network: Network Objects

In network: Classes for Relational Data

Network Objects

Description

Construct, coerce to, test for and print network objects.

Usage

is.network(x)

as.network(x, ...)

network(
  x,
  vertex.attr = NULL,
  vertex.attrnames = NULL,
  directed = TRUE,
  hyper = FALSE,
  loops = FALSE,
  multiple = FALSE,
  bipartite = FALSE,
  ...
)

network.copy(x)

## S3 method for class 'data.frame'
as.network(
  x,
  directed = TRUE,
  vertices = NULL,
  hyper = FALSE,
  loops = FALSE,
  multiple = FALSE,
  bipartite = FALSE,
  bipartite_col = "is_actor",
  ...
)

## S3 method for class 'network'
print(
  x,
  matrix.type = which.matrix.type(x),
  mixingmatrices = FALSE,
  na.omit = TRUE,
  print.adj = FALSE,
  ...
)

## S3 method for class 'network'
summary(object, na.omit = TRUE, mixingmatrices = FALSE, print.adj = TRUE, ...)

Arguments

x	for network, a matrix giving the network structure in adjacency, incidence, or edgelist form; otherwise, an object of class network.
...	additional arguments.
vertex.attr	optionally, a list containing vertex attributes.
vertex.attrnames	optionally, a list containing vertex attribute names.
directed	logical; should edges be interpreted as directed?
hyper	logical; are hyperedges allowed?
loops	logical; should loops be allowed?
multiple	logical; are multiplex edges allowed?
bipartite	count; should the network be interpreted as bipartite? If present (i.e., non-NULL, non-FALSE) it is the count of the number of actors in the bipartite network. In this case, the number of nodes is equal to the number of actors plus the number of events (with all actors preceeding all events). The edges are then interpreted as nondirected. Values of bipartite==0 are permited, indicating a bipartite network with zero-sized first partition.
vertices	If x is a data.frame, vertices is an optional data.frame containing the vertex attributes. The first column is assigned to the "vertex.names" and additional columns are used to set vertex attributes using their column names. If bipartite is TRUE, a logical column named "is_actor" (or the name of a column specified using the bipartite_col parameter) can be provided indicating which vertices should be considered as actors. If not provided, vertices referenced in the first column of x are assumed to be the network's actors. If your network has isolates (i.e. there are vertices referenced in vertices that are not referenced in x), the "is_actor" column is required.
bipartite_col	character(1L), default: "is_actor". The name of the logical column indicating which vertices should be considered as actors in bipartite networks.
matrix.type	one of "adjacency", "edgelist", "incidence". See edgeset.constructors for details and optional additional arguments
mixingmatrices	logical; print the mixing matrices for the discrete attributes?
na.omit	logical; omit summarization of missing attributes in network?
print.adj	logical; print the network adjacency structure?
object	an object of class network.

Details

network constructs a network class object from a matrix representation. If the matrix.type parameter is not specified, it will make a guess as to the intended edgeset.constructors function to call based on the format of these input matrices. If the class of x is not a matrix, network construction can be dispatched to other methods. For example, If the ergm package is loaded, network() can function as a shorthand for as.network.numeric with x as an integer specifying the number of nodes to be created in the random graph.

If the ergm package is loaded, network can function as a shorthand for as.network.numeric if x is an integer specifying the number of nodes. See the help page for as.network.numeric in ergm package for details.

network.copy creates a new network object which duplicates its supplied argument. (Direct assignment with <- should be used rather than network.copy in most cases.)

as.network tries to coerce its argument to a network, using the as.network.matrix functions if x is a matrix. (If the argument is already a network object, it is returned as-is and all other arguments are ignored.)

is.network tests whether its argument is a network (in the sense that it has class network).

print.network prints a network object in one of several possible formats. It also prints the list of global attributes of the network.

summary.network provides similar information.

Value

network, as.network, and print.network all return a network class object; is.network returns TRUE or FALSE.

Note

Between versions 0.5 and 1.2, direct assignment of a network object created a pointer to the original object, rather than a copy. As of version 1.2, direct assignment behaves in the same manner as network.copy. Direct use of the latter is thus superfluous in most situations, and is discouraged.

Many of the network package functions modify their network object arguments in-place. For example, set.network.attribute(net,"myVal",5) will have the same effect as net<-set.network.attribute(net,"myVal",5). Unfortunately, the current implementation of in-place assignment breaks when the network argument is an element of a list or a named part of another object. So set.network.attribute(myListOfNetworks[[1]],"myVal",5) will silently fail to modify its network argument, likely leading to incorrect output.

Author(s)

Carter T. Butts [e-mail] and David Hunter [e-mail]

References

Butts, C. T. (2008). “network: a Package for Managing Relational Data in R.” Journal of Statistical Software, 24(2). https://www.jstatsoft.org/v24/i02/

See Also

network.initialize, attribute.methods, as.network.matrix, as.matrix.network, deletion.methods, edgeset.constructors, network.indicators, plot.network

Examples

m <- matrix(rbinom(25,1,.4),5,5)
diag(m) <- 0
g <- network(m, directed=FALSE)
summary(g)

h <- network.copy(g)       #Note: same as h<-g
summary(h)

# networks from data frames ===========================================================
#* simple networks ====================================================================
simple_edge_df <- data.frame(
  from = c("b", "c", "c", "d", "a"),
  to = c("a", "b", "a", "a", "b"),
  weight = c(1, 1, 2, 2, 3),
  stringsAsFactors = FALSE
)
simple_edge_df

as.network(simple_edge_df)

# simple networks with vertices =======================================================
simple_vertex_df <- data.frame(
  name = letters[1:5],
  residence = c("urban", "rural", "suburban", "suburban", "rural"),
  stringsAsFactors = FALSE
)
simple_vertex_df

as.network(simple_edge_df, vertices = simple_vertex_df)

as.network(simple_edge_df,
  directed = FALSE, vertices = simple_vertex_df,
  multiple = TRUE
)

#* splitting multiplex data frames into multiple networks =============================
simple_edge_df$relationship <- c(rep("friends", 3), rep("colleagues", 2))
simple_edge_df

lapply(split(simple_edge_df, f = simple_edge_df$relationship),
  as.network,
  vertices = simple_vertex_df
)

#* bipartite networks without isolates ================================================
bip_edge_df <- data.frame(
  actor = c("a", "a", "b", "b", "c", "d", "d", "e"),
  event = c("e1", "e2", "e1", "e3", "e3", "e2", "e3", "e1"),
  actor_enjoyed_event = rep(c(TRUE, FALSE), 4),
  stringsAsFactors = FALSE
)
bip_edge_df

bip_node_df <- data.frame(
  node_id = c("a", "e1", "b", "e2", "c", "e3", "d", "e"),
  node_type = c(
    "person", "event", "person", "event", "person",
    "event", "person", "person"
  ),
  color = c(
    "red", "blue", "red", "blue", "red", "blue",
    "red", "red"
  ),
  stringsAsFactors = FALSE
)
bip_node_df

as.network(bip_edge_df, directed = FALSE, bipartite = TRUE)
as.network(bip_edge_df, directed = FALSE, vertices = bip_node_df, bipartite = TRUE)

#* bipartite networks with isolates ===================================================
bip_nodes_with_isolates <- rbind(
  bip_node_df,
  data.frame(
    node_id = c("f", "e4"),
    node_type = c("person", "event"),
    color = c("red", "blue"),
    stringsAsFactors = FALSE
  )
)
# indicate which vertices are actors via a column named `"is_actor"`
bip_nodes_with_isolates$is_actor <- bip_nodes_with_isolates$node_type == "person"
bip_nodes_with_isolates

as.network(bip_edge_df,
  directed = FALSE, vertices = bip_nodes_with_isolates,
  bipartite = TRUE
)

#* hyper networks from data frames ====================================================
hyper_edge_df <- data.frame(
  from = c("a/b", "b/c", "c/d/e", "d/e"),
  to = c("c/d", "a/b/e/d", "a/b", "d/e"),
  time = 1:4,
  stringsAsFactors = FALSE
)
tibble::as_tibble(hyper_edge_df)

# split "from" and "to" at `"/"`, coercing them to list columns
hyper_edge_df$from <- strsplit(hyper_edge_df$from, split = "/")
hyper_edge_df$to <- strsplit(hyper_edge_df$to, split = "/")
tibble::as_tibble(hyper_edge_df)

as.network(hyper_edge_df,
  directed = FALSE, vertices = simple_vertex_df,
  hyper = TRUE, loops = TRUE
)

# convert network objects back to data frames =========================================
simple_g <- as.network(simple_edge_df, vertices = simple_vertex_df)
as.data.frame(simple_g)
as.data.frame(simple_g, unit = "vertices")

bip_g <- as.network(bip_edge_df,
  directed = FALSE, vertices = bip_node_df,
  bipartite = TRUE
)
as.data.frame(bip_g)
as.data.frame(bip_g, unit = "vertices")

hyper_g <- as.network(hyper_edge_df,
  directed = FALSE, vertices = simple_vertex_df,
  hyper = TRUE, loops = TRUE
)
as.data.frame(hyper_g)
as.data.frame(hyper_g, unit = "vertices")

network documentation built on May 29, 2024, 6:07 a.m.