EpiContactTrace (version 0.8.8)

OutgoingContactChain-methods: 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.

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.

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

Value

• A data.frame with the following columns: [object Object],[object Object],[object Object],[object Object],[object Object]

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

## 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)