EpiContactTrace (version 0.18.0)

Trace: Trace Contacts.

Description

Contact tracing for a specied node(s) (root) during a specfied time period. The time period is divided into two parts, one for ingoing contacts and one for outgoing contacts.

Usage

Trace(
  movements,
  root,
  tEnd = NULL,
  days = NULL,
  inBegin = NULL,
  inEnd = NULL,
  outBegin = NULL,
  outEnd = NULL,
  maxDistance = NULL
)

Arguments

movements

a data.frame data.frame with movements, see details.

root

vector of roots to perform contact tracing for.

tEnd

the last date to include ingoing and outgoing movements. Defaults to NULL

days

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

inBegin

the first date to include ingoing movements. Defaults to NULL

inEnd

the last date to include ingoing 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

maxDistance

stop contact tracing at maxDistance (inclusive) from root. Default is NULL i.e. don't use the maxDistance stop criteria.

Details

The time period used for Trace can either be specified using tEnd and days or inBegin, inEnd, outBegin and outEnd.

If using tEnd and days, the time period for ingoing and outgoing contacts ends at tEnd and starts at days prior to tEnd. The tracing will be performed for each combination of root, tEnd and days.

An alternative way is to use inBegin, inEnd, outBegin and outEnd. The time period for ingoing contacts starts at inBegin and ends at inEndDate. For outgoing contacts the time period starts at outBegin and ends at outEnd. The vectors root inBegin, inEnd, outBegin and outEnd must have the same lengths and the tracing will be performed for each index of them.

The argument movements in Trace is a data.frame with the following columns:

source

an integer or character identifier of the source holding.

destination

an integer or character identifier of the destination holding.

t

the Date of the transfer

id

an optional character vector with the identity of the animal.

n

an optional numeric vector with the number of animals moved.

category

an optional character or factor with category of the animal e.g. Cattle.

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

## Load data
data(transfers)

## Perform contact tracing using tEnd and days
trace_1 <- Trace(movements = transfers,
                 root = 2645,
                 tEnd = "2005-10-31",
                 days = 91)

## Perform contact tracing using inBegin, inEnd
## outBegin and outEnd
trace_2 <- Trace(movements = transfers,
                 root = 2645,
                 inBegin = "2005-08-01",
                 inEnd = "2005-10-31",
                 outBegin = "2005-08-01",
                 outEnd = "2005-10-31")

## Check that the result is identical
identical(trace_1, trace_2)

## Show result of contact tracing
trace_1

## Create a network summary for 10 of the included herds
## First extract all source and destination from the dataset,
## then select the first ten.
root <- sort(unique(c(transfers$source,
                      transfers$destination)))
root <- root[1:10]

## Perform contact tracing using tEnd and days.
trace_3 <- Trace(movements = transfers,
                 root = root,
                 tEnd = "2005-10-31",
                 days = 91)

## Perform contact tracing using inBegin, inEnd
## outBegin and outEnd
trace_4 <- Trace(movements = transfers,
                 root = root,
                 inBegin = rep("2005-08-01", length(root)),
                 inEnd = rep("2005-10-31", length(root)),
                 outBegin=rep("2005-08-01", length(root)),
                 outEnd=rep("2005-10-31", length(root)))

## Check that the result is identical
identical(trace_3, trace_4)