CLIF ICU Transfer Analysis

CLIF version

2.1.0

Overview

Identifies hospitalizations coded as outside-hospital (OSH) admissions that are actually transfers linked to a prior encounter at the same site (discharged ≤6 hours before the OSH admission), plus the subset of those transferred directly to the ICU. Compares ICU length of stay, hospital length of stay, ICU/hospital type, mortality, and discharge category before vs. after the transfer.

How to run with uv

uv sync
uv run python 00_icu_transfer_analysis.py

config/config.json must be filled in first.

Outputs

Written to output_directory (from config/config.json, or overridden with --output-dir). Every file name ends in _<site_name> (the lowercased site_name from config).

File	Description
cohort_summary_<site>.csv	OSH cohort counts: total OSH, in-system OSH (linked prior encounter), direct-to-ICU transfers
icu_los_summary_<site>.csv	ICU length of stay (first-stay and cumulative), long format, by cohort/period
hospital_los_summary_<site>.csv	Hospital length of stay by cohort/period
icu_type_summary_in_system_osh_<site>.csv	ICU type counts/percentages, in-system OSH cohort, before vs. after transfer
icu_type_summary_direct_icu_<site>.csv	ICU type counts/percentages, direct-to-ICU transfer cohort
hospital_type_summary_in_system_osh_cohort_<site>.csv	Hospital type counts/percentages, in-system OSH cohort
hospital_type_summary_direct_icu_<site>.csv	Hospital type counts/percentages, direct-to-ICU transfer cohort
mortality_summary_<site>.csv	Mortality rate by cohort
discharge_summary_overall_osh_<site>.csv	Discharge category, overall OSH cohort
discharge_summary_in_system_osh_cohort_<site>.csv	Discharge category, in-system OSH cohort
discharge_summary_direct_icu_<site>.csv	Discharge category, direct-to-ICU transfer cohort
sankey_icu_type_in_system_osh_cohort_<site>.png	ICU type before → after transfer, in-system OSH cohort
sankey_icu_type_direct_icu_<site>.png	ICU type before → after transfer, direct-to-ICU transfer cohort
sankey_hospital_type_in_system_osh_cohort_<site>.png	Hospital type before → after transfer, in-system OSH cohort
sankey_hospital_type_direct_icu_<site>.png	Hospital type before → after transfer, direct-to-ICU transfer cohort
sankey_discharge_category_in_system_osh_cohort_<site>.png	Discharge category before → after transfer, in-system OSH cohort
sankey_discharge_category_direct_icu_<site>.png	Discharge category before → after transfer, direct-to-ICU transfer cohort