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[igraph] finding raw vertex index of a named vertex (R igraph)
From: |
Dr Gregory Jefferis |
Subject: |
[igraph] finding raw vertex index of a named vertex (R igraph) |
Date: |
Wed, 02 May 2018 10:46:55 +0100 |
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
- [igraph] finding raw vertex index of a named vertex (R igraph),
Dr Gregory Jefferis <=