This function runs the full process of creating the nodes, creating the edges and establishing priority edges to be used to enhance connectivity in the landscape for the focal species.
gDefrag.full(land_polyg, method, value_col = NULL,
min_length = 0, min_pol_area = 0, shape = FALSE,
shape_name_nodes = "shape_all_nodes", shape_name_edges = "shape_edges",
shape_name_out = "priorities_shape",
shape_name_nodes_edges = "nodes_with_edges",
scale_nodes = 10, col_nodes = "deepskyblue4", col_labels = "white",
cex_labels = 1, main = "Graph")SpatialPolygonsDataFrame loaded with readOGR function of the package rgdal (polygon shapefile). To be internally passed to as node.creation and as edge.creation.
Method to be used in the prioritization of the connectivity corridors. Detailed description in the 'details' section. To be internally passed to as prioritize.
Identification of the column in the 'land_polyg' object. To be internally passed to as prioritize.
Minimum length of the road segment to consider creating an edge representing it. To be internally passed to as edge.creation.
Minimum area of the polygon to consider creating a node representing it. To be internally passed to as node.creation.
Produce node and edges shapefiles as output? (TRUE/FALSE) To be internally passed to as node.creation and as edge.creation.
Name of the nodes shapefile to be created (all nodes).
Name of the edges shapefile to be created (without prioritization).
Name of the edges prioritization output shapefile to be created.
Instead of 'shape_name_nodes', that depicts all the nodes, 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).
Node size scaling factor for correct viewing in the plot. To be internally passed to as plotgraph.
Node colour. To be internally passed to as plotgraph.
Labels colour. To be internally passed to as plotgraph.
Text labels font size. To be internally passed to as plotgraph.
Main plot title. To be internally passed to as plotgraph.
This function produces a 'list' object. This list has two objects, one with the information of the nodes and the other with the information on the edges.
If shape = TRUE, this function produces four shapefiles: all nodes, nodes with area greater than 'min_pol_area', edges without prioritization metrics, edges with prioritization metrics. The prioritization of the connectivity corridors can be made with one of four methods (argument 'method'):
'value' - Give priority to edges connecting nodes with higher attribute value (e.g. suitability for the focal species);
'traffic' - Give priority to edges representing roads with more traffic;
'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' - Give priority to edges connecting nodes with more suitable area.
# NOT RUN {
data(road_P)
out1 <- gDefrag.full(land_polyg = road_P, method = "value",
value_col = "forest_sum", main = "value-based graph",
shape = TRUE)
# }
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