NetworkSummary {EpiContactTrace} | R Documentation |
NetworkSummary
NetworkSummary
gives a summary of the contact tracing including the
time-window, InDegree
, OutDegree
,
IngoingContactChain
and OutgoingContactChain
.
NetworkSummary(x, ...) ## S4 method for signature 'ContactTrace' NetworkSummary(x) ## S4 method for signature 'data.frame' NetworkSummary(x, root, tEnd = NULL, days = NULL, inBegin = NULL, inEnd = NULL, outBegin = NULL, outEnd = NULL)
x |
a ContactTrace object or a |
... |
Additional arguments to the method |
root |
vector of roots to calculate network summary 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 |
outBegin |
the first date to include outgoing
movements. Defaults to |
outEnd |
the last date to include outgoing movements. Defaults
to |
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:
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
Equals inBegin in Trace
Equals inEnd in Trace
Equals outBegin in Trace
Equals outEnd in Trace
The InDegree
of the contact tracing
The OutDegree
of the contact tracing
The IngoingContactChain
of the contact tracing
The OutgoingContactChain
of the contact tracing
signature(x = "ContactTrace")
Get the network summary for the ingoing and outgoing
Contacts
of a ContactTrace object.
signature(x = "data.frame")
Get the network summary 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 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)