IngoingContactChain {EpiContactTrace} | R Documentation |
IngoingContactChain
The ingoing contact chain is the number of holdings in the network of direct and indirect contacts to the root holding, with regard to temporal and order of the contacts during the defined time window used for contact tracing.
IngoingContactChain(x, ...) ## S4 method for signature 'Contacts' IngoingContactChain(x) ## S4 method for signature 'ContactTrace' IngoingContactChain(x) ## S4 method for signature 'data.frame' IngoingContactChain(x, root, tEnd = NULL, days = NULL, inBegin = NULL, inEnd = NULL)
x |
a ContactTrace object, or a list of ContactTrace objects
or a |
... |
Additional arguments to the method |
root |
vector of roots to calculate ingoing contact chain for. |
tEnd |
the last date to include ingoing movements. Defaults
to |
days |
the number of previous days before tEnd to include
ingoing movements. Defaults to |
inBegin |
the first date to include ingoing
movements. Defaults to |
inEnd |
the last date to include ingoing movements. Defaults
to |
The time period used for IngoingContactChain
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 IngoingContactChain
is a data.frame
with the following columns:
an integer or character identifier of the source holding.
an integer or character identifier of the destination holding.
the Date of the transfer
an optional character vector with the identity of the animal.
an optional numeric vector with the number of animals moved.
an optional character or factor with category of the animal e.g. Cattle.
A data.frame
with the following columns:
The root of the contact tracing
The first date to include ingoing movements
The last date to include ingoing movements
The number of days in the interval inBegin to inEnd
The IngoingContactChain
of the root within the time-interval
signature(x = "ContactTrace")
Get the IngoingContactChain of a ContactTrace
object.
signature(x = "data.frame")
Get the IngoingContactChain for a data.frame with movements, see details and examples.
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
## 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 ingoing contact chain from a ContactTrace object ic.1 <- IngoingContactChain(contactTrace) ## Calculate ingoing contact chain using tEnd and days ic.2 <- IngoingContactChain(transfers, root=2645, tEnd='2005-10-31', days=91) ## Check that the result is identical identical(ic.1, ic.2) ## Calculate ingoing contact chain for all included herds ## First extract all source and destination from the dataset root <- sort(unique(c(transfers$source, transfers$destination))) ## Calculate ingoing contact chain result <- IngoingContactChain(transfers, root=root, tEnd='2005-10-31', days=91) ## End(Not run)