Marathon is an R package to programmatically read concepts from a reference or pre-mapped list of codes into named concept sets for use in ATLAS
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Takes lists of codes and vocabulary identifiers and maps them to OMOP standard via the vocabulary lookup
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Can produce either spreadsheet or ATLAS concept set outputs
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Can provide a facile route to cohort and concept set population of new ATLAS environments.
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Without epidemiological expertise, peer reviewed reference libraries can be imported into ATLAS.
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[COMING SOON] Automatic input list cleaning, integration with sql, json and CapR cohort definitions.
Marathon is an R Package
Requires R (Version 4.0.0 or higher) Installation of HADES is recommended and many packages are required. Java is required.
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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
install.packages("remotes")
remotes::install_github("DrTTrousers/Marathon")
Coming soon
Alpha Build! Investigate column names first and then check if vocabularies need sanitsing!
Please open an issue with any suggestions, or a Pull request if you want to join in!