R: 'NetworkSummary'

NetworkSummary {EpiContactTrace}

R Documentation

`NetworkSummary`

Description

NetworkSummary gives a summary of the contact tracing including the time-window, InDegree, OutDegree, IngoingContactChain and OutgoingContactChain.

Usage

NetworkSummary(x, ...)

## S4 method for signature 'ContactTrace'
NetworkSummary(x)

## S4 method for signature 'list'
NetworkSummary(x)

## S4 method for signature 'data.frame'
NetworkSummary(
  x,
  root,
  tEnd = NULL,
  days = NULL,
  inBegin = NULL,
  inEnd = NULL,
  outBegin = NULL,
  outEnd = NULL
)

Arguments

`x`	a ContactTrace object, a `data.frame` with movements of animals between holdings (see `Trace` for details), or a list of `ContactTrace` objects where each item in the list must be a `ContactTrace` object.
`...`	Additional arguments to the method
`root`	vector of roots to calculate network summary for.
`tEnd`	the last date to include ingoing movements. Defaults to `NULL`
`days`	the number of previous days before tEnd to include ingoing 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`

Details

The time period used for NetworkSummary 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 network summary will be calculated 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 network summary will be calculated for each index of them.

The movements in NetworkSummary 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.

Value

A data.frame with the following columns:

root: The root of the contact tracing
inBegin: Equals inBegin in Trace
inEnd: Equals inEnd in Trace
outBegin: Equals outBegin in Trace
outEnd: Equals outEnd in Trace
inDegree: The InDegree of the contact tracing
outDegree: The OutDegree of the contact tracing
ingoingContactChain: The IngoingContactChain of the contact tracing
outgoingContactChain: The OutgoingContactChain of the contact tracing

Methods

signature(x = "ContactTrace"): Get the network summary for the ingoing and outgoing Contacts of a ContactTrace object.
signature(x = "list"): Get the network summary for a list of ContactTrace objects. Each item in the list must be a ContactTrace object.
signature(x = "data.frame"): Get the network summary for a data.frame with movements, see details and 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

Examples

## Not run: 

## Load data
data(transfers)

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

## Calculate network summary from a ContactTrace object
ns_1 <- NetworkSummary(contactTrace)

## Calculate network summary using tEnd and days
ns_2 <- NetworkSummary(transfers,
                       root = 2645,
                       tEnd = "2005-10-31",
                       days = 91)

## Check that the result is identical
identical(ns_1, ns_2)

## Calculate network summary using inBegin, inEnd
## outBegin and outEnd
ns_3 <- NetworkSummary(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(ns_2, ns_3)

## When calculating the network summary for a data.frame of movements
## a data.frame for each combination of root, tEnd and days are returned.
root <- c(1, 2, 3)
tEnd <- c("2005-09-01", "2005-10-01")
days <- c(30, 45)

## The network summary are calculated at the following
## 12 combinations.
## root = 1, tEnd = "2005-09-01", days = 30
## root = 1, tEnd = "2005-09-01", days = 45
## root = 1, tEnd = "2005-10-01", days = 30
## root = 1, tEnd = "2005-10-01", days = 45
## root = 2, tEnd = "2005-09-01", days = 30
## root = 2, tEnd = "2005-09-01", days = 45
## root = 2, tEnd = "2005-10-01", days = 30
## root = 2, tEnd = "2005-10-01", days = 45
## root = 3, tEnd = "2005-09-01", days = 30
## root = 3, tEnd = "2005-09-01", days = 45
## root = 3, tEnd = "2005-10-01", days = 30
## root = 3, tEnd = "2005-10-01", days = 45
NetworkSummary(transfers, root, tEnd, days)

## Create a network summary for all included herds
## First extract all source and destination from the dataset
root <- sort(unique(c(transfers$source,
                      transfers$destination)))

## Perform contact tracing using tEnd and days
result_1 <- NetworkSummary(transfers,
                           root = root,
                           tEnd = "2005-10-31",
                           days = 90)

## Perform contact tracing using inBegin, inEnd, outBegin and outEnd.
result_2 <- NetworkSummary(transfers,
                           root = root,
                           inBegin = rep("2005-08-02", length(root)),
                           inEnd = rep("2005-10-31", length(root)),
                           outBegin = rep("2005-08-02", length(root)),
                           outEnd = rep("2005-10-31", length(root)))

## End(Not run)

[Package EpiContactTrace version 0.17.0 Index]