HIV

This study aims to study HIV. (identify and characterize a cohort; showcase data elements available in that cohort)

Detailed information is available in the protocol.

To see an example of extracted aggregated data (no patient level data is being extracted), see folder extras/sample_output.

Requirements

• A database in Common Data Model version 5 in one of these platforms: SQL Server, Oracle, PostgreSQL, IBM Netezza, Apache Impala, Amazon RedShift, or Microsoft APS.
• R version 3.4.0 or newer
• On Windows: RTools
• Java

See this video for instructions on how to set up the R environment on Windows.

How to run

1. In R, use the following code to install the study package and its dependencies:

install.packages("devtools")
library(devtools)
install_github("ohdsi/SqlRender")
install_github("ohdsi/DatabaseConnector")
install_github("ohdsi/OhdsiRTools")
install_github("ohdsi/OhdsiSharing")
install_github("ohdsi/FeatureExtraction")
install_github("ohdsi/CohortMethod")
install_github("sigfried/HiVDescriptive")

If you experience problems on Windows where rJava can't find Java, one solution may be to add args = "--no-multiarch" to each install_github call, for example:

install_github("ohdsi/SqlRender", args = "--no-multiarch")

Alternatively, ensure that you have installed both 32-bit and 64-bit JDK versions, as mentioned in the video tutorial.

2. Once installed, you can execute the study by modifying and using the following code:

library(HivDescritive)

connectionDetails <- createConnectionDetails(dbms = "postgresql",
					     user = "joe",
					     password = "secret",
					     server = "myserver")
cdmDatabaseSchema <- "cdm_data"
cohortDatabaseSchema <- "results"
cohortTable <- "hiv_descriptive"
outputfolder <- "c:/temp/study_results"

execute(connectionDetails = connectionDetails,
	cdmDatabaseSchema = cdmDatabaseSchema,
	cohortDatabaseSchema = cohortDatabaseSchema,
	cohortTable = cohortTable,
	oracleTempSchema = NULL,
	outputFolder = outputfolder,
	createCohorts = TRUE,
	packageResults = TRUE,
	#maxCores = 30
	)

• For details on how to configurecreateConnectionDetails in your environment type this for help:

?createConnectionDetails

• cdmDatabaseSchema should specify the schema name where your data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.

• cohortDatabaseSchema should specify the schema name where intermediate results can be stored. Note that for SQL Server, this should include both the database and schema name, for example 'results.dbo'.

• cohortTable should specify the name of the table that will be created in the work database schema where the exposure and outcomes cohorts will be stored. The default value is 'ohdsi_alendronate_raloxifene'.

• oracleTempSchema should be used only by Oracle users to specify a schema where the user has write priviliges for storing temporary tables. This can be the same as the work database schema.

• outputFolder a location in your local file system where results can be written. Make sure to use forward slashes (/). Do not use a folder on a network drive since this greatly impacts performance.

3. Email the file export/studyResult.zip in the output folder to the study coordinator (Sigfried Gold) (extracted data is on aggregated level only) Optionaly, you can use the OHDSI encrypted submission using key and secret credentials.

Getting Involved

• Developer questions/comments/feedback: http://forums.ohdsi.org/t/hiv-research-in-the-cdm/6789
• We use the GitHub issue tracker for all bugs/issues/enhancements

Development

Package was developed in R Studio.

Development status

In production. Version 1 with simple output is being piloted at 2 initial sites.