omopify_xml: Create an OMOP database from ICNARC XML

In CC-HIC/icnarc2omop: Conversion of ICNARC XML to OMOP CDM 6

Description

This function instantiates an OHDSI CDM (referred to throughout as OMOP for brevity) database from raw ICNARC XML. It can be specfied to output either version 5.3.1 or 6.0.0. In doing so, it creates an extremely spartan instance of OMOP. This behaviour is intentional to short cut the creation of an OMOP database, which can be a daunting process. After the OMOP database has been created, you have the option to add more data directly from additional ICNARC XML in the future, or begin to populate the database directly with data from another source, with your patient and their outcomes already populated.

Usage

omopify_xml(
  project_path,
  nhs_trust,
  cdm_version = "5.3.1",
  vocabulary_version = "5",
  database_name = NULL,
  database_engine = "postgres",
  host_name = "localhost",
  port_no = 5432,
  username = NULL,
  from_empty = TRUE,
  vocabulary = TRUE,
  indexes = TRUE,
  constraints = TRUE,
  sqlite_file = NULL,
  dummy_data = FALSE
)

Arguments

project_path	the path to your project folder with the following populated folders: vocab - contains ATHENA vocabularies. meta - constains metadata on the ICNARC ETL process. xml - contains raw ICNARC XML in lexicographical order.
nhs_trust	a character string with the full name of the trust.
cdm_version	the version of the CDM you are using, choose from: 5.3.1 6.0.0
vocabulary_version	the version of the vocabulary you are using
database_name	the name of the database you are connecting to
database_engine	the database engine, choose from: sqlite: SQLite postgres: PostgreSQL mysql: Microsoft SQL Server (or similar varients)
host_name	host ip address
port_no	port number
username	username to database (*must* have write privaleges)
from_empty	logical flag: do you want to create the OMOP database from stratch. If you want to first write out the tables yourself this can be set to FALSE
vocabulary	logical flag: do you want to write out vocabularies
indexes	logical flag: do you want to create db with indexes
constraints	logical flag: do you want to create db with relational constraints
sqlite_file	a filename if using sqlite
dummy_data	logical flag: do you want to ignore XML files and use local dummy data instead

Value

TRUE if completed without errors

CC-HIC/icnarc2omop documentation built on March 4, 2020, 11:11 a.m.