[R] Calculating Betweenness - Efficiency problem

[Gabor Csardi]

Senthil,

sending a 12Mb file to the list is not a good idea. 
I've run the code in my previous email without any problem, so you need
to be a bit more specific about what went wrong for you.

This is what I get:

> library(igraph)
> tab <- read.csv("/tmp/Test.csv")
> dim(tab)
[1] 304711      2
> length(unique(tab))
[1] 2
> g <- graph.data.frame(tab)
> summary(g)
Vertices: 48072 
Edges: 304711 
Directed: TRUE 
No graph attributes.
Vertex attributes: name.
No edge attributes.
> system.time(bet <- betweenness(g))
   user  system elapsed 
661.180   0.098 661.716 
> length(bet)
[1] 48072
> bet <- data.frame(city=V(g)$name, betweenness=bet)
> dim(bet)
[1] 48072     2

Best,
Gabor

On Tue, Jul 22, 2008 at 11:58:37AM -0700, Senthil Purushothaman wrote:
> Dear Gabor,
>    Thank you very much for the insights. I have been using the igraph
> package for my computations. But I did not know about
> graph.data.frame(). Thanks again for that. So I did run my data using
> the steps you had provided. Weirdly, even though the .csv file has
> approximately 300,000 records (remember that the file gets truncated to
> 65536 rows when opened in Excel 2003), not all of them are pulled in
> during the operation and the final betweenness list contains only ~1000+
> records but it should be tens of thousands. 
> 
> I know that you are a busy person. This problem seems to be a very
> different challenge. I am attaching the Test.csv file for your
> experiments. Thank you very much again.
> 
> Best regards,
> Senthil
> (909) 267-0799
> 
> -----Original Message-----
> From: Gabor Csardi [mailto:csardi at rmki.kfki.hu] 
> Sent: Monday, July 21, 2008 1:57 AM
> To: Senthil Purushothaman
> Cc: jim holtman; r-help at r-project.org
> Subject: Re: [R] Calculating Betweenness - Efficiency problem
> 
> Senthil,
> 
> you can try the 'igraph' package. Export your two-column Excel file
> as a .csv, use 'read.csv' to read that into R, then 'graph.data.frame'
> to create an igraph graph from it. Finally, call 'betweenness' on 
> the graph. It is really just three/four lines, something like this:
> 
> tab <- read.csv(...)
> g <- graph.data.frame(tab)
> bet <- betweenness(g)
> bet <- data.frame(city=V(g)$name, betweenness=bet)
> 
> The last line creates a two column data frame with the betweenness 
> score of each city. 
> 
> Best,
> Gabor
[...]

-- 
Csardi Gabor <csardi at rmki.kfki.hu>    UNIL DGM