R: 'InDegree'

InDegree {EpiContactTrace}

R Documentation

`InDegree`

Description

The number of herds with direct movements of animals to the root herd during the defined time window used for tracing.

Usage

InDegree(x, ...)

## S4 method for signature 'Contacts'
InDegree(x)

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

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

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 indegree 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`

Details

The time period used for InDegree can either be specified using tEnd and days or inBegin and inEnd.

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

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

The movements in InDegree 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: The first date to include ingoing movements
inEnd: The last date to include ingoing movements
inDays: The number of days in the interval inBegin to inEnd
inDegree: The InDegree of the root within the time-interval

Methods

signature(x = "ContactTrace"): Get the InDegree of a ContactTrace object.
signature(x = "data.frame"): Get the InDegree 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 indegree from a ContactTrace object
id.1 <- InDegree(contactTrace)

## Calculate indegree using tEnd and days
id.2 <- InDegree(transfers,
                 root = 2645,
                 tEnd = "2005-10-31",
                 days = 91)

## Check that the result is identical
identical(id.1, id.2)

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

## Calculate indegree
result <- InDegree(transfers,
                   root = root,
                   tEnd = "2005-10-31",
                   days = 91)

## End(Not run)

[Package EpiContactTrace version 0.17.0 Index]

InDegree