Reusable utilities for the ACS NSQIP benign lung resection study, extracted to avoid duplicating constants and helpers across analyses.

• Configuration constants for years and output directories (2010-2024).
• CPT metadata for lung resection procedures plus ICD prefix sets for benign, cancer, and structural diagnoses.
• Column detection helpers, NSQIP field candidate lists, and normalization utilities (ASA, Yes/No, BMI).
• ICD classification, cohort prep, 30-day outcomes, and stratified outcome tables.
• Regression prep, imputation, and optional risk-adjusted rate analysis with statsmodels/scipy support.

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Python implementation of the Charlson-Deyo comorbidity index using ICD-9 and ICD-10 rules.

• Rule table for ICD-9/ICD-10 prefixes and ranges for each comorbidity group.
• Normalization and matching helpers for claims diagnoses and ICD version inference.
• Long-format conversion for claims data and time-window filtering around diagnosis date.
• Outputs per-condition counts, validity flags, Charlson score, binned score, and NCI index.

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R implementation of the Charlson-Deyo comorbidity index using tidyverse workflows.

• Same ICD-9/ICD-10 rule set as the Python version for parity.
• Tidyverse helpers for normalization, prefix/range matching, and long-format DX data.
• Calculates comorbidity flags, Charlson score, and NCI index for downstream analysis.

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Document ingestion script that builds a FAISS vector store for retrieval workflows.

• Recursively loads files with type-specific loaders (text, Markdown, HTML, PDF, Office).
• Chooses a faster PDF loader for larger files based on PDF_FAST_SIZE_MB.
• Splits documents into overlapping chunks for fine-grained retrieval.
• Creates OpenAI embeddings and saves the FAISS index to ./vectorstore.

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CPT code groupings for lung procedures, organized by resection extent.

• Maps extent labels (pneumonectomy, lobectomy, segmentectomy, wedge, biopsy, tumor resection) to CPT code lists.
• Includes open and thoracoscopic (VATS) codes for consistent grouping.
• Useful for collapsing procedure codes into analysis-ready categories.
• Contains overlapping codes across years where applicable.

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Year-range lookup for CPT codes with descriptions and procedure types.

• Organizes codes by time windows (2010-2012, 2013-2023).
• Each CPT entry includes a human-readable description and extent type.
• Captures coding changes over time (biopsy, wedge, and resection updates).
• Supports time-aware classification in longitudinal analyses.

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Lookup table mapping ICD-O-3 topography codes to site descriptions.

• Columns include icdo3_code and description.
• Covers anatomic sites across head/neck, GI, respiratory, skin, bone, and more.
• Useful for decoding SEER or registry tumor site fields.

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