OHDSI Home | Forums | Wiki | Github

How to use the latest version of HADES in new study packages generated by ATLAS

(Martijn Schuemie) #1

As most of you know, you can generate estimation and prediction study packages directly from ATLAS. However, the current version of ATLAS is lagging behind a bit in the versions of the HADES packages used in the generated study packages. Most importantly, the study packages generated by ATLAS still use ff, even though we migrated to Andromeda for good reasons a while ago.

If you want to use the latest versions of the study packages (which use the latest version of the HADES packages), you can generate the study packages from the ATLAS JSON yourself. This is done through the Hydra package. See these instructions for how to use Hydra to generate study packages based on the ATLAS JSON.

Not only do the new versions use Andromeda, avoiding issues with ff like this one and many others related to zero-row tables, they also use the latest version of Circe to generate the cohort SQL (thus supporting BigQuery). The estimation study package now also uses renv to handle package dependencies (see the README file in the generated study package).

HADES development announcements
Estimation R - Covariate computing error
Solving “Error: object ‘is.factor.ff’ is not exported by 'namespace:ff'”
(Jose Posada) #2

hi @schuemie, this is awesome. Thank you for posting the instructions

(Gregory Klebanov) #3

just to add that the Andromeda upgrade is going to be released as a part of the upcoming ATLAS 2.8 release (still few weeks away).

(Pascal Mattiocco) #4

Hi Martijn, I really like the capabilities that Hydra provides. I wanted to try but I run into a problem and I’m not sure what is causing this error.
Here the error message I’m getting when running the sample code:

specifications <- loadSpecifications(“c:/Hydra/stroke.json”)
hydrate(specifications = specifications,

  •     outputFolder = "c:/Hydra/MyStudyPackage",
  •     packageName = "Stroke")

Error in .jcall(“RJavaTools”, “Ljava/lang/Object;”, “invokeMethod”, cl, :
java.lang.RuntimeException: java.io.FileNotFoundException: C:\Users\G456584a\Documents\R\win-library\3.5\Hydra\skeletons\CohortCharacterizationStudy_v0.0.1.zip (The system cannot find the file specified)
Any clue to will be appreciated, Thanks

(Martijn Schuemie) #5

Hi Pascal,

It seems your specifications are for a cohort characterization study, which is not something that is currently implemented as an R package. The only study types currently supported are prediction and estimation studies, so things where in ATLAS you have the option to “Download study package”.

(I do hope that in the future we’ll have characterization R packages as well, as that will greatly facilitate distributing them across the OHDSI network, but we’re not there yet).

(Martijn Schuemie) #6

For those of you searching for this error message:

Error: object ‘is.factor.ff’ is not exported by 'namespace:ff'

This is also caused by the fact that the R packages generated by ATLAS are out of date (and require an older version of the ff package than currently in CRAN). I recommend everyone use these instructions to generate study packages, instead of generating them using ATLAS.