multinet (version 4.0)

multinet.IO: Reading and writing multilayer networks from/to file

Description

These functions are used to store a multilayer network to a file or load it from a file.

There are two network formats accepted: multiplex (default) or multilayer. A full multiplex network input file has the following format:

-- comment lines start with two dashes (--) #VERSION 3.0

#TYPE multiplex

#ACTOR ATTRIBUTES AttributeName1,STRING AttributeName2,NUMERIC -- etc.

#NODE ATTRIBUTES LayerName1,AttributeName1,STRING LayerName1,AttributeName2,NUMERIC LayerName2,AttributeName3,STRING -- etc.

#EDGE ATTRIBUTES -- edge attributes can be defined for specific layers (called local attributes): LayerName1,AttributeName,STRING LayerName1,AttributeName,NUMERIC -- or for all layers (called global attributes): AnotherAttributeName,NUMERIC -- etc.

#LAYERS LayerName1,UNDIRECTED LayerName2,DIRECTED LayerName3,UNDIRECTED,LOOPS -- etc. -- LOOPS indicates that edges from one vertex to itself (called loops) are allowed on that layer

#ACTORS ActorName1,AttributeValueList... ActorName2,AttributeValueList... -- etc.

#VERTICES ActorName1,LayerName1,AttributeValueList... ActorName1,LayerName2,AttributeValueList... -- etc.

#EDGES ActorName1,ActorName2,LayerName1,LocalAttributeValueList,GlobalAttributeValueList... -- etc. -- the attribute values must be specified in the same order in which they are defined above

----------------------------------

If the #LAYERS section is empty, all edges are created as undirected.

If the #ACTOR ATTRIBUTES, #VERTEX ATTRIBUTES or #EDGE ATTRIBUTES sections are empty, no attributes are created.

The #LAYERS, #ACTORS and #VERTICES sections are useful only if attributes are present, or if there are actors that are not present in any layer (#ACTORS), or if there are isolated vertices (#VERTICES), otherwise they can be omitted.

If no section is specified, #EDGES is the default.

Therefore, a non attributed, undirected multiplex network file can be as simple as: ---------------------------------- Actor1,Actor2,Layer1 Actor1,Actor3,Layer1 Actor4,Actor2,Layer2 ----------------------------------

If interlayer edges exist, then type "multilayer" must be specified, and layers and edges are formatted in a different way:

#VERSION 3.0

#TYPE multilayer

#ACTOR ATTRIBUTES AttributeName1,STRING AttributeName2,NUMERIC -- etc.

#NODE ATTRIBUTES LayerName1,AttributeName1,STRING LayerName1,AttributeName2,NUMERIC LayerName2,AttributeName3,STRING -- etc.

#EDGE ATTRIBUTES -- edge attributes can be defined for specific layers: LayerName1,AttributeName,STRING LayerName1,AttributeName,NUMERIC -- or for all layers (called global attributes): AnotherAttributeName,NUMERIC -- etc.

#LAYERS -- LayerName1,LayerName1,UNDIRECTED -- LayerName2,LayerName2,DIRECTED -- LayerName3,LayerName3,DIRECTED,LOOPS -- LayerName1,LayerName2,DIRECTED -- etc. -- all intra-layer specifications (where the first and second layers are the same) -- should be listed first. -- LOOPS is only allowed for intra-layer specifications.

#ACTORS ActorName1,AttributeValueList... ActorName2,AttributeValueList... -- etc.

#VERTICES ActorName1,LayerName1,AttributeValueList... ActorName1,LayerName2,AttributeValueList... -- etc.

#EDGES -- ActorName1,LayerName1,ActorName2,LayerName2,LocalAttributeValueList,GlobalAttributeValueList... -- etc.

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Usage

read_ml(file, name = "unnamed", sep = ',', aligned = FALSE)
write_ml(n, file, format = "multilayer", layers = character(0),
  sep = ',', merge.actors = TRUE, all.actors = FALSE)

Arguments

file

The path of the file storing the multilayer network.

name

The name of the multilayer network.

n

A multilayer network.

layers

If specific layers are passed to the function, only those layers are saved to file.

format

Either "multilayer", to use the package's internal format, or "graphml".

sep

The character used in the file to separate text fields.

aligned

If true, all actors are added to all layers.

merge.actors

Whether the nodes corresponding to each single actor should be merged into a single node (true) or kept separated (false), when format = "graphml" is used.

all.actors

Whether all actors in the multilayer network should be included in the output file (true) or only those present in at least one of the input layers (false), when format = "graphml" and merge.actors = TRUE are used.

Value

read_ml returns a multilayer network. write_ml does not return any value.

See Also

multinet.predefined, multinet.generation

Examples

# NOT RUN {
# writing a network to file...
file <- tempfile("aucs.mpx")
net <- ml_aucs()
write_ml(net,file)
# ...and reading it back into a variable
net <- read_ml(file,"AUCS")
net
# the following network has more nodes, because all
# actors are replicated to all graphs
net_aligned <- read_ml(file,"AUCS",aligned=TRUE)
net_aligned
# }