Re: [igraph] finding raw vertex index of a named vertex (R igraph)

[Gábor Csárdi]

I think the important thing here, is to vectorize the query, if you can do
that.

For a single vertex, I think

match('1001', vertex_attr(gt, "name"))

is as fast as this gets. igraph does not have a special index for vertex
names.

Gabor
On Wed, May 2, 2018 at 10:47 AM Dr Gregory Jefferis <
address@hidden> wrote:

> Hello,

> In R igraph I want to find the raw vertex index from the vertex name

> For example:

> library(igraph)
> gt=graph.tree(1000)
> gt=set.vertex.attribute(gt, name = 'name', value = 1001:2000)

> Now I want to find the integer vertex index of the vertex named 1001
> (i.e. 1 in this toy example). One could do:

> > as.integer(V(gt)['1001'])
> [1] 1

> I want to do this a lot with some big graphs, so I would like to take
> the most direct and efficient approach.

> > library(microbenchmark)
> >  microbenchmark(as.integer(V(gt)['1001']))
> Unit: microseconds
>                         expr     min       lq     mean   median       uq
>       max neval
>    as.integer(V(gt)["1001"]) 559.399 580.2445 640.5165 605.1565 663.3915
> 1044.307   100
> > microbenchmark(match(1001, names(V(gt))))
> Unit: microseconds
>                         expr    min      lq     mean median      uq
> max neval
>    match(1001, names(V(gt))) 71.686 75.9195 86.37762 78.813 92.5785
> 221.455   100

> Doing:

> > match(1001, names(V(gt)))

> does not seem very elegant or particularly efficient, but strangely is
> the fastest approach that I have found so far.

> Many thanks for any alternative suggestions,

> Greg.

> PS timings with CRAN igraph 1.1.2 on R 3.4.3 on macosx 10.12.6

> --
> 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

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