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Convert to Cograph Network

Source: R/class-network.R
as_cograph.Rd

as_cograph() creates a cograph_network object from a matrix, an edge list, or a network object of another package. to_cograph() is an alias. The object is a named list that every cograph function accepts.

Usage

as_cograph(x, directed = NULL, simplify = FALSE, ...)

to_cograph(x, directed = NULL, ...)

# S3 method for class 'cograph_network'
as.data.frame(
  x,
  row.names = NULL,
  optional = FALSE,
  ...,
  what = c("edges", "nodes")
)

Arguments

x

Network input. One of a square numeric weight matrix, a data frame edge list, an igraph object, a statnet network object, a qgraph object, a tna object, or an existing cograph_network, which is returned as it is. In an edge list the endpoint columns are found by name, ignoring case (from, source, src, v1, node1 or i, and to, target, tgt, v2, node2 or j), and otherwise the first two columns are used. An optional weight column is found by the names weight, w, value or strength. For as.data.frame(), a cograph_network.

directed

Logical. Forces a directed or undirected interpretation. NULL (default) detects it from the input.

simplify

Logical or character. If FALSE (default), every transition from tna sequence data is a separate edge. If TRUE (equivalent to "sum") or one of "sum", "mean", "max", "min", duplicate transitions are aggregated with that function. Other inputs are not affected.

...

Passed from to_cograph() to as_cograph(); otherwise unused.

row.names

NULL or a character vector of row names, as for as.data.frame.

optional

Logical, as for as.data.frame. It is ignored, and the column names are always the documented ones.

what

Which table as.data.frame() returns, "edges" (default) or "nodes".

Value

as_cograph() and to_cograph() return a cograph_network object, a named list with components:

nodes

Data frame with id, label, and optional layout or metadata columns.

edges

Data frame with integer from and to columns (row numbers into nodes), weight, and extra columns such as session and time for tna input. Repeated rows of an edge list are kept as separate edges.

directed

Logical. Whether the network is directed.

weights

The n x n weight matrix for matrix and tna input, or NULL (for example for an edge list).

data

The original estimation data (sequence data, edge list), or NULL.

meta

Metadata list with source (input type), a tna entry for tna input (type, group name and group index) and, optionally, splot (rendering hints read by splot).

node_groups

Optional data frame of node groupings.

as.data.frame() returns a base data frame. For what = "edges" it has one row per edge with columns from and to (node labels), weight, and any extra edge columns the network carries, such as session or columns computed by mutate_edges. For what = "nodes" it has one row per node with the node table columns (id, label, layout coordinates and any custom columns). to_df returns only from, to and weight.

Details

A cograph_network prints a short description of its nodes, edges and source, summary() reports counts and edge weight statistics, plot() plots it with sn_render, and as.data.frame() returns its edge or node table. The accessor and setter functions are documented in get_nodes.

Producer packages may attach plotting hints under meta$splot. The recognized fields are renderer (the cograph renderer to use), weight (the edge column or matrix plotted as weight), and defaults (a named list of renderer arguments). Entries in defaults are defaults only, and arguments passed to splot override them. renderer and weight define which view is plotted and are not overridden by plot arguments.

See also

get_nodes, splot, to_df

Examples

net <- as_cograph(regulation_net)
as.data.frame(net, what = "edges")
#>          from         to weight
#> 1       Adapt    Explore   0.28
#> 2     Reflect    Explore   0.05
#> 3     Discuss    Explore   0.30
#> 4      Create    Explore   0.14
#> 5  Synthesize       Plan   0.11
#> 6       Share       Plan   0.21
#> 7        Plan    Monitor   0.13
#> 8     Reflect    Monitor   0.15
#> 9  Synthesize    Monitor   0.07
#> 10   Evaluate    Monitor   0.33
#> 11     Create    Monitor   0.17
#> 12      Share    Monitor   0.49
#> 13    Monitor      Adapt   0.16
#> 14   Evaluate      Adapt   0.43
#> 15      Share      Adapt   0.39
#> 16    Explore    Reflect   0.35
#> 17    Discuss    Reflect   0.35
#> 18 Synthesize    Reflect   0.42
#> 19   Evaluate    Reflect   0.07
#> 20       Plan    Discuss   0.40
#> 21      Adapt    Discuss   0.34
#> 22      Adapt Synthesize   0.17
#> 23       Plan   Evaluate   0.49
#> 24     Create   Evaluate   0.39
#> 25       Plan     Create   0.20
#> 26    Monitor     Create   0.37
#> 27    Discuss     Create   0.14
#> 28    Explore      Share   0.27
#> 29       Plan      Share   0.36
#> 30     Create      Share   0.23