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

Usage

read_ml(file, name = "unnamed", 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.

Examples

# 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

multinet documentation built on Nov. 2, 2024, 5:06 p.m.