complete_network: compare two given networks (original and augmented, presented...

In SDDE: Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks

Description

This function computes the number of paths in each category for all pairs of nodes of the original network.

Usage

	complete_network(g1,g2,
					     taxnames,
					     maxdistance=0,
					     maxtime=3600,
					     maxnode=0,
					     verbose=FALSE,
					     file="log.txt",
					    maxcores=1,
					    node1,
					    node2
					) 

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)
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)
verbose	flag to save into a file additionnal informations regarding the obtained paths (default=FALSE, the file name should be indicated)
file	filename to save the additionnal informations
node1	if node1 is set,we look only for paths starting from node1
node2	if node2 is set, we will only look at the paths starting at node1 and ending at node2
maxcores	maximum number of cores to use (default=1, use 0 to use half of the total cores available )

Value

This function returns the number of paths of each category: Shortcuts, Detours, Dead ends, Equal paths and disconnected nodes.

If some of the augmented nodes are not visited because of the limits defined by maxnode, maxtime or maxdistance, a path can also be classified as Detour or Dead End.

Examples

## Searching the sample data (containing 11 original nodes and 3 augmented nodes)
data(Sample_1)
result <- complete_network(g1, g2)
print(result)
## Results:
##
##          disconnected nodes shortcuts equals detours dead ends
##user.self                 18         4      5      26         2
##          Dead ends or detour total user time system time real time
##user.self                   0    55     0.997       0.111     2.186
##
## Searching for path x1 -> x2 in the sample data
## Not run: complete_network(g1, g2,node1="x1", node2="x2")
##
## Specifying a limit on time (60 seconds) and maximum distance (2) of 
## an original node to an augmented node
## Not run: complete_network(g1, g2, maxtime=60, maxdistance=2)

SDDE documentation built on May 1, 2019, 9:01 p.m.