[igraph] R igraph 1.0 and return.vs.es

[Dr Gregory Jefferis]

Hello,

I have recently upgraded to v1.0.1 of the R igraph package. Thanks for 
all your hard work on this. A lot has happened since 0.7.1!

One thing I have noticed is that some of my functions (in CRAN package 
nat) now run ~50x slower. I've traced this to a change in behaviour, 
where functions like graph.dfs return vertex sequences rather than plain 
(integer) vertex ids. subsetting those vertex sequences can be very 
slow. This can be changed by the igraph_option return.vs.es=F (which 
incidentally does not seem to be documented)

Here is a (stupid) toy example:

> g3=graph.tree(500) %du% graph.tree(500)
> system.time({d=graph.dfs(g3, root=1, neimode = 'all', father = T); 
> for(i in 1:length(d$order)) d$order[i] })
   user  system elapsed
  0.713   0.007   0.719
> igraph_options(return.vs.es=F)
> system.time({d=graph.dfs(g3, root=1, neimode = 'all', father = T); 
> for(i in 1:length(d$order)) d$order[i] })
   user  system elapsed
  0.001   0.000   0.001

Obviously in this case one can do this:

> igraph_options(return.vs.es=T)
> system.time({d=graph.dfs(g3, root=1, neimode = 'all', father = T); 
> do=as.integer(d$order) ; for(i in 1:length(do)) do[i] })
   user  system elapsed
  0.003   0.000   0.002

But this means changing quite a bit of code and there are places where 
similar issues cannot be so easily side-stepped.

Two questions:

1. Is this slow down expected?

2. As a package developer, is there any way to ensure I have the 
behaviour of igraph_options(return.vs.es=F) when I import the igraph 
package (while still giving other users the chance to set  
igraph_options(return.vs.es=T) if that is what they want) ?

As a comment, my feeling is that this behaviour should probably be 
controlled both at a per function as well as a package option level.

Many thanks for your help,

Greg.


--
Gregory Jefferis, PhD
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://flybrain.stanford.edu