R/connectivity_matrix.R
connectivity_matrix.RdConverts 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
)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().
a logical value. If TRUE (default), keep values in the
lower triangle of the matrix. Otherwise they will be replaced by NA
(or 0).
a logical value. If TRUE (default), keep values in the
upper triangle of the matrix. Otherwise they will be replaced by NA
(or 0).
a logical value. If TRUE (default), keep values in the
diagonal of the matrix. Otherwise they will be replaced by NA
(or 0).
a logical value. If TRUE (default), missing edges are
coded as 0. Otherwise they will be coded as NA.
A connectivity matrix of dimensions n x n, where n is the number
of nodes.
# 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)
#> 1-1 1-2 1-3 1-4 1-5 2-1 2-2 2-3 2-4 2-5 3-1 3-2 3-3 3-4 3-5
#> 1-1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
#> 1-2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
#> 1-3 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
#> 1-4 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
#> 1-5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> 2-1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
#> 2-2 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
#> 2-3 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
#> 2-4 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
#> 2-5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> 3-1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
#> 3-2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
#> 3-3 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
#> 3-4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
#> 3-5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
# Get connectivity matrix ----
connectivity_matrix(adour_edges, na_to_zero = FALSE)
#> 1-1 1-2 1-3 1-4 1-5 2-1 2-2 2-3 2-4 2-5 3-1 3-2 3-3 3-4 3-5
#> 1-1 NA 1 NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 1-2 NA NA 1 NA NA NA NA NA NA NA NA NA NA NA NA
#> 1-3 NA NA NA 1 NA NA NA NA NA NA NA NA NA NA NA
#> 1-4 NA NA NA NA 1 NA NA NA NA NA NA NA NA NA NA
#> 1-5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 2-1 NA NA NA NA NA NA 1 NA NA NA NA NA NA NA NA
#> 2-2 NA NA NA NA NA NA NA 1 NA NA NA NA NA NA NA
#> 2-3 NA NA NA NA NA NA NA NA 1 NA NA NA NA NA NA
#> 2-4 NA NA NA NA NA NA NA NA NA 1 NA NA NA NA NA
#> 2-5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> 3-1 NA NA NA NA NA NA NA NA NA NA NA 1 NA NA NA
#> 3-2 NA NA NA NA NA NA NA NA NA NA NA NA 1 NA NA
#> 3-3 NA NA NA NA NA NA NA NA NA NA NA NA NA 1 NA
#> 3-4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1
#> 3-5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA