SDDE (version 1.0.1)

complete_trace: return properties of a single path in two given networks (original and augmented, presented as undirected graphs) using a path analysis

Description

This function is equivalent to the complete_network function, but it analyses a single path returning information about the: path type, the enumeration of traversed nodes, the traversed node taxa, the original path length and the augmented path length.

Usage

complete_trace(g1,g2,
					  taxnames,
					  node1,
					  node2,
					  maxdistance=0,
					  maxtime=3600,
					  maxnode=0,
					  maxcores=1
					)

Arguments

g1

the original network X

g2

the augmented network Y with additional nodes (all the original nodes from X must be present in the augmented network Y)

taxnames

the taxon name of the nodes added to the original graph (default: we select all nodes that are not in g1)

node1

the from node (either the node name or the node number) of the path to investigate

node2

the to node (either the node name or the node number) of the path to investigate

maxnode

the maximum number of augmented nodes in network Y to take into account (default=0, no maximum number of augmented nodes to take into account. The augmented nodes are sorted by distance to the investigated node pairs by the algorithm.)

maxtime

the maximum search time per pathway (default=3600 seconds)

maxdistance

the maximum search distance to the added nodes in network Y (default=0, no maximum distance for augmented nodes to take into account)

maxcores

maximum number of cores to use (default=1, use 0 to use half of the total cores available )

Value

• This function returns a list containing the from and to node names, the path type (Shortcut, Detour, Dead end and Equal paths or disconnected node), the original path length, the augmented path length, the traversed path nodes and the path_visited_taxa (taxa of each visited node).

encoding

ISO-8859-2

Examples

## Searching the sample data for the path type between node x1 and x5
data(Sample_1)
##
complete_trace(g1,g2,node1="x1", node2="x5")
## Expected results:
## $from
## [1] "x1"
## $to
## [1] "x5"
## $path_type
## [1] "Detour"
## $original_path_length
## [1] 2
## $augmented_path_length
## [1] 3
## $path
## [1] "x1" "x14" "x6" "x5" 
## $path_visited_taxa
## [1] 1 2 1 1