Use and manipulate persistent ids of network elements
Persistent ids (pids) are unique values attached to vertices or edges which remain unchanged throughout network manipulation and extraction processes. The “vertex.pid” of a vertex is an overall data-set id, unlike the “vertex.id” which is an index dependent on network size. These functions provide ways to look up vertex.pids from vertex.ids (and the other way around) and also provide necessary modifications to some standard network functions to safely work with pids.
get.vertex.id(nd, pid) get.vertex.pid(nd, id) get.edge.id(nd, pid) get.edge.pid(nd, id) initialize.pids(nd) vertex.pid.check(nd) edge.pid.check(nd)
nd |
a |
pid |
persistent id(s) of the network element(s) for which the network-specific id(s) should be returned |
id |
network-specific (index) id(s) of the network element for which the persistent id(s) should be returned |
The persistent id functionality is an optional feature of networkDynamic objects. If a network-level attribute named vertex.pid exists, its value is required to be the name of a vertex attribute that can safely be used as a vertex.pid. If it is set to NULL, pids will be ignored. A vertex.pid must have a unique value for all vertices. Persistent ids for edges function in the same way, except the attribute is named edge.pid.
Some existing network code uses the vertex.names attributes of networks as a persistent id without checking that it is unique. It is possible to indicate that vertex.names can safely be used as a vertex.pid by setting vertex.pid to 'vertex.names'
The function initialize.pids can be used to create a set of pids on all existing vertices (named vertex.pid and edges named edge.pid). The pids are currently initialized with pseudo-random hex strings using the tempfile function (something like '4ad912252bc2'). It is especially useful if called after a network object as been constructed and before any extractions are performed.
The element addition functions (add.vertices) override their network-package counterparts in order to permit assigning pids to newly-added elements if the pid is defined. They can be defined by the user with the vertex.pids argument, or, if not specified, a unique random id will be generated. (Note that any new values added by default to a vertex.names pid will not be numeric.)
Some of the import/conversion methods may set pids. See network.
User-specified pids are checked for uniqueness. The the current auto-generated pid implementation produces ids that are unique within the current network. They are also almost certain to be unique within an R session (so that vertices will have a unique id if added and removed) and quite likely across sessions, but we need more details on the tempfile's implementation.
With the exception of the "check" utilities, all of these functions modify their network argument in place.
Get methods:
get.vertex.id returns the vertex.id(s) of vertices corresponding to the vertex.pid(s) provided.
get.vertex.pid returns the vertex.pid(s) of vertices corresponding to the vertex.id(s) provided.
get.edge.id returns the edge.id(s) of edge corresponding to the edge.pid(s) provided.
get.edge.pid returns the edge.pid(s) of edges corresponding to the edge.id(s) provided.
Each of the above return NA values where no match is found.
vertex.pid.check throws an error if the vertex.pid is found to not meet specifications. Otherwise returns TRUE or FALSE and gives a warning if vertex.pid does not exist
edge.pid.check throws an error if the edge.pid is found to not meet specifications. Otherwise returns TRUE or FALSE and gives a warning if edge.pid does not exist
Adding edges via the extraction/replacement operators [,] bypasses the pid code and will break the edge pids defined for the network. Similarly, add.vertices.active and add.edges.active do not yet support including pids.
lxwang, skyebend, the statnet team
See also add.vertices in network.
# use vertex.names as a persistent id net<-network.initialize(5) set.network.attribute(net, 'vertex.pid','vertex.names') # find original vertex corresponding to vertex in smaller extracted net haystack<-network.initialize(30) activate.vertices(haystack,v=10:20) # hide a needle somewhere in the haystack set.vertex.attribute(haystack,'needle',TRUE,v=sample(1:30,1)) # set up the persistand ids with defaults initialize.pids(haystack) # some hay is removed over time ... newstack<-network.extract(haystack,at=100,active.default=FALSE) network.size(newstack) # we find the needle! needleId <-which(get.vertex.attribute(newstack,'needle')) needleId # which vertex is the corresponding one in original stack? oldId<-get.vertex.id(haystack,get.vertex.pid(newstack,needleId)) oldId # check if we got it right.. get.vertex.attribute(haystack,'needle')[oldId] # one reason you wouldn't want to use ordinary vertex.names net<-network.initialize(3) add.vertices(net,3) network.vertex.names(net) # but if you make it a persistant id, new names will be created net<-network.initialize(3) set.network.attribute(net,'vertex.pid','vertex.names') add.vertices(net,3) network.vertex.names(net) # try with edges and add/remove vertices net <-network.initialize(10) add.edges(net,1:9,2:10) set.edge.attribute(net,'test',"you found me!",e=7) initialize.pids(net) changed<-net add.vertices(changed,5) delete.vertices(changed,c(1,3,5,15)) delete.edges(changed,eid=1:3) # which edge in changed corresponds to edge 7 in net? network.edgecount(changed) get.edge.id(changed,get.edge.pid(net,7)) # actually, they are the same because of NULL edges in edgelist get.edge.attribute(changed,'test',unlist=FALSE)[[7]] # however, the ids of the vertices have changed changed$mel[[7]]$inl net$mel[[7]]$inl # do they still match up? get.vertex.pid(changed,changed$mel[[7]]$inl)==get.vertex.pid(net,net$mel[[7]]$inl)
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