sample_network {SDDE} | R Documentation |
This function allows the user to compare two related networks (undirected graphs) by computing the number of paths of each category for a sample of nodes from the original graph.
sample_network(g1,g2, size, taxnames, maxdistance=0, maxtime=3600, maxnode=0, verbose=FALSE, file='log.txt', maxcores=1, node1, node2, sample_paths=c(), old_path=c() )
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) |
size |
the number of pathways to sample or the percent of node to sample if smaller than 1.0 (default=10) |
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) |
sample_paths |
vector containing a list of node numbers to sample. Note: this override the size argument |
old_path |
vector containing a list of node numbers already sampled |
This function returns the number of paths of each category: Shortcuts, Detours, Dead ends, Equal paths or disconnected nodes.
If not all augmented nodes are visited because of the maxnode, maxtime or maxdistance limits, a path can also be classified as 'Detour or Dead End'.
## Sample 10 of the 55 pathways in Sample_1 data(Sample_1) sample_network(g1,g2, size=10) ## Repeated sampling (5) of 10 pathways ## Not run: old_path <- c() for (i in 1:5) { sample_paths <- sample_path(10, length(V(g1)), old_path=old_path); sample_network(g1,g2, sample_paths=sample_paths); old_path <- c(old_path,sample_paths); } ## End(Not run)