get_patient: Retrieve Patient Data

In simon-hans/CEDARS: Simple and Efficient Pipeline for Electronic Health Record Annotation

Retrieve Patient Data

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,
  replica_set,
  port,
  database,
  end_user,
  search_query,
  use_negation,
  hide_duplicates,
  patient_id = NA,
  tag_query = 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.
replica_set	MongoDB replica set, if indicated.
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.
tag_query	If desired, text metadata tags will be used for search.

simon-hans/CEDARS documentation built on Feb. 14, 2024, 3:16 a.m.