c_ij_fun {riverconn}

Calculates c_ij: the structural contribution to the dispersal probability I_ij

Description

Calculates c_ij: the structural contribution to the dispersal probability I_ij

Usage

c_ij_fun(
  graph,
  dir_fragmentation_type = "symmetric",
  pass_confluence = 1,
  pass_u = "pass_u",
  pass_d = "pass_d"
)

Arguments

graph

an object of class igraph. Can be both directed or undirected.

dir_fragmentation_type

how directionality in c_ij calculations is dealt with: "symmetric" (i.e. undirected graph) or "asymmetric" (i.e. directed graph). See details.

pass_confluence

a value in the range [0,1] that defines the passability of confluences (default is 1).

pass_u

the 'graph' edge attribute to be used as upstream passability. Default is "pass_u".

pass_d

the 'graph' edge attribute to be used as downstream passability. Default is "pass_d".

Details

dir_fragmentation_type = "symmetric" is to be used when the directionality of the river network is not relevant. The equivalent passability for each barrier is calculated as the product of upstream and downstream passabilities. dir_fragmentation_type = "asymmetric" is to be used when the directionality is relevant. The equivalent passability of each barrier is calculated as a function of the path connecting each couple of reaches and depends on the direction of the path. Check the package vignette for more details.

Value

a square matrix of size length(V(graph)) containing c_ij values. The matrix is organized with "from" nodes on the columns and "to" nodes on the rows

Examples

library(igraph)
g <- igraph::graph_from_literal(1-+2, 2-+5, 3-+4, 4-+5, 6-+7, 7-+10,
8-+9, 9-+10, 5-+11, 11-+12, 10-+13, 13-+12, 12-+14, 14-+15, 15-+16)
E(g)$id_dam <- c("1", NA, "2", "3", NA, "4", NA, "5", "6", NA,  NA, NA, NA, "7", NA)
E(g)$type <- ifelse(is.na(E(g)$id_dam), "joint", "dam")
V(g)$length <- c(1, 1, 2, 3, 4, 1, 5, 1, 7, 7, 3, 2, 4, 5, 6, 9)
V(g)$HSI <- c(0.2, 0.1, 0.3, 0.4, 0.5, 0.5, 0.5, 0.6, 0.7, 0.8, 0.8, 0.8, 0.8, 0.8, 0.8, 0.8)
V(g)$Id <- V(g)$name
E(g)$pass_u <- E(g)$pass_d <- ifelse(!is.na(E(g)$id_dam),0.1,NA)
dist_mat <- c_ij_fun(g)