Re: [igraph] Translate code from r to python

[simone gabbriellini]

Hi Tamas,

your code gives me an error:

TypeError: argument 1 must be list, not int
WARNING: Failure executing file: <analisi_venezia.py>

is this a correct solution?

g_sw = Graph.Lattice([1, g.vcount()], nei=sum(g.degree())/g.vcount(),  
dir=True, mutual=True)

If I understand the rewire procedure correctly, it changes in this  
case the 25% of the edges in the graph. How can it be that the average  
path after the rewire is longer than in the regular lattice??? This is  
what I have:

In [4]: g = Graph.Read_GraphML("200403.graphml")

In [5]: print g.summary()
37 nodes, 728 edges, directed

Number of components: 2
Diameter: 4
Density: 0.5465
Reciprocity: 0.9259
Average path length: 1.4754

In [6]: gSW = Graph.Lattice([1, g.vcount()], nei=sum(g.degree())/ 
g.vcount(), directed=True, mutual=True)

In [7]: print gSW.summary()
37 nodes, 740 edges, directed

Number of components: 1
Diameter: 3
Density: 0.5556
Reciprocity: 0.0556
Average path length: 1.8686

In [8]: gSW.rewire(0.25*gSW.ecount())
/Library/Frameworks/Python.framework/Versions/4.1.30101/bin/ipython:1:  
DeprecationWarning: integer argument expected, got float
  #!/Library/Frameworks/Python.framework/Versions/4.1.30101/Resources/ 
Python.app/Contents/MacOS/Python
Out[8]: <igraph.Graph object at 0x1570d470>

In [9]: print gSW.summary()
37 nodes, 740 edges, directed

Number of components: 1
Diameter: 14
Density: 0.5556
Reciprocity: 0.0571
Average path length: 3.7523

maybe this is an expected behaviour, or maybe I am doing something  
wrong...

best regards,
Simone


Il giorno 26/giu/09, alle ore 13:19, Tamas Nepusz ha scritto:

> > g.sw=rewire.edges(graph.lattice(vcount(g), nei=mean(degree(g)),  
> > dir=TRUE, mutual=TRUE), p=0.25)
> g_sw = Graph.Lattice(g.vcount(), nei=sum(g.degree())/g.vcount(),  
> dir=True, mutual=True)
> g_sw.rewire(0.25 * g_sw.ecount())
>
> Note that rewire() does not have a p= argument in Python, only n=...  
> which lets you specify the number of rewirings. That's why I've  
> written g_sw.ecount() * 0.25. Another difference is that  
> Graph.rewire() rewires the graph in-place in Python, so you must  
> construct the graph first and then invoke its rewire() method.
>
> --
> T.
>
>
>
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