clifR is an R port of the Python library clifpy for standardizing and analyzing critical care (ICU) data using the Common Longitudinal ICU data Format (CLIF) version 2.0.

Transform heterogeneous ICU data into standardized, analysis-ready datasets with built-in validation, clinical calculations, and high-performance data processing.

• CLIF 2.0 Tables: 18 core table classes implemented (Patient, Hospitalization, ADT, Vitals, Labs, Diagnoses, Medications, Respiratory Support, Code Status, CRRT, ECMO/MCS, Microbiology, Assessments, Procedures, Position)
• Schema Validation: Automatic validation against CLIF specification
• Clinical Calculations:
  • SOFA (Sequential Organ Failure Assessment) scores
  • Charlson Comorbidity Index (CCI) from ICD-9/ICD-10 codes
  • P/F ratio calculation
  • Ventilator settings analysis
• Medication Analysis:
  • Vasopressor and sedation tracking
  • Antibiotic administration timing
  • Dose unit conversion
• Respiratory Support: Ventilator modes, settings, and compliance metrics
• Unit Conversion: Smart conversion between medical units (doses, temperature, pressure, labs)
• Encounter Stitching: Link related hospital stays
• Wide Dataset Creation: Transform narrow clinical data to time-series format
• High Performance: Leverages DuckDB and arrow for efficient processing
• Timezone-Aware: Proper handling of timestamps across timezones

# Install development version from GitHub
# install.packages("devtools")
devtools::install_github("AartikSarma/clifR")

library(clifR)

# Load and validate CLIF data
orchestrator <- ClifOrchestrator$new(
  data_directory = "path/to/clif/data",
  timezone = "US/Eastern"
)

# Validate all tables
orchestrator$validate_all()

# Access data
vitals <- orchestrator$vitals$df
labs <- orchestrator$labs$df

# Create wide dataset
wide_data <- orchestrator$create_wide_dataset()

# Calculate SOFA scores
sofa_scores <- orchestrator$calculate_sofa_scores()

This package implements the CLIF 2.0 specification for standardized ICU data.

• Patient demographics
• Hospitalization records
• ADT (Admission/Discharge/Transfer) events
• Vital signs
• Laboratory results
• Respiratory support
• Medications (continuous and intermittent)
• Microbiology (culture, non-culture, susceptibility)
• Diagnoses, procedures, assessments
• And more...

• CLIF Specification: https://clif-icu.com/data-dictionary
• Python Library (clifpy): https://github.com/Common-Longitudinal-ICU-data-Format/clifpy
• Package Documentation: [Coming soon]

🚧 This package is under active development. Core functionality is being ported from the Python library with systematic cross-validation.

This is an R port of clifpy. Contributions are welcome! Please ensure:

• R implementations match Python outputs (see cross-validation tests)
• Code follows tidyverse style guide
• All functions have roxygen2 documentation
• Tests pass with devtools::check()

• clifpy: Python implementation (GitHub)
• CLIF Consortium: https://clif-icu.com/

Apache License 2.0

If you use this package in your research, please cite the CLIF Consortium and the original clifpy library.