download_events: Download Event Data

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

Download Event Data

Description

Downloads patient event data. Typically done after all records have been annotated and the project is complete.

Usage

download_events(
  uri_fun,
  user,
  password,
  host,
  replica_set,
  port,
  database,
  dates = FALSE,
  sentences_only = FALSE
)

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.
dates	Provide dates of first and last note for each patient; this is needed to assess duration of follow-up, however can take a long time with large cohorts.
sentences_only	Should only a list of sentences be provided?

Value

Object of class data.frame containing patient ID for all cohort members, date of recorded event if any, abstractor comments, sentences reviewed along with statistics about review process.

Examples

## Not run: 
download_events(uri_fun = mongo_uri_standard, user = 'John', password = 'db_password_1234',
host = 'server1234', port = NA)

## End(Not run)

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