connectivity_matrix function

Create a connectivity matrix from an edge list

Converts an edge list to an connectivity matrix (also known as adjacency matrix).

connectivity_matrix(
  edges,
  lower = TRUE,
  upper = TRUE,
  diag = TRUE,
  na_to_zero = TRUE
)

Arguments

• edges: a data.frame with the following two columns: from (the first node of the edge) and to (the second node of the edge). The output of the functions create_edge_list() or append_edge_lists().

• lower: a logical value. If TRUE (default), keep values in the lower triangle of the matrix. Otherwise they will be replaced by NA

  (or 0).

• upper: a logical value. If TRUE (default), keep values in the upper triangle of the matrix. Otherwise they will be replaced by NA

  (or 0).

• diag: a logical value. If TRUE (default), keep values in the diagonal of the matrix. Otherwise they will be replaced by NA

  (or 0).

• na_to_zero: a logical value. If TRUE (default), missing edges are coded as 0. Otherwise they will be coded as NA.

Returns

A connectivity matrix of dimensions n x n, where n is the number of nodes.

Examples

# Import Adour sites ----
path_to_file <- system.file("extdata", "adour_survey_sampling.csv", 
                            package = "chessboard")
adour_sites  <- read.csv(path_to_file)

# Select first location ----
adour_sites <- adour_sites[adour_sites$"location" == 1, ]

# Create node labels ----
adour_nodes <- create_node_labels(data     = adour_sites, 
                                  location = "location", 
                                  transect = "transect", 
                                  quadrat = "quadrat")

# Find edges with 1 degree of neighborhood (pawn method) ----
adour_edges <- create_edge_list(adour_nodes, method = "pawn", 
                                directed = TRUE)

# Get connectivity matrix ----
connectivity_matrix(adour_edges)

# Get connectivity matrix ----
connectivity_matrix(adour_edges, na_to_zero = FALSE)