Convert to Cograph Network

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

# From adjacency matrix
mat <- matrix(c(0, 1, 1, 1, 0, 1, 1, 1, 0), nrow = 3)
net <- as_cograph(mat)

# Direct $ access to core data
net$nodes      # nodes data frame
#>   id label name  x  y
#> 1  1     1    1 NA NA
#> 2  2     2    2 NA NA
#> 3  3     3    3 NA NA
net$edges      # edges data frame
#>   from to weight
#> 1    1  2      1
#> 2    1  3      1
#> 3    2  3      1
net$directed   # TRUE/FALSE
#> [1] FALSE

# Getter functions (recommended for programmatic use)
get_nodes(net)   # nodes data frame
#>   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)   # edges data frame (from, to, weight)
#>   from to weight
#> 1    1  2      1
#> 2    1  3      1
#> 3    2  3      1
get_labels(net)  # character vector of labels
#> [1] "1" "2" "3"
n_nodes(net)     # 3
#> [1] 3
n_edges(net)     # 3
#> [1] 3
cograph::is_directed(net) # FALSE (symmetric matrix)
#> [1] FALSE

# Setter functions
net <- set_nodes(net, data.frame(id = 1:3, label = c("A", "B", "C")))
net <- set_edges(net, data.frame(from = c(1,2), to = c(2,3), weight = c(0.5, 0.8)))
net <- set_layout(net, data.frame(x = c(0, 1, 0.5), y = c(0, 0, 1)))

# Plot it
splot(net)


# From igraph (if installed)
if (requireNamespace("igraph", quietly = TRUE)) {
  g <- igraph::make_ring(10)
  net <- as_cograph(g)
  splot(net)
}

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