prioritize: Prioritizing connectivity corridors

In gDefrag: Graph-Based Landscape De-Fragmentation

Description

Function to stablish a priority on the edges (connections) to be created in order to de-fragment a landscape.

Usage

prioritize(nodes, edges, method, shape=FALSE, shape_name_out = "priorities_shape", 
shape_name_nodes_edges = "nodes_with_edges")

Arguments

nodes	Output of node.creation.
edges	Output of edge.creation.
method	Method to be used in the prioritization of the connectivity corridors. Detailed description in the 'details' section.
shape	Create a shapefiles? (TRUE/FALSE).
shape_name_out	Name of the shapefile to be created.
shape_name_nodes_edges	Name of the nodes shapefile to be created. This shape has only nodes considered in the prioritization procedure (those with an area greater that the argument 'min_pol_area' in the function edge.creation).

Details

If shape = TRUE, this function produces two shapefiles: nodes with area greater than 'min_pol_area' (in edge.creation), edges with prioritization metrics. The prioritization of the connectivity corridors can be made with one of these methods (argument 'method'):

• 'value' - Give priority to edges connecting nodes with higher attribute value (e.g. suitability for the focal species);

• 'IIC' - Give priority to edges with higher overall impact in the connectivity. This was implemented by using the Integral Index of Connectivity (IIC) developed by Pascual-Hortal and Saura (2006). The connectivity relevance of each edge was evaluated usinf the approach described in Pascual-Hortal and Saura (2006): dIIC=((I1-I2)/I1)*100, where I1 is the IIC before edge removal and I2 is the IIC after.

• 'between' - Give priority to edges with higher betweenness using the function edge.beetweenness.estimate from the igraph package.

• 'AWM' - Area Weighted Metric - The user should provide the value of the variable to be weighted by area (e.g. habitat area) in the 'value_col' argument of the function node.creation. The expression for the Area Weighted Metric is: AWM = (value_A*area_B)+(value_B*area_A), where: 'value_A' and 'area_B' are the node A argument and the habitat in polygon B, respectively and 'value_B' and 'area_A' are the node B argument and the habitat in polygon A, respectively.

Value

The output is a SpatialLinesDataFrame with an additional field, 'priorization'. This field provides the desired priorization value.

Note

The computation of IIC is made resorting to the node attribute in place of the 'habitat patch areas' (ai and aj) as originally devised by Pascual-Hortal & Saura (2006).

Author(s)

Frederico Mestre, Fernando Ascensao and A. Marcia Barbosa

References

Pascual-Hortal, L., Saura, S. (2006). Comparison and development of new graph-based landscape connectivity indices: towards the priorization of habitat patches and corridors for conservation. Landscape Ecology, 21(7), 959-967.

See Also

node.creation, edge.creation

Examples

data(road_P)

####### To the value, betweenness and connectivity metrics #######

#Obtaining nodes
out1 <- node.creation(land_polyg = road_P, value_col = "forest_sum", 
scale_nodes = 10, col_nodes = "pink", cex_labels = 1)

#Obtaining edges
out2 <- edge.creation(nodes = out1, land_polyg = road_P, 
min_length = 0, min_pol_area = 0)

#Prioritize
out3 <- prioritize(nodes = out1, edges = out2, 
	method = "value")#Raster value
out4 <- prioritize(nodes = out1, edges = out2, 
	method = "between")#Betweenness
out5 <- prioritize(nodes = out1, edges = out2, 
	method = "IIC")  #Connectivity

####### To the area weighted metric #######

#Obtaining nodes
out6 <- node.creation(land_polyg = road_P, value_col = "proportion", 
scale_nodes = 10, col_nodes = "pink", cex_labels = 1)

#Obtaining edges
out7 <- edge.creation(nodes = out6, land_polyg = road_P, 
min_length = 0, min_pol_area = 0)

#Prioritize
out8 <- prioritize(nodes = out6, edges = out7, 
	method = "AWM")#Habitat proportion

gDefrag documentation built on Sept. 3, 2020, 1:07 a.m.