R: 'ShortestPaths'

ShortestPaths {EpiContactTrace}

R Documentation

`ShortestPaths`

Description

Methods for function ShortestPaths in package EpiContactTrace to get the shortest distance from/to the root given by the contact tracing.

Usage

ShortestPaths(x, ...)

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

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

Arguments

`x`	a `ContactTrace` object, 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 shortest path 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 contact tracing performs a depth first search starting at the root. The ShortestPaths gives the shortest distance from root at each node. The network tree structure given by the depth first search is shown by show.

Value

A data.frame with the following columns:

root: The root of the contact tracing
inBegin: If the direction is ingoing, then inBegin equals inBegin in Trace else NA.
inEnd: If the direction is ingoing, then inEnd equals inEnd in Trace else NA.
outBegin: If the direction is outgoing, then outBegin equals outBegin in Trace else NA.
outEnd: If the direction is outgoing, then outEnd equals outEnd in Trace else NA.
direction: If the direction is ingoing, then direction equals 'in' else 'out'
source: The source of the contact at distance from root
destination: The destination of the contact at distance from root
distance: The shortest distance from/to root in the depth first search

Methods

signature(object = "ContactTrace"): Get the shortest paths for the ingoing and outgoing Contacts of a ContactTrace object.
signature(x = "data.frame"): Get the shortest paths for a data.frame with movements, see details and examples.

Examples

## Not run: 

## Load data
data(transfers)

## Perform contact tracing
contactTrace <- Trace(movements = transfers,
                      root = 2645,
                      tEnd = "2005-10-31",
                      days = 90)

ShortestPaths(contactTrace)

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

sp <- ShortestPaths(transfers,
                    root = root,
                    tEnd = "2005-10-31",
                    days = 90)

## End(Not run)

[Package EpiContactTrace version 0.17.0 Index]

ShortestPaths