ohdsi-circe 0.2.3

Python wrapper for the OHDSI R packages

python-ohdsi

Python wrappers for (some) OHDSI tools. This project has been initiated for supporting OMOP data sources in vantage6.

Make sure you have a working R environment with the OHDSI packages installed.

Building documentation

cd docs
export
make html

cd docs
Set-Item -Path Env:IGNORE_R_IMPORTS -Value True
make html

You can set the IGNORE_R_IMPORTS environment variable to ignore the R imports in the documentation. This is useful when you don't have the R packages installed but want to build the documentation anyway.

TODO

Packages to be wrapped:

• Capr
• CirceR
• CohortGenerator
• SqlRender
• DatabaseConnector
• FeatureExtraction
• FeatureExtractionApi (custom package to wrap FeatureExtraction module in a REST API)

Release packages: ohdsi-circe, ohdsi-capr, ohdsi-cohortgenerator, ohdsi-sqlrender, ohdsi-databaseconnector, ohdsi-featureextraction

Some notes

• installing some OHDSI packages required the --no-multiarch flag: INSTALL_opts=c("--no-multiarch").