kesernetwork

Overview

The kesernetwork builds a shiny app to visualize the knowledge networks for the code concepts. Using co-occurrence matrices of EHR codes from Veterans Affairs (VA) and Massachusetts General Brigham (MGB), the knowledge extraction via sparse embedding regression (KESER) algorithm was used to construct knowledge networks for the code concepts.

Installation

Install the released version of kesernetwork from CRAN:

install.packages("kesernetwork")

Or install the development version from GitHub with:

install.packages("remotes")
remotes::install_github("celehs/kesernetwork")

Usage

This is a basic example which shows you how to run the kesernetwork app. Remember you need to get access to the data and save it to your local computer. In order to guarantee some dependencies are loaded, you must use library(kesernetwork) beforehand, instead of directly running kesernetwork::run_app().

library(kesernetwork)
run_app(Rdata_path = "path/to/kesernetwork.RData")

See the getting started guide to learn how to use kesernetwork.

Citations

• Hong, C., Rush, E., Liu, M. et al. Clinical knowledge extraction via sparse embedding regression (KESER) with multi-center large scale electronic health record data. npj Digit. Med. 4, 151 (2021). https://doi.org/10.1038/s41746-021-00519-z