get_patient: Retrieve Patient Data

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

Description

Retrieves annotated electronic health record sentences for one patient. Returns basic info, along with a dataframe containing sentences and corresponding notes.

Usage

get_patient(
  uri_fun,
  user,
  password,
  host,
  port,
  database,
  end_user,
  search_query,
  use_negation,
  hide_duplicates,
  patient_id = NA
)

Arguments

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.
end_user	CEDARS end user name.
search_query	Medical corpus query containg keywords/CUI's, boolean elements and other operators ('AND', 'OR', '!', '(', or ')').
use_negation	Should negated items be ignored in the keyword/concept search?
hide_duplicates	Should duplicated sentences be removed for search results?
patient_id	Used if a specific patient record is requested, instead of a search for next record to annotate.

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