Netfrac: Title

In XPHenry/Netfrac: Netfrac - Community distance calculation within sequence similarity networks

Description

Title

Usage

NetFrac(x, distances = "UniFrac", paths = "single", mats = "",
  maxcores = 1, share_weight = 0)

Arguments

x	The network(or tree) that will be analyzed. The network must be in the igraph format, the edges being accessible with E(x) and vertices with V(x). The communities are under V(x)$tax and the branch weights under E(x)$weight. These functions are applicable with igraph objects only
distances	Distances or indices to calculate: Transfer, Transfer2, Spaths, UniFrac and Motifs. The transfer, paths and Unifrac distances can also be calculated for trees
paths	this parameter is used to decide whether all the shortest paths between network nodes should be calculated ("all"), or only one of them ("single"). The last option can significantly reduce the time of computation. For Motifs distance, decide the size of the motifs (i.e. 2 or 3)
mats	the similarity matrix used to reconnect the network. See also reconnect
maxcores	uses the multicore function to set up the number of cores to be used
share_weight	weight if there are mixed communities. For now, only 0 is implemented

Value

$'Spp'
A B
A 0.0000000 0.5555556
B 0.5555556 0.0000000

$Spep
A B
A 0.0000000 0.6296296
B 0.6296296 0.0000000

$Spelp
A B
A 0.0000000 0.6296296
B 0.6296296 0.0000000

$Spinp
A B
A 0.0000000 0.9907407
B 0.9907407 0.0000000
$Transfer
A B
A 0.0000000 0.6666667
B 0.3333333 0.0000000

Examples

NetFrac(net_a)
NetFrac(net_a,"Spaths","all")

XPHenry/Netfrac documentation built on Jan. 29, 2020, 12:14 p.m.