OutDegree {EpiContactTrace} | R Documentation |
OutDegree
Description
The number of herds with direct movements of animals from the root herd during the defined time window used for tracing
Usage
OutDegree(x, ...)
## S4 method for signature 'Contacts'
OutDegree(x)
## S4 method for signature 'ContactTrace'
OutDegree(x)
## S4 method for signature 'data.frame'
OutDegree(x, root, tEnd = NULL, days = NULL, outBegin = NULL, outEnd = NULL)
Arguments
x |
a ContactTrace object, or a list of ContactTrace objects
or a |
... |
Additional arguments to the method |
root |
vector of roots to calculate outdegree for. |
tEnd |
the last date to include outgoing movements. Defaults
to |
days |
the number of previous days before tEnd to include
outgoing movements. Defaults to |
outBegin |
the first date to include outgoing
movements. Defaults to |
outEnd |
the last date to include outgoing movements. Defaults
to |
Details
The time period used for OutDegree
can either be specified
using tEnd
and days
or outBegin
and
outEnd
.
If using tEnd
and days
, the time period for outgoing
contacts ends at tEnd
and starts at days
prior to
tEnd
. The outdegree will be calculated for each combination
of root
, tEnd
and days
.
An alternative way is to use outBegin
and outEnd
.
The time period for outgoing contacts starts at outBegin and ends
at outEndDate. The vectors root
outBegin
,
outEnd
must have the same lengths and the outdegree will be
calculated for each index of them.
The movements in OutDegree
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
- outBegin
-
The first date to include outgoing movements
- outEnd
-
The last date to include outgoing movements
- outDays
-
The number of days in the interval outBegin to outEnd
- outDegree
-
The
OutDegree
of the root within the time-interval
Methods
signature(x = "ContactTrace")
-
Get the OutDegree of a
ContactTrace
object. signature(x = "data.frame")
-
Get the OutDegree 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
See Also
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 outdegree from a ContactTrace object
od.1 <- OutDegree(contactTrace)
## Calculate outdegree using tEnd and days
od.2 <- OutDegree(transfers,
root = 2645,
tEnd = "2005-10-31",
days = 91)
## Check that the result is identical
identical(od.1, od.2)
## Calculate outdegree for all included herds
## First extract all source and destination from the dataset
root <- sort(unique(c(transfers$source,
transfers$destination)))
## Calculate outdegree
result <- OutDegree(transfers,
root = root,
tEnd = "2005-10-31",
days = 91)
## End(Not run)