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ohdsi-studies / Covid19SubjectsAesiIncidenceRate

Extending on our previous work by Li et al. in understanding the incidence rates of adverse events of special interest (AESI) for COVID-19, this work will look at the rates of these AESIs in patients who had COVDI-19 disease.
https://ohdsi-studies.github.io/Covid19SubjectsAesiIncidenceRate/Protocol.html
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Update codeToRun.R #33

Closed fdefalco closed 2 years ago

fdefalco commented 2 years ago

add pathToDriver to connectionDetails

schuemie commented 2 years ago

I'm not sure just adding a mysterious path for people to set will help. Especially since the recommended practice is to set the path to the jars in an environmental variable.

We have the DatabaseConnector vignette we could point to for people that haven't yet figured out how to use DatabaseConnector to connect to their database. Or maybe we could create a separate vignette or page on the HADES website?

fdefalco commented 2 years ago

Yes, your suggestions sound better. As it stands, it just throws an error when you try to run it as is, my fix only prevents that.

schuemie commented 2 years ago

I've split the DatabaseConnector vignette, so we have a separate one just on getting to the point where people can connect, which is what people will need to run network studies. The new vignette is currently available as PDF only, but will be an HTML webpage once I've released a new version of DatabaseConnector (which hopefully will be soon).

I recommend we point people to this in our network studies.

schuemie commented 2 years ago

(I've also improved the error messages when the pathToDriver isn't specified)

schuemie commented 2 years ago

The instructions for how to connect to a database are now available as a website. I recommend linking to that in the instructions.

ericaVoss commented 2 years ago

Based on what is discussed above, I will perform this in another pull request.

Here is what I added: https://github.com/ohdsi-studies/Covid19SubjectsAesiIncidenceRate/commit/81d1fecce8b17814a895c487235c9503a99bc284