CohortMethod is part of HADES.
An R package with a Shiny viewer to explore profiles of patients in a cohort. The output of this R-package is a self contained R shiny that contain person level data for review.
- Contains person level data. This package is not to be considered de-identified.
- Please do not share the output with others as it may violate protected health information.
- .RData file in output contains PHI.
- From an instantiated cohort, identifies specified number of random persons. It also allows for non random selection by specifying a set of personId as input.
- Extracts person level data for each person from the common data model, and constructs a results object in rds form. This rds object has person level data with personId and dates.
- Accepts a set of configurable parameters for the shiny application. This parameters will be chosen in the shiny app. e.g. regular expression.
- Allows additional de-identification using two optional mechanisms (shift dates and replace OMOP personId with a new random id). Shift date: shifts all dates so that the first observation_period_start_date for a person is set to January 1st 2000, and all other dates are shifted in relation to this date. Also creates and replaces the source personId with a new randomly generated id.
- Creates a R shiny app in a specified local folder, that can then be published to a shiny server or explored locally.
- The output of createCohortExplorerApp is a Shiny App with person level data in .RData. It is in the output folder.
- Go the output location in your file browser (e.g. windows file explorer in a Windows computer) and start 'CohortExplorer.Rproj'.
- In R console now run renv::restore() to enable renv. This will download all required packages and dependencies and set up the run environment.
- Next call to shiny::runApp()
- If you want to run this Shiny App on a remote Shiny Server, you may copy all the files in the outpu to the remote shiny servers new app file folder. run renv::restore() in the shiny server and restart app.
CohortExplorer is an R package.
Requires R (version 3.6.0 or higher).
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See the instructions here for configuring your R environment, including RTools and Java.
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In R, use the following commands to download and install CohortExplorer:
install.packages("remotes")
remotes::install_github("ohdsi/CohortExplorer")Documentation can be found on the package website.
PDF versions of the documentation are also available:
- Package manual: CohortExplorer.pdf
- Developer questions/comments/feedback: OHDSI Forum
- We use the GitHub issue tracker for all bugs/issues/enhancements
Read here how you can contribute to this package.
CohortExplorer is licensed under Apache License 2.0
CohortExplorer is being developed in R Studio.
CohortExplorer is under development.