Title: Epidemiological Tool for Contact Tracing
Version: 0.18.0
Description: Routines for epidemiological contact tracing and visualisation of network of contacts.
License: EUPL version 1.1 | EUPL version 1.2 [expanded from: EUPL]
URL: https://github.com/stewid/EpiContactTrace
BugReports: https://github.com/stewid/EpiContactTrace/issues
Type: Package
LazyData: true
Depends: R(≥ 3.0.2)
Imports: graphics, methods, tools, utils
Collate: 'Contacts.R' 'ContactTrace.R' 'EpiContactTrace-package.R' 'in-degree.R' 'ingoing-contact-chain.R' 'network-structure.R' 'network-summary.R' 'out-degree.R' 'outgoing-contact-chain.R' 'plot.R' 'report.R' 'shortest-paths.R' 'show.R' 'trace.R' 'tree.R'
Encoding: UTF-8
RoxygenNote: 7.3.2
NeedsCompilation: yes
Packaged: 2024-10-04 17:54:02 UTC; stefan
Author: Maria Noremark ORCID iD [aut], Stefan Widgren ORCID iD [aut, cre]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Repository: CRAN
Date/Publication: 2024-10-04 18:20:02 UTC

Epidemiological tool for contact tracing.

Description

Routines for epidemiological contact tracing and visualisation of network of contacts.

Details

In many countries, livestock movement data are collected with the major objective to enable contact tracing during disease outbreaks. Livestock movement data can also be of relevance for risk based surveillance - both during outbreak or when investigating if a disease is present in the population. However, the livestock movement databases are not always structured in such a way that relevant information for contact tracing or surveillance design is easily retrieved. EpiContactTrace uses the network parameters in-degree, out-degree, ingoing contact-chain and outgoing contact-chain, which are relevant for forward- and backward contact-tracing respectively. The measures can also be used for identifying herds with many contacts, which can be used in risk based disease surveillance. Different time periods for ingoing and outgoing contacts can be of interest in the contact tracing, based on possible window of introduction, and this can be adjusted in the tool. The output from the analysis is available as a dataset, but moreover, the tool automatically generates a report on farm level. The report both contains an overview of the situation on the farm, including a graph, as well as detailed information including dates of movements on group or individual level on all contacts.

Author(s)

Maintainer: Stefan Widgren stefan.widgren@gmail.com (ORCID)

Authors:

References

See Also

Useful links:

Examples


## Load data
data(transfers)

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

contactTrace

## Generate an html report showing details of the contact tracing
## for root 2645. Note: Creates the files 2645.html and 2645.png
## in the temporary directory.
Report(contactTrace, dir = tempdir())

Class "ContactTrace"

Description

Class to handle contact tracing.

Details

The ContactTrace class holds information for the ingoing and outgoing contact chain for a specific root within the time window used for contact tracing.

Slots

root

A character vector of length one with the identifier of the root.

ingoingContacts

A Contacts object with the contacts for the ingoing contact chain.

outgoingContacts

A Contacts object with the contacts for the outgoing contact chain.

Objects from the Class

Objects can be created by calls of the form new("ContactTrace",root, ingoingContacts, outgoingContacts,...)

Examples


## Load data
data(transfers)

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

## Show structure
str(contactTrace)

Class "Contacts"

Description

Class to handle contacts.

Details

The Contacts class keeps track of all ingoing or outgoing livstock transfers in the contact chain for a specific root within the time window used for contact tracing. The slots; source, destination, t, id, n and category contains contact information extracted from the movement dataset during contact tracing. The index slot is an index to the extracted contacts within the class that together with the distance slot can be used to rebuild the exact contacts that were extracted from each search step during the contact tracing.

Slots

root

A character vector of length one with the identifier of the root.

tBegin

A Date vector of length one with the start date of the time window used for contact tracing.

tEnd

A Date vector of length one with the end date of the time window used for contact tracing.

source

A character vector with the identifiers of the source holdings of the livestock transfer.

destination

A character vector with the identifier of the destination holdings of the livestock transfer.

t

A Date vector of the livestock transfer.

id

A character vector with the identifiers of the animals.

n

A numeric vector with the number of animals transfered.

category

A character vector with the category of animals e.g. cattle.

index

A integer index vector.

distance

A integer vector with the distance from root for the contact[index]

direction

A character vector of length one equal to the direction "in" or "out"

Objects from the Class

Objects can be created by calls of the form new("Contacts", root, startDate, days, source, destination, t, id, n, category, level, direction, ...).

Examples


## Load data
data(transfers)

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

## Show structure of ingoing contacts
str(contactTrace@ingoingContacts)

## Show structure of ougoing contacts
str(contactTrace@outgoingContacts)

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

See Also

NetworkSummary

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)

IngoingContactChain

Description

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.

Usage

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
)

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 ingoing contact chain 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 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:

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

ingoingContactChain

The IngoingContactChain of the root within the time-interval

Methods

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.

References

See Also

NetworkSummary

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 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)

NetworkStructure

Description

Methods for function NetworkStructure in package EpiContactTrace to get the network tree structure from the contact tracing.

Usage

NetworkStructure(object)

## S4 method for signature 'Contacts'
NetworkStructure(object)

## S4 method for signature 'ContactTrace'
NetworkStructure(object)

## S4 method for signature 'list'
NetworkStructure(object)

Arguments

object

A Contacts or linkS4class{ContactTrace} object.

Details

The contact tracing performs a depth first search starting at the root. The NetworkStructure gives the 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 contacts in the depth first search

destination

The destination of the contacts in the depth first search

distance

The distance from the destination to root in the depth first search

Methods

signature(object = "Contacts")

Get the network structure for the Contacts object.

signature(object = "ContactTrace")

Get the network structure for the ingoing and outgoing Contacts of a ContactTrace object.

signature(object = "list")

Get the network structure for a list of ContactTrace objects. Each item in the list must be a ContactTrace object.

See Also

show.

Examples

## Load data
data(transfers)

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

NetworkStructure(contactTrace)

NetworkSummary

Description

NetworkSummary gives a summary of the contact tracing including the time-window, InDegree, OutDegree, IngoingContactChain and OutgoingContactChain.

Usage

NetworkSummary(x, ...)

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

## S4 method for signature 'list'
NetworkSummary(x)

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

Arguments

x

a ContactTrace object, a data.frame with movements of animals between holdings (see Trace for details), or a list of ContactTrace objects where each item in the list must be a ContactTrace object.

...

Additional arguments to the method

root

vector of roots to calculate network summary 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 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:

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

Equals inBegin in Trace

inEnd

Equals inEnd in Trace

outBegin

Equals outBegin in Trace

outEnd

Equals outEnd in Trace

inDegree

The InDegree of the contact tracing

outDegree

The OutDegree of the contact tracing

ingoingContactChain

The IngoingContactChain of the contact tracing

outgoingContactChain

The OutgoingContactChain of the contact tracing

Methods

signature(x = "ContactTrace")

Get the network summary for the ingoing and outgoing Contacts of a ContactTrace object.

signature(x = "list")

Get the network summary for a list of ContactTrace objects. Each item in the list must be a ContactTrace object.

signature(x = "data.frame")

Get the network summary for a data.frame with movements, see details and examples.

References

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 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)

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 data.frame with movements of animals between holdings, see Trace for details.

...

Additional arguments to the method

root

vector of roots to calculate outdegree for.

tEnd

the last date to include outgoing movements. Defaults to NULL

days

the number of previous days before tEnd to include outgoing 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 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

See Also

NetworkSummary

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)

OutgoingContactChain

Description

The outgoing contact chain is the number of holdings in the network of direct and indirect contacts from the root holding, with regard to temporal and order of the contacts during the defined time window used for contact tracing.

Usage

OutgoingContactChain(x, ...)

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

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

## S4 method for signature 'data.frame'
OutgoingContactChain(
  x,
  root,
  tEnd = NULL,
  days = NULL,
  outBegin = NULL,
  outEnd = 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 outgoing contact chain for.

tEnd

the last date to include outgoing movements. Defaults to NULL

days

the number of previous days before tEnd to include outgoing 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

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 OutgoingContactChain of the root within the time-interval

Methods

signature(x = "ContactTrace")

Get the OutgoingContactChain of a ContactTrace object.

signature(x = "data.frame")

Get the OutgoingContactChain for a data.frame with movements, see examples.

References

See Also

NetworkSummary

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 outgoing contact chain from a ContactTrace object
oc_1 <- OutgoingContactChain(contactTrace)

## Calculate outgoing contact chain using tEnd and days
oc_2 <- OutgoingContactChain(transfers,
                             root = 2645,
                             tEnd = "2005-10-31",
                             days = 91)

## Check that the result is identical
identical(oc_1, oc_2)

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

## Calculate outgoing contact chain
result <- OutgoingContactChain(transfers,
                               root = root,
                               tEnd = "2005-10-31",
                               days = 91)

## End(Not run)

Generate a contact tracing Report

Description

EpiContatTrace contains report templates to generate pdf- or html reports for the farm specific contacts. These reports can be useful for hands-on disease tracing in the field. The templates are used by Sweave and can be adapted by the end user. However, in the default setting the report has the following layout; first the contacts are visualised graphically in a plot, as to give an immediate signal to the reader of the report of the number of contacts. In the following, the contact data are presented with different levels of detail split by ingoing and outgoing contacts. The first includes collapsed data and the sequential contact structure at group level (i.e. no information on individuals or dates). In this summary, the sequential structure of each part of the chain is included, and a holding that appears in several different parts of the chain can therefore be included more than once in the summary. The reason for this is to facilitate sequential tracing and getting an overview of each part of the chain. After the summary all details of all contacts included in the contact chains is presented, i.e. date of contact and data on individual level when available. To generate pdf files a TeX installation must exist to compile the latex file. The report is saved in the working directory with the name of the root as filename.

Usage

Report(object, format = c("html", "pdf"), dir = ".", template = NULL)

## S4 method for signature 'ContactTrace'
Report(object, format = c("html", "pdf"), dir = ".", template = NULL)

## S4 method for signature 'list'
Report(object, format = c("html", "pdf"), dir = ".", template = NULL)

Arguments

object

the object

format

the format to use, can be either 'html' or 'pdf'. The default is 'html'

dir

the generated report is written to the directory folder. The default (".") is the current working directory.

template

the Sweave template file to use. If none is provided, the default is used.

Methods

signature(object = "ContactTrace")

Generate a report for a ContactTrace object.

signature(object = "list")

Generate reports for a list of ContactTrace objects.

References

See Also

Sweave, texi2pdf.

Examples

## Load data
data(transfers)

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

## Generate an html report showing details of the contact tracing for
## root 2646.
## Creates the file 2645.html in the temporary directory.
Report(contactTrace, dir = tempdir())

## It's possible to generate reports for a list of ContactTrace objects.
## Perform contact tracing for ten of the included herds
root <- sort(unique(c(transfers$source, transfers$destination)))[1:10]

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

## Generate reports
## Creates the files 1.html, 2.html, ..., 10.html
## in the temporary directory
Report(contactTrace, dir = tempdir())

Get current ContactTrace object when generating a report

Description

EpiContatTrace contains report templates to generate pdf- or html reports for the farm specific contacts. These reports can be useful for hands-on disease tracing in the field. The templates are used by Sweave and can be adapted by the end user. This method enables communication of the current ContactTrace object to the report.

Usage

ReportObject()

Value

The current ContactTrace object when generating a report

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.

See Also

show and NetworkStructure.

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)

Trace Contacts.

Description

Contact tracing for a specied node(s) (root) during a specfied time period. The time period is divided into two parts, one for ingoing contacts and one for outgoing contacts.

Usage

Trace(
  movements,
  root,
  tEnd = NULL,
  days = NULL,
  inBegin = NULL,
  inEnd = NULL,
  outBegin = NULL,
  outEnd = NULL,
  maxDistance = NULL
)

Arguments

movements

a data.frame data.frame with movements, see details.

root

vector of roots to perform contact tracing for.

tEnd

the last date to include ingoing and outgoing movements. Defaults to NULL

days

the number of previous days before tEnd to include ingoing and outgoing 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

maxDistance

stop contact tracing at maxDistance (inclusive) from root. Default is NULL i.e. don't use the maxDistance stop criteria.

Details

The time period used for Trace 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 tracing will be performed 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 tracing will be performed for each index of them.

The argument movements in Trace 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.

References

Examples

## Load data
data(transfers)

## Perform contact tracing using tEnd and days
trace_1 <- Trace(movements = transfers,
                 root = 2645,
                 tEnd = "2005-10-31",
                 days = 91)

## Perform contact tracing using inBegin, inEnd
## outBegin and outEnd
trace_2 <- Trace(movements = 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(trace_1, trace_2)

## Show result of contact tracing
trace_1

## Create a network summary for 10 of the included herds
## First extract all source and destination from the dataset,
## then select the first ten.
root <- sort(unique(c(transfers$source,
                      transfers$destination)))
root <- root[1:10]

## Perform contact tracing using tEnd and days.
trace_3 <- Trace(movements = transfers,
                 root = root,
                 tEnd = "2005-10-31",
                 days = 91)

## Perform contact tracing using inBegin, inEnd
## outBegin and outEnd
trace_4 <- Trace(movements = transfers,
                 root = root,
                 inBegin = rep("2005-08-01", length(root)),
                 inEnd = rep("2005-10-31", length(root)),
                 outBegin=rep("2005-08-01", length(root)),
                 outEnd=rep("2005-10-31", length(root)))

## Check that the result is identical
identical(trace_3, trace_4)

plot,-method

Description

The contact structure can be visualized graphically with a plot. The plot gives an overview of the number of ingoing and outgoing holdings connected to the root holding. The black node is the root holding and all white nodes represent holdings that are direct or indirect holdings with ingoing contacts to root. Grey nodes represent holdings that are direct or indirect holdings with outgoing contacts from root.

Usage

## S4 method for signature 'ContactTrace'
plot(x, y, ...)

Arguments

x

The ContactTrace object to plot

y

Not used

...

Additional arguments affecting the plot

References

See Also

show.

Examples

## Not run: 

## Load data
data(transfers)

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

## Plot in- and outgoing contact chain for the root 2645
plot(contactTrace)

## End(Not run)

Show

Description

Shows information of the time-window used for contact tracing and summary of network parameters. It also visualize the contact structure.

Usage

## S4 method for signature 'Contacts'
show(object)

Arguments

object

The Contacts or ContactTrace object

Value

None (invisible 'NULL').

Methods

signature(object = "Contacts")

Show information for the Contacts object.

signature(object = "ContactTrace")

Show information for the ingoing and outgoing Contacts of a ContactTrace object.

References

Examples

## Not run: 

## Load data
data(transfers)

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

show(contactTrace)

## End(Not run)

Movement Example Data

Description

Movement data included in the package. The data contains fictitious example data of cattle movements during the period 2005-08-01 – 2005-10-31.

Usage

data(transfers)

Format

A data frame with 70190 observations on the following 6 variables.

source

a numeric vector with the holding identifier of the source.

destination

a numeric vector with holding identifier of the destination.

id

a character vector with the identity of the animal. In this dataset an 5 character hexadecimal vector.

t

a Date of the transfers

n

a numeric vector with the number of animals moved. Always 1 in this dataset.

category

a factor describing the category of the animal. Always Cattle in this dataset.

Examples

data(transfers)

Trace(movements = transfers, root = 2645, tEnd = "2005-10-31", days = 90)