phecodemap

Overview

The phecodemap package builds a shiny app to visualize the hierarchy of PheCode Mapping with ICD-9 and ICD-10-cm. The same PheCode hierarchy is displayed in two ways: as a sunburst plot and as a tree.

Installation

Install development version from GitHub:

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

Usage

This is a basic example which shows you how to run the phecodemap 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(phecodemap) beforehand, instead of directly running phecodemap::run_app().

library(phecodemap)
run_app()

App instructions

See the App instructions guide to learn how to use the app.

Citations

• Wei WQ, Bastarache LA, Carroll RJ, Marlo JE, Osterman TJ, Gamazon ER, Cox NJ, Roden DM, Denny JC. Evaluating phecodes, clinical classification software, and ICD-9-CM codes for phenome-wide association studies in the electronic health record. PLoS One. 2017 Jul 7;12(7):e0175508. https://doi.org/10.1371/journal.pone.0175508

• Wu, P., Gifford, A., Meng, X., Li, X., Campbell, H., Varley, T., Zhao, J., Carroll, R., Bastarache, L., Denny, J. C., Theodoratou, E., & Wei, W. Q. (2019). Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation. JMIR medical informatics, 7(4), e14325. https://doi.org/10.2196/14325