B_ij_fun: Calculates B_ij: the functional contribution to dispersal...

In riverconn: Fragmentation and Connectivity Indices for Riverscapes

Calculates B_ij: the functional contribution to dispersal probability I_ij

Description

Calculates B_ij: the functional contribution to dispersal probability I_ij

Usage

B_ij_fun(
  graph,
  field_B = "length",
  dir_distance_type = "symmetric",
  disp_type = "exponential",
  param_u,
  param_d,
  param,
  param_l
)

Arguments

graph	an object of class igraph. Can be both directed or undirected.
field_B	the 'graph' edge attribute to be used to calculate the distance. Default is "length".
dir_distance_type	how directionality in B_ij calculations is dealt with: "symmetric" (i.e. undirected graph) or "asymmetric" (i.e. directed graph). See details.
disp_type	the formula used to calculate the probabilities in the B_ij matrix. Use "exponential" for exponential decay, "threshold" for setting a distance threshold, or "leptokurtic" for leptokurtic dispersal.
param_u	the upstream dispersal parameter. Must be a numeric value. Only used if dir_distance_type = "asymmetric". See details.
param_d	the downstream dispersal parameter. Must be a numeric value. Only used if dir_distance_type = "asymmetric". See details.
param	the dispersal parameter. Must be a numeric value. Only used if dir_distance_type = "symmetric". See details.
param_l	the parameters for the leptokurtic dispersal mode. Must be a numeric vector of the type c(sigma_stat, sigma_mob, p). See details below.

Details

dir_distance_type = "symmetric" is to be used when the directionality of the river network is not relevant. The distance between reaches midpoints is calculated for each couple of reaches. dir_distance_type = "asymmetric" is to be used when the directionality is relevant. The distance between reaches midpoints is calculated for each couple of reaches and splitted between 'upstream travelled' distance and 'downstream travelled' distance. When disp_type ="leptokurtic" is selected, symmetric dispersal is assumed.

The 'param_u', 'param_d', and 'param' values are interpreted differently based on the formula used to relate distance (d_ij) and probability (B_ij). When disp_type ="exponential", those values are used as the base of the exponential dispersal kernel: B_ij = param^d_ij. When disp_type ="threshold", those values are used to define the maximum dispersal length: B_ij = ifelse(d_ij < param, 1, 0).

When disp_type ="leptokurtic" is selected, a leptokurtic dispersal kernel is used to calculate B_ij. A leptokurtic dispersal kernel is a mixture of two zero-centered gaussian distributions with standard deviations sigma_stat (static part of the population), and sigma_mob (mobile part of the population). The probability of dispersal is calculated as: B_ij = p F(0, sigma_stat, d_ij) + (1-p) F(0, sigma_mob, d_ij) where F is the upper tail of the gaussian cumulative density function.

Value

a square matrix of size length(V(graph)) containing B_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 <- B_ij_fun(g, param = 0.9)

riverconn documentation built on May 31, 2023, 8:02 p.m.