Contacts-class: Class '"Contacts"'

In EpiContactTrace: Epidemiological Tool for Contact Tracing

Class "Contacts"

Description

Class to handle contacts.

Details

The Contacts class keeps track of all ingoing or outgoing livstock transfers in the contact chain for a specific root within the time window used for contact tracing. The slots; source, destination, t, id, n and category contains contact information extracted from the movement dataset during contact tracing. The index slot is an index to the extracted contacts within the class that together with the distance slot can be used to rebuild the exact contacts that were extracted from each search step during the contact tracing.

Slots

root

A character vector of length one with the identifier of the root.

tBegin

A Date vector of length one with the start date of the time window used for contact tracing.

tEnd

A Date vector of length one with the end date of the time window used for contact tracing.

source

A character vector with the identifiers of the source holdings of the livestock transfer.

destination

A character vector with the identifier of the destination holdings of the livestock transfer.

t

A Date vector of the livestock transfer.

id

A character vector with the identifiers of the animals.

n

A numeric vector with the number of animals transfered.

category

A character vector with the category of animals e.g. cattle.

index

A integer index vector.

distance

A integer vector with the distance from root for the contact[index]

direction

A character vector of length one equal to the direction "in" or "out"

Objects from the Class

Objects can be created by calls of the form new("Contacts", root, startDate, days, source, destination, t, id, n, category, level, direction, ...).

Examples

## Load data
data(transfers)

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

## Show structure of ingoing contacts
str(contactTrace@ingoingContacts)

## Show structure of ougoing contacts
str(contactTrace@outgoingContacts)

EpiContactTrace documentation built on Oct. 5, 2024, 1:07 a.m.