Note, these instructions are under development
This is a reproducibility repository documenting procedure for a study of antibiotic hepatotoxicity in the intensive care unit setting.
To reproduce this work (which is possible because you can use the exact same data that we did), you will first have to obtain the MIMIC III dataset. For a direct link to the application site, click here.
Study preparation requires setting up a PostgreSQL database with MIMIC III data, and then running an ETL to the OMOP CDM V5.
After setting up your database, enter its credentials in the cdmdb/R/db-config.R file. If you prefer not to write your password in plaintext, you can have RStudio prompt for a password by uncommenting the line including .rs.askForPassword('Enter password:'). Note that this doesn't work for knitting the file, however, and requires you to run and open a script/Rmd in RStudio.
From there, assuming you have a working installation of R and relevant dependencies, you may knit the report with make report.