Add CDC Adult Sepsis Event (ASE) criteria implementation

[Copilot]

Implements CDC Adult Sepsis Event surveillance criteria as compute_sepsis() function based on reference implementations in ASE_revised_thresholds_wbc_temp and CLIF_sepsis repositories.

Changes

New module: clifpy/utils/sepsis.py

• compute_sepsis() - Main function implementing ASE criteria
• Helper functions for each component:
  • _identify_presumed_infection() - Blood culture + QAD ≥4 (or ≥1 with early death/transfer)
  • _identify_organ_dysfunction_vasopressors() - Vasopressor initiation within window
  • _identify_organ_dysfunction_ventilation() - IMV within window
  • _identify_organ_dysfunction_labs() - AKI, hyperbilirubinemia, thrombocytopenia, lactate

ASE criteria (both required):

• Presumed infection: Blood culture + qualifying antibiotic days
• Organ dysfunction: Vasopressors OR IMV OR lab dysfunction (within ±2 days)

Testing & documentation:

• 14 unit tests covering all criteria paths and edge cases
• Working demo in examples/sepsis_demo.py
• Complete API documentation in docs/sepsis_module.md

Usage

from clifpy.utils import compute_sepsis

sepsis_df = compute_sepsis(
    blood_cultures=bc_df,           # hospitalization_id, collect_dttm, fluid_category
    antibiotics=abx_df,             # hospitalization_id, admin_dttm, med_group
    hospitalization=hosp_df,        # hospitalization_id, discharge_dttm, discharge_category
    labs=labs_df,                   # hospitalization_id, lab_category, lab_value_numeric, lab_result_dttm
    continuous_meds=meds_df,        # Optional: vasopressor data
    respiratory_support=resp_df,    # Optional: IMV data
    window_days=2,                  # Configurable
    include_lactate=True            # Optional criterion
)
# Returns: hospitalization_id, ase_flag, presumed_infection_time, first_organ_dysfunction_time, organ_dysfunction_type

Follows existing patterns (DuckDB-based like compute_sofa), handles missing data gracefully, includes configurable time windows.

References:

• https://github.com/dmh0817/ASE_revised_thresholds_wbc_temp
• https://github.com/Common-Longitudinal-ICU-data-Format/CLIF_sepsis
• CDC Sepsis Surveillance Toolkit

Original prompt

---

This section details on the original issue you should resolve

<issue_title>add sepsis flag</issue_title>
<issue_description>start with the sepsis ASE critiera as implemented in two projects:

https://github.com/dmh0817/ASE_revised_thresholds_wbc_temp

https://github.com/Common-Longitudinal-ICU-data-Format/CLIF_sepsis</issue_description>

<agent_instructions>Read the repositories linked in the issue, find the code that implements the sepsis criteria and convert to a clifpy function</agent_instructions>

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

• Fixes add sepsis function  #109

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