get_data: Get one Sentence for Review

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

Description

Gets one sentence, one note and date of note for one patient. Main way for an end user to query CEDARS.

Usage

get_data(
  uri_fun,
  user,
  password,
  host,
  port,
  database,
  end_user,
  end_user_password,
  html = TRUE,
  position,
  patient_id = NA,
  ldap = FALSE
)

Arguments

uri_fun	Uniform resource identifier (URI) string generating function for MongoDB credentials.
user	MongoDB user name.
password	MongoDB user password.
host	MongoDB server host.
port	MongoDB port.
database	MongoDB database name.
end_user	CEDARS end user name.
end_user_password	CEDARS end user password.
html	Should output keywords/concepts be highlighted with HTML markup? Default is TRUE.
position	Sentence position within the sequence of selected sentences for a given patient.
patient_id	Used if a specific patient record is requested, instead of a search for next record to annotate.
ldap	Is LDAP authentication being used? If so, password will not be checked and access will be granted automatically.

Value

A list with patient-specific information and a dataframe with selected sentences along with sentence-specific data.

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