EpiContactTrace-package: Epidemiological tool for contact tracing.

Description

Routines for epidemiological contact tracing and visualisation of network of contacts.

Arguments

Author

Maintainer: Stefan Widgren stefan.widgren@gmail.com (ORCID)

Authors:

Maria Noremark (ORCID)

Details

In many countries, livestock movement data are collected with the major objective to enable contact tracing during disease outbreaks. Livestock movement data can also be of relevance for risk based surveillance - both during outbreak or when investigating if a disease is present in the population. However, the livestock movement databases are not always structured in such a way that relevant information for contact tracing or surveillance design is easily retrieved. EpiContactTrace uses the network parameters in-degree, out-degree, ingoing contact-chain and outgoing contact-chain, which are relevant for forward- and backward contact-tracing respectively. The measures can also be used for identifying herds with many contacts, which can be used in risk based disease surveillance. Different time periods for ingoing and outgoing contacts can be of interest in the contact tracing, based on possible window of introduction, and this can be adjusted in the tool. The output from the analysis is available as a dataset, but moreover, the tool automatically generates a report on farm level. The report both contains an overview of the situation on the farm, including a graph, as well as detailed information including dates of movements on group or individual level on all contacts.

References

Dube, C., et al., A review of network analysis terminology and its application to foot-and-mouth disease modelling and policy development. Transbound Emerg Dis 56 (2009) 73-85, doi: 10.1111/j.1865-1682.2008.01064.x
Noremark, M., et al., Network analysis of cattle and pig movements in Sweden: Measures relevant for disease control and riskbased surveillance. Preventive Veterinary Medicine 99 (2011) 78-90, doi: 10.1016/j.prevetmed.2010.12.009

Examples

Run this code


## Load data
data(transfers)

## Perform contact tracing
contactTrace <- Trace(movements = transfers,
                      root = 2645,
                      tEnd = "2005-10-31",
                      days = 90)

contactTrace

## Generate an html report showing details of the contact tracing
## for root 2645. Note: Creates the files 2645.html and 2645.png
## in the temporary directory.
Report(contactTrace, dir = tempdir())