Automated Characterization of Health Information at Large-scale Longitudinal Evidence Systems (ACHILLES) - descriptive statistics about a OMOP CDM v4/v5 database
(Please review the Achilles Wiki for specific details for Linux)
Make sure you have your data in the OMOP CDM v4/v5 format.
Make sure that you have Java installed. If you don't have Java already intalled on your computed (on most computers it already is installed), go to java.com to get the latest version. (If you have trouble building with rJava below, be sure on Windows that your Path variable includes the path to jvm.dll (Windows Button --> type "path" --> Edit Environmental Variables --> Edit PATH variable, add to end ;C:/Program Files/Java/jre/bin/server) or wherever it is on your system.)
in R, use the following commands to install Achilles:
r
install.packages("devtools")
library(devtools)
install_github("ohdsi/SqlRender")
install_github("ohdsi/DatabaseConnector")
install_github("ohdsi/Achilles")
r
library(Achilles)
connectionDetails <- createConnectionDetails(dbms="sql server", server="server.com")
achillesResults <- achilles(connectionDetails, cdmDatabaseSchema="cdm4_inst", resultsDatabaseSchema="results", sourceName="My Source Name", cdmVersion = "cdm version")
"cdm4_inst" cdmDatabaseSchema parmater and "results" resultsDatabaseSchema parameter are the names of the schemas holding the CDM data and target results respectively.
See the DatabaseConnector package for details on settings the connection details for your database, for example by typing
r
?createConnectionDetails
Currently "sql server", "oracle", "postgresql", and "redshift" are supported as dbms.
"cdmVersion" can be either 4 or 5.
r
exportToJson(connectionDetails, cdmDatabaseSchema = "cdm4_inst", resultsDatabaseSchema = "results", outputPath = "c:/myPath/AchillesExport", cdmVersion = "cdm version")
This is an alternative method for running Achilles that does not require R and Java installations, using a Docker container instead.
Install Docker and Docker Compose.
Clone this repository with git (git clone https://github.com/OHDSI/Achilles.git
) and make it your working directory (cd Achilles
).
Copy env_vars.sample
to env_vars
and fill in the variable definitions. The ACHILLES_DB_URI
should be formatted as <dbms>://<username>:<password>@<host>/<schema>
.
Copy docker-compose.yml.sample
to docker-compose.yml
and fill in the data output directory.
Build the docker image with docker-compose build
.
Run Achilles in the background with docker-compose run -d achilles
.
Achilles is licensed under Apache License 2.0
Achilles is being developed in R Studio.
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