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LABTNSCPSS

LABTNSCPSS is an R package that implements a reproducible pipeline to process episode-level clinical data and compute chronic pathology, frailty, and comorbidity indices from diagnosis codes.

The package computes:

• Charlson Comorbidity Index (CCI)
• Elixhauser Comorbidity Index (ECI)
• Combined Comorbidity Index
• Frailty Index
• Morbidity-Frailty Index

from episode-level clinical data.

Installation

Install from CRAN:

install.packages("LABTNSCPSS")

Load the package:

library(LABTNSCPSS)

##Quick Start Example

The example below uses the sample dataset included in the package.

# Load example dataset included in the package
input_file <- system.file("extdata", "testpackage.csv", package = "LABTNSCPSS")

# Define column mapping
col_mapping <- list(
  patient_id = "trajectoire_id",
  ICD        = "diagnostic_code",
  start_date = "date_debut",
  end_date   = "date_fin",
  episode_id = "episode_id"
)

# Choose output directory
out_dir <- tempdir()

# Run the pipeline
results <- run_pipeline(
  input_file   = input_file,
  col_mapping  = col_mapping,
  coding_system = "ICD-10-CA",
  out_dir      = out_dir
)

results

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.