chronic_pathologies

This function assigns chronic categories to ICD codes, propagates chronic
conditions forward in time (category 2 indefinitely; category 1 within 1 year),
adds basal codes, and writes an updated episode file with `updated_icd_codes`.

Computes comorbidity indices and combined frailty scores for multiple ICD coding systems, including ICD-10-CA, ICD-10-CM, and ICD-11. The package provides tools to preprocess episode data, map diagnosis codes to chronic categories, propagate conditions across episodes, and generate comorbidity and frailty measures. The methods implemented are original to this package and were developed by the authors for research applications; a manuscript describing the methodology is currently in preparation.

Azadeh Bayani

LABTNSCPSS

Calculation of Comorbidity and Frailty Scores

Jean Noel Nikiema

Michèle Bally

chronic_pathologies function

<dl><dt>file_path_main</dt>
<dd>Path to cleaned episode-level CSV (must include patient_id, episode_id, start_date, ICD).</dd>
<dt>updated_path</dt>
<dd>Output CSV path. If NULL, a temp file is created.</dd>
<dt>coding_system</dt>
<dd>One of "ICD-10-CA", "ICD-10-CM", "ICD-11".</dd></dl>

Arguments

Carry-forward chronic ICD codes and build updated episode-level ICD history — chronic_pathologies

<dl>

<dt>file_path_main</dt>
<dd>Path to cleaned episode-level CSV (must include patient_id, episode_id, start_date, ICD).</dd>


<dt>updated_path</dt>
<dd>Output CSV path. If NULL, a temp file is created.</dd>


<dt>coding_system</dt>
<dd>One of "ICD-10-CA", "ICD-10-CM", "ICD-11".</dd>

</dl>

chronic_pathologies: Carry-forward chronic ICD codes and build updated episode-level ICD history

Description

Usage

Value

Arguments