obkContacts: Formal class "obkContacts"
In thibautjombart/OutbreakTools: Basic Tools for the Analysis of Disease Outbreaks

Description Usage Arguments Objects from the class obkContacts Slots Methods Author(s) Examples

The class obkContacts is a formal (S4) class for storing contact data between individuals. Contacts can be static, or change in time (dynamic) at specified dates. Contacts are handled as network and networkDynamic objects, for static and dynamic contacts, respectively. See the corresponding packages for more information on this data structure.

An obkContacts object can be constructed from individual identifiers (stored as character vectors), representing the 'sender' and 'receiver' individuals, whether the contacts should be regarded as directed, with optional information about the timing of contacts.

get.contacts(x, ...)
get.ncontacts(x, ...)
## S4 method for signature 'obkContacts'
get.ncontacts(x, from=NULL, to=NULL, ...)
## S4 method for signature 'obkContacts'
get.contacts(x, from=NULL, to=NULL, ...)

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

## S4 method for signature 'obkContacts'
plot(x, y=NULL, labels=get.individuals(x),
...)

## S4 method for signature 'obkContacts'
as.matrix(x,
         matrix.type=c("adjacency","incidence","edgelist"),
         use.labels=TRUE, ...)

## S4 method for signature 'obkContacts'
as.data.frame(x, row.names=NULL, optional=FALSE,
         use.labels=TRUE, ...)

`x,object`	an obkContacts object.
`y`	used for compatibility with the generic definition of `plot`; unused.
`labels`	a vector of characters giving annotation for the vertices.
`matrix.type`	a character indicating which type of matrix to extract(adjacency, incidence, or edge matrix).
`from,to`	dates indicating the time span to consider for active contacts (for dynamic networks only).
`...`	arguments passed to other methods; currently not used, except for `plot`.
`row.names,optional`	unused arguments, there for compatibility with the generic `as.data.frame`.
`use.labels`	a logical indicating whether labels should be used to indicate individuals, as opposed to their index in the network.

obkContacts objects can be created by calls to new("obkContacts", ...), where '...' can be the following arguments:

from: a vector of individual identifiers in character format representing the source of the contact.
to: a vector of individual identifiers in character format representing the sink of the contact.
directed: a Boolean for whether contacts should be regarded as directed (TRUE) or not (FALSE).
start: an optional vector of times representing the start of a contact; can be dates or numeric values.
end: an optional vector of times representing the end of a contact; can be dates or numeric values..
duration: an optional vector of durations of a contact, as an alternative way of representing dynamic contacts than using end; if numeric values are used together with dates in 'start' and 'end', these will be interpreted as numbers of days.

The following slots are the content of instances of the class obkContacts; note that in most cases, it is better to retrieve information via accessors (see below), rather than by accessing the slots manually.

contacts:: an object of class network or networkDynamic.
origin:: an object of class Date indicating the origin of the contacts (i.e., this corresponds to "day 0".

Here is a list of methods available for obkContacts objects. Most of these methods are accessors, that is, functions which are used to retrieve the content of the object. Specific manpages can exist for accessors with more than one argument. These are indicated by a '*' symbol next to the method's name. This list also contains methods for conversion from obkContacts to other classes.

show: signature(x = "obkContacts"): printing of the object.
plot: signature(x = "obkContacts", y=NULL): plot the contact network; relies on plot.network, to which arguments can be passed via ....
get.ncontacts: signature(x = "obkContacts"): returns the number of contacts; for dynamic contact networks, starting dates can be specified by the argument from, and end date by the argument to.
get.contacts: signature(x = "obkContacts"): returns the contacts (as network or networkDynamic); for dynamic contact networks, starting dates can be specified by the argument from, and end date by the argument to.
get.nindividuals*: signature(x = "obkContacts"): returns the number of individuals in the contact data (see manpage of get.individuals for details)..
get.individuals*: signature(x = "obkContacts"): returns the identifiers of individuals in the contact data(see manpage of get.individuals for details)..
get.ndates*: signature(x = "obkContacts"): returns the number of dates at which contact structure changes (see manpage of get.dates for details).
get.dates*: signature(x = "obkContacts"): returns the dates at which contact structure changes (see manpage of get.dates for details).
as.matrix: signature(x = "obkContacts", matrix.type=c("adjacency","incidence","edgelist")): extract an adjacency, incidence, or edge matrix from the object.
as.data.frame: signature(x = "obkContacts", ...): for static contacts, returns an edge list; for dynamic contacts, returns and edge list with information on the timing of contacts.

Original class: Simon Frost (sdwfrost@gmail.com)
Plot, various accessors, conversion methods: Thibaut Jombart (tjombart@imperial.ac.uk)

## THIS IS A TOY EXAMPLE ##
cf <- c("a", "b", "a", "c", "d")
ct <- c("b", "c", "c", "d", "b")
onset <- c(1, 2, 3, 4, 5)
terminus <- c(1.2, 4, 3.5, 4.1, 6)
oc.static <- new("obkContacts",cf,ct,FALSE) # static network
oc.dynamic <- new("obkContacts",cf,ct,FALSE,onset,terminus)
oc.static
oc.dynamic

plot(oc.static, main="Contact network")



## PLOTTING A DYNAMIC CONTACT NETWORK ##
## LOAD DATA
data(ToyOutbreak) # ToyOutbreak includes a dynamic contact network

## PLOT THE STATIC NETWORK
plot(ToyOutbreak@contacts)

## PLOT THE DYNAMIC NETWORK OVER THE FIRST 4 DAYS OF THE OUTBREAK
par(mfrow=c(2,2))

plot(ToyOutbreak@contacts)

plot(get.contacts(ToyOutbreak, from=0, to=2), displaylabels=TRUE,
     main="Contact network - days 1-2")

plot(get.contacts(ToyOutbreak, from=2.9, to=3.1), displaylabels=TRUE,
     main="Contact network - day 3")

plot(get.contacts(ToyOutbreak, from=3.9, to=4.1), displaylabels=TRUE,
     main="Contact network - day 4")

par(mfrow=c(1,1))

# extract matrices of adjacency, incidence, or edge list
as.matrix(ToyOutbreak@contacts)
as.matrix(ToyOutbreak@contacts, "incidence")
as.matrix(ToyOutbreak@contacts, "edgelist")

as.data.frame(ToyOutbreak@contacts)