execute: Execute OHDSI Iris

Usage Arguments Details Value Examples

Usage

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execute(dbms, user = NULL, domain = NULL, password = NULL, server,
  port = NULL, cdmSchema, cdmVersion = 5, file)

Arguments

dbms

The type of DBMS running on the server. Valid values are

  • "mysql" for MySQL

  • "oracle" for Oracle

  • "postgresql" for PostgreSQL

  • "redshift" for Amazon Redshift

  • "sql server" for Microsoft SQL Server

  • "pdw" for Microsoft Parallel Data Warehouse (PDW)

  • "netezza" for IBM Netezza

user

The user name used to access the server. If the user is not specified for SQL Server, Windows Integrated Security will be used, which requires the SQL Server JDBC drivers to be installed.

domain

(optional) The Windows domain for SQL Server only.

password

The password for that user

server

The name of the server

port

(optional) The port on the server to connect to

cdmSchema

Schema name where your patient-level data in OMOP CDM format resides

cdmVersion

Define the OMOP CDM version used: currently support 4 and 5. Default = 4

file

(Optional) Name of local file to place results; makre sure to use forward slashes (/)

Details

This function executes OHDSI Iris. Iris computes some basic parameters about a dataset.

Value

Study results are placed in CSV format files in specified local folder and returned as an R object class OhdsiStudy when sufficiently small. The properties of an OhdsiStudy may differ from study to study.

Examples

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## Not run: 
# Run study
execute(dbms = "postgresql",
        user = "joebruin",
        password = "supersecret",
        server = "myserver",
        cdmSchema = "cdm_schema",
        cdmVersion = 4)

# Email result file
email(from = "collaborator@ohdsi.org",
      dataDescription = "CDM4 Simulated Data")

## End(Not run)

OHDSI/Iris documentation built on May 7, 2019, 8:26 p.m.