pre_search: Execute Search on a Set of Records

In CEDARS: Simple and Efficient Pipeline for Electronic Health Record Annotation

Description

Batches a keyword/CUI search for a cohort of patients. Useful to speed up the process by end users, since search results will be pre-populated. Locks each record before proceeding with search on existing NLP annotations. Patient records with no matching sentences or a known event date at or before the earliest matching sentence will be marked as reviewed. The latter assumes the query orders to skip sentences after events.

Usage

pre_search(patient_vect = NA, uri_fun, user, password, host, port, database)

Arguments

patient_vect	Vector of patient ID's. Default is NA, in which case all unlocked records will be searched.
uri_fun	Uniform resource identifier (URI) string generating function for MongoDB credentials.
user	MongoDB user name.
password	MongoDB user password.
host	MongoDB host server.
port	MongoDB port.
database	MongoDB database name.

Value

No return value, called to execute a query in the database.

Examples

## Not run: 
pre_search(patient_vect = NA, uri_fun = mongo_uri_standard, user = 'John',
password = 'db_password_1234', host = 'server1234', database = 'TEST_PROJECT')

## End(Not run)

CEDARS documentation built on Feb. 7, 2021, 5:06 p.m.