README.md

In resplab/codex: The CODEX (Comorbidity, Obstruction, Dyspnea, and Previous Severe Exacerbations) Index: Short and Medium-Term Prognosis in Patients Hospitalized for Chronic Obstructive Pulmonary Disease (COPD) Exacerbations

codexcopd

R package for the CODEX (comorbidity, obstruction, dyspnea, and previous severe exacerbations) index: Short and Medium-term (3 to 12 months) Prognosis in Patients Hospitalized for COPD Exacerbations described in https://www.sciencedirect.com/science/article/pii/S0012369215345888.

Installation

You can download the latest development version from GitHub:

install.packages("remotes")
remotes::install_github("resplab/codexcopd")

CODEX Index

To get CODEX index, you will need to pass in patient's risk factors. For example:

codex (age = 40,charlson = 8 , FEV1 = 40, mMRC = 3, exacerbation = 2)

The codex() function returns a CODEX index with possible values range from 0 to 10, with higher scores indicating a greater risk of death. It was a successful predictor of survival and readmission at 3 months and 1 year after hospital discharge for a COPD exacerbation.

Cloud-based API Access

The Peer Models Network allows users to access CODEXindex through the cloud. A MACRO-enabled Excel-file can be used to interact with the model and see the results. To download the PRISM Excel template file for CODEX index please refer to the model repository.

Cloud Access through R

Users can access models on the Peer Models Network using the peermodels R package, available on GitHub. The following code snippet illustrates how you can run the model for example patient provided in the codexcopd package:

remotes::install_github (resplab/peermodels)
library(peermodels)
connect_to_model("codexcopd", api_key = YOUR_API_KEY)
input <- get_default_input()
results <- model_run(input)

Cloud Access through Linux Bash

In Ubuntu, you can call the API with curl:

curl \
-X POST \
-H "x-prism-auth-user: REPLACE_WITH_API_KEY" \
-H "Content-Type: application/json" \
-d '{"func":["prism_model_run"],"model_input":[{"age":40,"charlson":8,"FEV1":40,"mMRC":3,"exacerbation":2}]}' \
http


### Citation

Please cite: 

Almagro, P., Soriano, J. B., Cabrera, F. J., Boixeda, R., Alonso-Ortiz, M. B., Barreiro, B., ... & Heredia, J. L. (2014). Short-and medium-term prognosis in patients hospitalized for COPD exacerbation: the CODEX index. Chest, 145(5), 972-980. ```

resplab/codex documentation built on June 25, 2020, 9:08 p.m.