Comments on: Clustering in Two-mode Networks

By: Tore Opsahl

Tore Opsahl — Tue, 05 Mar 2013 17:32:54 +0000

Hi Yaseswini,

You are running out of memory.. The R-functions were written to be faster than memory efficient due to loops being really really slow in R. For larger networks, I have c++ functions that are very fast and very memory efficient; however, they require some knowledge to work. Email me and I will send them to you.

Best,
Tore

By: Yaseswini

Yaseswini — Tue, 05 Mar 2013 06:50:37 +0000

Hi Tore,

I am using the clustering_local_tm function for my two mode data which has 6029 vertices in the primary node set and 9313 vertices in the secondary node set with 57912 edges connecting them.When i tried using the function, i got an error message stating:

Error: cannot allocate vector of size 1.4 Gb
In addition: Warning messages:
1: In `[.data.frame`(x, c(m$xi, if (all.x) m$x.alone), c(by.x, seq_len(ncx)[-by.x]), :
Reached total allocation of 4043Mb: see help(memory.size)
2: In `[.data.frame`(x, c(m$xi, if (all.x) m$x.alone), c(by.x, seq_len(ncx)[-by.x]), :
Reached total allocation of 4043Mb: see help(memory.size)
3: In `[.data.frame`(x, c(m$xi, if (all.x) m$x.alone), c(by.x, seq_len(ncx)[-by.x]), :
Reached total allocation of 4043Mb: see help(memory.size)
4: In `[.data.frame`(x, c(m$xi, if (all.x) m$x.alone), c(by.x, seq_len(ncx)[-by.x]), :
Reached total allocation of 4043Mb: see help(memory.size)

can u please help me out with the problem.

Thanks
Yaseswini

By: Yaseswini

Yaseswini — Mon, 04 Mar 2013 04:28:45 +0000

Thanks for the reply.I shall try that.

Yaseswini

By: Tore Opsahl

Tore Opsahl — Sun, 03 Mar 2013 21:14:24 +0000

Hi Yaseswini,

You can swap the columns to get local clustering scores for the secondary nodes. For example, if you network is in an object called net which has two columns, you can simply type net <- net[,2:1] to reverse the columns.

Best,
Tore

By: Yaseswini

Yaseswini — Sun, 03 Mar 2013 13:08:14 +0000

hi,
I am using the tnet package for bipartite graph analysis. Iam particularly interested in calculating the clustering coefficient of all the vertices of the network. But the documentation says that the clustering coefficient function “clustering_local_tm(net)” returns the values for the primary node set.How do i calculate the clustering coefficient of the second set? could you please explain

Thanks
Yaseswini

By: Tore Opsahl

Tore Opsahl — Mon, 27 Feb 2012 21:24:01 +0000

Hi John,

Thanks for spotting a missing piece of the documentation. The second column called lc is simply the binary local clustering coefficient for two-mode networks.

Let me know if there is anything else – I will incorporate this in the upcoming version of tnet!

Best,
Tore

By: John T Scholz

John T Scholz — Mon, 27 Feb 2012 21:02:31 +0000

For a weighted 2-mode network, the command “clustering_local_tm(net2)” produces the follow output for the first lines:
node lc lc.am lc.gm lc.ma lc.mi
1 1 0.5789474 0.5756300 0.5568930 0.5759220 0.4851772
2 2 0.3787879 0.4117520 0.4336639 0.3799618 0.5025974
3 3 0.2736781 0.2912917 0.2849269 0.2914947 0.2684981
4 4 0.3240741 0.3355950 0.3482124 0.3313095 0.3813559
5 5 NaN NaN NaN NaN NaN
6 6 NaN NaN NaN NaN NaN

I assume that the columns with suffixes am, gm, ma, and mi are calculated with the arithmetic and geometric mean and the maximum and minimum value for the 4-paths, but how is the first lc column calculated? I could not find an explanation in the manual or online.

Thanks, John