EpiContactTrace (version 0.18.0)

OutgoingContactChain: OutgoingContactChain

Description

The outgoing contact chain is the number of holdings in the network of direct and indirect contacts from the root holding, with regard to temporal and order of the contacts during the defined time window used for contact tracing.

Usage

OutgoingContactChain(x, ...)
# S4 method for Contacts
OutgoingContactChain(x)
# S4 method for ContactTrace
OutgoingContactChain(x)
# S4 method for data.frame
OutgoingContactChain(
  x,
  root,
  tEnd = NULL,
  days = NULL,
  outBegin = NULL,
  outEnd = NULL
)

Value

A data.frame with the following columns:

root

The root of the contact tracing

outBegin

The first date to include outgoing movements

outEnd

The last date to include outgoing movements

outDays

The number of days in the interval outBegin to outEnd

outDegree

The OutgoingContactChain of the root within the time-interval

Arguments

x

a ContactTrace object, or a list of ContactTrace objects or a data.frame with movements of animals between holdings, see Trace for details.

...

Additional arguments to the method

root

vector of roots to calculate outgoing contact chain for.

tEnd

the last date to include outgoing movements. Defaults to NULL

days

the number of previous days before tEnd to include outgoing movements. Defaults to NULL

outBegin

the first date to include outgoing movements. Defaults to NULL

outEnd

the last date to include outgoing movements. Defaults to NULL

Methods

signature(x = "ContactTrace")

Get the OutgoingContactChain of a ContactTrace object.

signature(x = "data.frame")

Get the OutgoingContactChain for a data.frame with movements, see examples.

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

See Also

NetworkSummary

Examples

if (FALSE) {

## Load data
data(transfers)

## Perform contact tracing using tEnd and days
contactTrace <- Trace(movements = transfers,
                      root = 2645,
                      tEnd = "2005-10-31",
                      days = 91)

## Calculate outgoing contact chain from a ContactTrace object
oc_1 <- OutgoingContactChain(contactTrace)

## Calculate outgoing contact chain using tEnd and days
oc_2 <- OutgoingContactChain(transfers,
                             root = 2645,
                             tEnd = "2005-10-31",
                             days = 91)

## Check that the result is identical
identical(oc_1, oc_2)

## Calculate outgoing contact chain for all included herds
## First extract all source and destination from the dataset
root <- sort(unique(c(transfers$source,
                      transfers$destination)))

## Calculate outgoing contact chain
result <- OutgoingContactChain(transfers,
                               root = root,
                               tEnd = "2005-10-31",
                               days = 91)
}