuse but only mapped to the last one encountered.

Changes

src/comorbidipy/calculators/comorbidity.py

• Replace dictionary reverse mapping with list of (code, comorbidity) pairs
• Use DataFrame join to handle one-to-many code→comorbidity relationships
• Deduplicate at (id, comorbidity) level to prevent double-counting

Before:

reverse_mapping = {
    i: k
    for i in codes
    for k, v in mapping[score_icd_variant].items()
    if i.startswith(tuple(v))
}
working_df = working_df.with_columns(
    pl.col(code).replace_strict(reverse_mapping, default=None).alias("mapped_code")
)

After:

code_to_comorbidities = []
for icd_code in codes:
    for comorbidity_name, icd_patterns in mapping[score_icd_variant].items():
        if icd_code.startswith(tuple(icd_patterns)):
            code_to_comorbidities.append((icd_code, comorbidity_name))

mapping_df = pl.DataFrame(code_to_comorbidities, schema=[code, "mapped_code"], orient="row")
working_df = working_df.join(mapping_df, on=code, how="inner")
working_df = working_df.unique(subset=[id, "mapped_code"])

Affected Codes

All codes now correctly map to multiple comorbidities:

• I426, F315, I2782 (ICD-10 Elixhauser)
• 40403, 40413, 40493, 4255 (ICD-9 Charlson/Elixhauser)

Example

df = pl.DataFrame({'id': [1, 1, 1], 'code': ['I2782', 'I426', 'F315']})
result = comorbidity(df, score='elixhauser', icd='icd10', variant='quan')

# Before: alcohol=1, chf=0, cpd=1, depre=1, pcd=0, psycho=0
# After:  alcohol=1, chf=1, cpd=1, depre=1, pcd=1, psycho=1

Original prompt

---

This section details on the original issue you should resolve

<issue_title>ICD10 codes map to only one comorbidity when they should map to two</issue_title>
<issue_description>### General info

• comorbidipy version: 0.4.4 (latest)
• Python version: 3.7.12
• Operating System: linux

Description

When a patient has a list of icd codes, each icd code is supposed to be mapped to its corresponding comorbidities. This works as expected for most codes. However, an issue arises when a code corresponds to multiple different comorbidities. For instance, ICD10 code I42.6, alcoholic cardiomyopathy, is supposed to map to both alcohol abuse as well as congestive heart failure (per quan ICD10 mapping). When the comorbidity function does its mapping/calculation, the icd code is only mapped once (to alcohol) instead of twice, to both alcohol & chf.

Ultimately, a code that should essentially count for 10 points (swiss: -3 alcohol, 13 chf) counts as -3 points if a patient does not have other codes recorded for chf.

It is also worth noting that this method deviates from the way that the R comorbidity package, which this repo is modeled after, calculates and maps comorbidities. When using that package, a patient with code I42.6 is mapped to both the alcohol & the chf comorbidities.

What I Did

Example using 3 different icd10 codes where this problem can be seen:

id = [1,1,1]
age = [50,50,50]
code = ['I2782','I426','F315']
df_example = pd.DataFrame({'id': id, 'age': age, 'code': code})

## These 3 codes should return 1s for pcd, cpd, psycho, depre, alcohol, chf
## Instead, each code is only mapped to one comorbidity

df_out = comorbidipy.comorbidity(df_example,  
                                 age="age",
                                 score="elixhauser",
                                 icd="icd10",
                                 variant="quan",
                                 weighting="swiss")

df_out[['alcohol','chf','cpd', 'depre', 'pcd', 'psycho']]

df_out output:

	id	alcohol	chf	cpd	depre	pcd	psycho
0	1	1	0	1	1	0	0

</issue_description>

<agent_instructions>This issue was raised against an older version of this package (v0.5.0) but is certainly still relevant. Implement the correct approach to address what @kyliewillis and @rpomponio have reported. </agent_instructions>

Comments on the Issue (you are @copilot in this section)

@vvcb @kyliewillis - Thank you for reporting this! 🙏 I didn't think anyone else was using this library. So it was a pleasant surprise to find this issue raised, albeit an embarrassing one as I missed it for an entire month.

@rpomponio - thanks for the fantastic work on the tests comparing the parent R package and this one 🚀. Are you please able to share anonymised data for the cases where the two packages differ?

I will find some time to dig into this and fix it. (And will document it better as well - especially if people are using it!)</comment_new>
<comment_new>@vvcb
I suspect the reason for this bug is this code section here - https://github.com/vvcb/comorbidipy/blob/main/comorbidipy/calculator.py#L111-L116

It will be easy enough to find all the codes that map to more than one category. I will have to think about how this section can be modified. Should be straightforward (:coldsweat:)!</comment_new>
<comment_new>@vvcb
Having reviewed all the codes across all the comorbidity risk scores, there are a very small number of codes that cause this issue.

A workaround specific to these codes may be the most pragmatic and simple solution.

code	comorbidity 1	comorbidity 2
charlson_icd9_quan
40403	chf	rend
40413	chf	rend
40493	chf	rend
charlson_icd10_se
K703	mld	mld
charlson_icd10_am
C80	canc	metacanc
elixhauser_icd9_quan
40403	chf	rf
40413	chf	rf
40493	chf	rf
4255	chf	alcohol
elixhauser_icd10_quan
I426	chf	alcohol
F315	psycho ...

• Fixes ICD10 codes map to only one comorbidity when they should map to two #2

---

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[Copilot]

Pull request overview

This PR fixes a critical bug where ICD codes that should map to multiple comorbidities only mapped to one due to dictionary-based reverse mapping. The fix replaces the dictionary with a list of tuples and uses DataFrame joins to handle one-to-many relationships correctly.

Changes:

• Replaced dictionary reverse mapping with list-based approach allowing codes to map to multiple comorbidities
• Added DataFrame join operation to handle one-to-many code→comorbidity mappings
• Implemented deduplication at the (patient ID, comorbidity) level to prevent double-counting
• Added comprehensive test suite covering all affected codes across ICD-9 and ICD-10

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
src/comorbidipy/calculators/comorbidity.py	Core fix replacing dictionary mapping with list-based approach and DataFrame join to enable one-to-many code→comorbidity relationships
tests/test_multiple_comorbidity_mapping.py	Comprehensive test suite covering all affected codes (I426, F315, I2782, 40403, 4255) with edge cases for duplicate codes and multiple patients