Package 'autotracer'

Title: Probabilistically Identify Clusters in Electronic Medical Records
Description: What the package does (one paragraph).
Authors: Michael DeWitt [aut, cre] (ORCID: <https://orcid.org/0000-0001-8940-1967>), Cone Health [aut, cph]
Maintainer: Michael DeWitt <[email protected]>
License: MIT + file LICENSE
Version: 0.0.1
Built: 2026-04-28 05:24:35 UTC
Source: https://github.com/conedatascience/autotracer

Help Index

Simulated Patient Data Synthetic data that can be used to explore "autotracer"

Description

Simulated Patient Data Synthetic data that can be used to explore "autotracer"

Usage

autotracer_linelist

Format

a data.frame with 10500 rows and 9 columns:

x

Latitude

y

Longitude

Race

Race indentifier

patient_id

Unique patient indentifier (e.g. MRN)

Age

Age of the patient in years

Sex

Biological sex of the patient

Language

Primary spoken language of the patient

Age10

Age given as a ten year age group

date

Date of test or infection identification

Connect Probable Cases

Description

Probabilistically estimates a likely tranmission chain using EMR derrived data.

Usage

connect_probable_cases(
  dat,
  weights_in = NULL,
  threshold = 30,
  exposure_link = NULL
)

Arguments

dat

the dataframe of likely connect cases with a column named "date" indicating the onset or positive test date and "patient_id", a unique identifier for the record.
weights_in

the weights to use for the serial interval if available
threshold

integer, the threshold in days at which to discard a connected case (e.g. >30 days from previous case, then discard).
exposure_link

string or column name, how these cases are connected