run_pipeline

Runs data cleaning, chronic pathology propagation, frailty calculation,
and comorbidity/frailty scoring.

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

run_pipeline function

<dl><dt>input_file</dt>
<dd>Path to the input CSV file.</dd>
<dt>col_mapping</dt>
<dd>Named list mapping standard names to the user's column names.</dd>
<dt>coding_system</dt>
<dd>Coding system used (e.g., "ICD-10-CA"). Optional; used by internal functions when applicable.</dd>
<dt>out_dir</dt>
<dd>Output directory for generated files. If NULL, writes next to `input_file`.</dd></dl>

Arguments

Run the LABTNSCPSS comorbidity + frailty pipeline — run_pipeline

<dl>

<dt>input_file</dt>
<dd>Path to the input CSV file.</dd>


<dt>col_mapping</dt>
<dd>Named list mapping standard names to the user's column names.</dd>


<dt>coding_system</dt>
<dd>Coding system used (e.g., "ICD-10-CA"). Optional; used by internal functions when applicable.</dd>


<dt>out_dir</dt>
<dd>Output directory for generated files. If NULL, writes next to `input_file`.</dd>

</dl>

run_pipeline: Run the LABTNSCPSS comorbidity + frailty pipeline

Description

Usage

Value

Arguments