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Convert to Cograph Network

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

Creates a lightweight cograph_network object from various network inputs. The resulting object is a named list with all data accessible via $.

Usage

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

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

Arguments

x

Network input. Can be:

  • A square numeric matrix (adjacency/weight matrix)

  • A data frame with edge list (from, to, optional weight columns)

  • An igraph object

  • A statnet network object

  • A qgraph object

  • A tna object

  • An existing cograph_network object (returned as-is)

directed

Logical. Force directed interpretation. NULL for auto-detect.

simplify

Logical or character. If FALSE (default), every transition from tna sequence data is a separate edge. If TRUE or a string ("sum", "mean", "max", "min"), duplicate edges are aggregated.

...

Additional arguments (currently unused).

Value

A cograph_network object: a named list with components:

nodes

Data frame with id, label, (x, y if layout applied)

edges

Data frame with from, to, weight columns

directed

Logical indicating if network is directed

weights

Full n×n weight matrix (for to_matrix round-trip)

data

Original estimation data (sequence matrix, edge list, etc.), or NULL

meta

Consolidated metadata list with sub-fields: source (input type string), layout (layout info list or NULL), tna (TNA metadata or NULL)

node_groups

Optional node groupings data frame

A cograph_network object. See as_cograph.

Details

The cograph_network format is designed to be:

  • Lean: Only essential data stored, computed values derived on demand

  • Modern: Uses named list elements instead of attributes for clean $ access

  • Compatible: Works seamlessly with splot() and other cograph functions

Use getter functions for programmatic access: get_nodes, get_edges, get_labels, n_nodes, n_edges

Use setter functions to modify: set_nodes, set_edges, set_layout

See also

get_nodes to extract the nodes data frame, get_edges to extract edges as a data frame, n_nodes and n_edges for counts, is_directed to check directedness, splot for plotting

Examples

mat <- matrix(c(0, 1, 1, 1, 0, 1, 1, 1, 0), nrow = 3)
net <- as_cograph(mat)
get_nodes(net)
#>   id label name  x  y
#> 1  1     1    1 NA NA
#> 2  2     2    2 NA NA
#> 3  3     3    3 NA NA
get_edges(net)
#>   from to weight
#> 1    1  2      1
#> 2    1  3      1
#> 3    2  3      1
splot(net)

mat <- matrix(c(0, 1, 1, 1, 0, 1, 1, 1, 0), nrow = 3)
net <- to_cograph(mat)