README.md

In chrisknoll/CohortManager: OHDSI Cohort Manager Util

CohortManager

======== An R tool that lets you manage cohort definitions sourced from CSVs

Getting Started

1. in R, use the following commands to install CohortManager (if you have prior package installations of aony of these packages, you may need to first unistall them using the command remove.packages()). r install.packages("devtools") library(devtools) install_github("chrisknoll/CohortManager")

2. If you do not have existing CSV files, create an empty directory to store these, and execute the following to create empty files: r directoryPath <- "{path to empty directory}"; CohortManager::initCsv(directoryPath)

3. Edit the CSV files. The CSV files needed for cohort manager are:
4. ConcpetSets.csv: Contains the names and IDs of the concept set expressions used across all cohort definitions. One row per concept set.
5. ConceptSetItems.csv: Contains the items, defining the concept_id and if you should include/exclude, use descendants or use mapped. Many rows per concept set.
6. CohortDefinitions.csv: Contains the cohort definitions, specifying the event limits, prior/post observation requirements, and end date strategy. One row per cohort definition.
7. CohortCriteria.csv: Contains the universe of cohort criteria referenced in the cohort definitions.
8. CohortPrimaryEvents.csv: Specifies which CohortCriteria should be associated to a cohort as the 'primary events' used to define the cohort start date.
9. Cohort CorrelatedCriteria: Specifies one or more criteria that validates the Primary Events. These criteria are AND'd together when validating the Primary Event.
10. CohortDemographicCriteria.csv: Specifies one or more demographic criteria (used to specify age, gender or time window of the primary event.
11. DateOffsetStrategy.csv: Specifies the data used when the cohort defintion exit strategy is set to 'DateOffset'. One row per cohort definition.
12. CustomEraStrategy.csv: Specifies the data used when the cohort defintion exit strategy is set to 'CustomEra'. One row per cohort definition.
13. CohortCensoringEvents.csv: Specifies one or more cohort criteria to use as censoring events.

14. Set the CohortManager options for the WebAPI path and sourceKey: directoryPath <- {path to empty directory}; CohortManager::initCsv(directoryPath)

15. Call CohortManager::setDataDirectory(path). This will verify all tequired files and columns are found.

16. Call CohortManager::sync() to create/update cohort definitions hosted in the specified WebAPI.

Troubleshooting

Ensure that all files are saved before calling sync(). Do hot have the CohortDefinitions.csv file open in excell when calling sync() because the file is modified with he server-side cohort definition IDs, and if the file is open, it will report 'access deined'.

License

CohortManager is licensed under Apache License 2.0

Development

CohortManager is being developed in R Studio.

chrisknoll/CohortManager documentation built on May 13, 2019, 6:55 p.m.