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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.
Install development version from GitHub:
install.packages("remotes")
remotes::install_github("celehs/phecodemap")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()See the App instructions guide to learn how to use the app.
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
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.