LABTNSCPSS (version 1.0.2)

run_pipeline: Run the LABTNSCPSS Comorbidity-Frailty Pipeline

Description

Computes Charlson, Elixhauser, Combined Comorbidity, Frailty, and Morbidity-Frailty scores from episode-level data.

Usage

run_pipeline(
  input_file,
  col_mapping,
  coding_system = c("ICD-10-CA", "ICD-10-CM", "ICD-11"),
  out_dir = tempdir()
)

Value

A named list containing:

scores_final

Final combined scores (comorbidity + frailty).

final_data_charlson

Charlson scores by episode.

final_data_elixhauser

Elixhauser scores by episode.

final_data_combined

Combined comorbidity scores by episode.

score_pop_Elixh

Weighted Elixhauser score (ICD-10-CA only; may be NULL).

Arguments

input_file

Path to input CSV file.

col_mapping

Named list mapping required fields to column names in `input_file`. Must include: `patient_id`, `ICD`, `start_date`, `end_date`, `episode_id`.

coding_system

One of: "ICD-10-CA", "ICD-10-CM", "ICD-11".

out_dir

Directory where output CSV files will be written (default: `tempdir()`).

Examples

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

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

res <- run_pipeline(
  input_file = f,
  col_mapping = col_mapping,
  coding_system = "ICD-10-CA",
  out_dir = tempdir()
)
names(res)