inner_d_index_calculation: Calculate index improvement for scenarios of barriers removal...

In riverconn: Fragmentation and Connectivity Indices for Riverscapes

Calculate index improvement for scenarios of barriers removal - function not for export

Description

Calculate index improvement for scenarios of barriers removal - function not for export

Usage

inner_d_index_calculation(
  graph,
  barriers_metadata,
  id_barrier,
  pass_u_updated,
  pass_d_updated,
  mode = "leave_one_out",
  parallel,
  ncores,
  weight,
  nodes_id,
  index_type,
  index_mode,
  c_ij_flag,
  B_ij_flag,
  dir_fragmentation_type,
  pass_confluence,
  pass_u,
  pass_d,
  field_B,
  dir_distance_type,
  disp_type,
  param_u,
  param_d,
  param,
  param_l
)

Arguments

graph	an object of class igraph. Can be both directed or undirected.
barriers_metadata	data.frame that must contain a column having the same name as the 'id_barrier' attribute of the graph, and two columns with the corresponding upstream and downstream improved passabilities (see pass_u_updated and pass_d_updated).
id_barrier	graph edges attribute used to label barriers. Default is "id_barrier".
pass_u_updated	field in barrier_metadata where updated value for upstream passability is stored (recommended values higher than the original passability).
pass_d_updated	field in barrier_metadata where updated value for downstream passability is stored (recommended values higher than the original passability).
mode	currentlym only "leave_one_out" is implemented.
parallel	logical value to flag if parallel option is to be used.
ncores	define how many cores are used in parallel processing. Active only when parallel = TRUE
weight	check index_calculation function.
nodes_id	check index_calculation function.
index_type	check index_calculation function.
index_mode	check index_calculation function.
c_ij_flag	check index_calculation function.
B_ij_flag	check index_calculation function.
dir_fragmentation_type	check index_calculation function.
pass_confluence	check index_calculation function.
pass_u	check index_calculation function.
pass_d	check index_calculation function.
field_B	check index_calculation function.
dir_distance_type	check index_calculation function.
disp_type	check index_calculation function.
param_u	check index_calculation function.
param_d	check index_calculation function.
param	check index_calculation function.

Details

Setting c_ij_flag = FALSE removes from the calculations the effect of barriers, i.e. the c_ij contribution is not used in the calculation of the index. Setting B_ij_flag = FALSE removes from the calculations the effect of movement/dispersal, i.e. the B_ij contribution is not used in the calculation of the index. Note that it is not possible to set both c_ij_flag = FALSE and B_ij_flag = FALSE.

The setting 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. The setting 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

The 'param_u', 'param_d', and 'param' values are interpreted differently based on the formula used to relate distance and probability. 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).

Value

returns a data.frame containing the percent improvement of the index for each barrier present in the 'barriers_metadata' variable. If index_type = "full", the data.frame is organized by 'id_barrier'. If index_type = "reach", the data.frame is organized by 'id_barrier' and 'name'. In both cases, both numerator and denominator used in the index calculations are reported in the columns 'num' and 'den'. The column 'd_index' contains the relative index improvement when each barrier is removed.

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