riverconn (version 0.3.31)

c_ij_fun: 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"
)

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

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.

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)