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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. URL of the paper: https://doi.org/10.1016/j.ijmedinf.2026.106709 —

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.

tarball <- "./CRAN/LABTNSCPSS_1.0.4.tar.gz"

install.packages(
  tarball,
  repos = NULL,
  type = "source"
)
library(LABTNSCPSS)
packageVersion("LABTNSCPSS")
args(LABTNSCPSS::run_pipeline)

# Load example dataset included in the package

input_file <- system.file(
  "extdata",
  "testpackage.csv",
  package = "LABTNSCPSS"
)

if (input_file == "") {
  stop("The example file was not found in the installed package.")
}

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

out_dir <- tempdir()

# To use a different system, simply change the coding_system from here; possible values ("ICD-10-CA", "ICD-10-CM", "ICD-11"):
results <- LABTNSCPSS::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.