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Important update to the OHDSI R packages


(Martijn Schuemie) #1

At the beginning of the next week (June 8-9) we will be switching many of the OHDSI R packages from ff to Andromeda. To find out more, see this forum thread. In short, almost all of our packages rely on ff to handle objects that may be too large to fit in memory, but ff has always had some serious issues, and wasn’t maintained well. Also, CRAN no longer accepts our package updates (e.g. for DatabaseConnector) because we still depend on ff. For this reason we developed Andromeda to replace ff.

By necessity, we will need to switch all packages pretty much at once, dropping ff in favor of Andromeda. The following packages will be affected:

  • ParallelLogger
  • DatabaseConnector
  • Cyclops
  • FeatureExtraction
  • CohortDiagnostics
  • CohortMethod
  • MethodEvaluation
  • BigKnn
  • PatientLevelPrediction

Going forward, people should use the latest versions of these packages, as for example an older version of CohortMethod will not work with the newer version of DatabaseConnector.

For ongoing studies you can still use and install the current versions of these packages:

install.packages("remotes")
library(remotes)
install_github("ohdsi/ParallelLogger", ref = "v1.2.0")
install_github("ohdsi/DatabaseConnector", ref = "v2.4.4")
install_github("ohdsi/Cyclops", ref = "v2.0.1")
install_github("ohdsi/FeatureExtraction", ref = "v2.2.5")
install_github("ohdsi/CohortDiagnostics", ref = "v0.1.3")
install_github("ohdsi/CohortMethod", ref = "v3.1.1")
install_github("ohdsi/MethodEvaluation", ref = "v1.1.0")
install_github("ohdsi/BigKnn", ref = "v0.0.3")
install_github("ohdsi/PatientLevelPrediction", ref = "v3.0.16")

(Martijn Schuemie) #2

The update has been completed!

Next, we will update the study package skeletons for prediction and estimation studies to use these newer versions, and add them to ATLAS. This may take a while. I’ll keep you updated.


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