[igraph] slow rewire performance after subsetting a graph

[Murat Tasan]

hi all - i've noticed some drastic performance changes in the rewire method after i added some clean-up steps prior to rewiring a graph.

this was done using the R package (v0.6, with 1-indexing):

G is a random graph where i artificially add a collection of zero-degree vertices, which i'll remove later to demonstrate the speed issue.

> G <- graph.data.frame(data.frame(v1 = sample(100, 100, replace = TRUE), v2 = sample(100, 100, replace = TRUE)), vertices = data.frame(1:200))

> H <- delete.vertices(G, which(degree(G) == 0))

the second line removes any zero-degree vertices from the graph object.

the edges (and any connected vertices) remain the same between G and H.

> G

IGRAPH DN-- 200 100 --

+ attr: name (v/c)

> H

IGRAPH DN-- 86 100 --

+ attr: name (v/c)

now some basic re-wiring.

> system.time(rewire(G, niter = 5e5))

   user  system elapsed

  1.070   0.000   1.078

> system.time(rewire(H, niter = 5e5))

   user  system elapsed

  4.930   0.000   4.929

i'm guessing "H" is kept in memory as a view on a backing "G", leading to the slow-down as boundary checks have to be made and calls forwarded to the underlying object.

for some large (real data) graphs i'm working with, the slow-down is magnified by a lot and becomes a substantial problem.

if my "view" guess is right, is there any way in R to force "H" to be treated as a completely new object (i.e. a clone-like call)?

cheers, and thanks for any insight here,

-m