README.md

In ohdsi-studies/AlcoholicLiverDisease: Alcoholic liver disease treatment effects

Alcoholic Liver Disease (ALD): Medication and clinical parameters associated with course of disease

• Analytics use case(s): Characterization, Population-Level Estimation
• Study type: Clinical Application
• Tags: Liver, Alcoholic liver disease, Drug, Gender
• Study lead: Prof. Dr. Dr. Andreas Teufel, Medical Faculty Mannheim, Heidelberg University, Germany
• Study lead forums tag: Andreas Teufel
• Study start date: -
• Study end date: -
• Protocol: Here
• Publications: -
• Results explorer: -

Within this study we are interested in investigating new treatment options for patients with alcoholic liver disease respectively inside different sub groups as well as gender specific in respect of the overall survival of the patients.

How to run

1. Requirements for executing this package:
2. DatabaseConnector ( >= 2.1.4 )
3. SqlRender ( >= 1.5.2 )

4. survival ( >= 2.42-4 )

5. The package needs to be installed into the R environment.

6. with the devtools package inside a R session it could be done with r devtools::install_github("ohdsi-studies/AlcoholicLiverDisease") If you get the error message: "No CurrentVersion entry in Software/JavaSoft registry!", use the following command r devtools::install_github("ohdsi-studies/AlcoholicLiveDisease, INSTALL_opts="--no-multiarch")

7. from the command line on linux machines it could be done with bash R CMD build AlcoholicLiverDisease R CMD INSTALL AlcoholicLiverDisease_0.0.1.tar.gz

8. Then, within an interactive R session, execute the adapted commands below.

```r library(AlcoholicLiverDisease)

  connectionDetails <- DatabaseConnector::createConnectionDetails(
      dbms = "sql server",          # DB Server type
      server = "localhost",         # URL / IP
      user = "<user>",              # user for connection
      password = "<password>",      # password for connection
  )

  execute(
      connectionDetails,
      sourceName="abbreviation",    # Abbreviation for the origin of DB
      schema="<schema>"             # Schema name of the DB
  )

``` The parameter sourceName is only used to connect the results with the origin. Therefore, please provide your institution or DB abbreviation as the sourceName parameter.

Depending on the package version of "DatabaseConnector", the schema version is removed within the function "createConnectionDetails". Therefore, the schema parameter is includd into the "execute" function.

Example configuration: - "sql server": r dbms = "sql server": server = "<URL>" # "localhost" schema = "<DB>.<schema>" # "testdb.dbo" - "postgresql": r dbms = "posgresql" server = "<URL>/<DB>" # "localhost/testdb" schema = "<schema>" # "public"

1. Once the execution is finished, the results will be placed as ZIP files inside the temporary directory of the R session. Please send them back to the study coordinator.

ohdsi-studies/AlcoholicLiverDisease documentation built on Dec. 22, 2021, 4:16 a.m.