Scalar Assortativity - Definition
Hello Tiago, I have a quick question about how the scalar assortativity is calculated. You reference "M. E. J. Newman, “Mixing patterns in networks”, Phys. Rev. E 67, 026126 (2003)" as source for the equation. In the paper the equation seems to consider edges connecting nodes of indegree x to those of outdegree y (or rather "j" and "k"). In your implementation I am able to choose in-degree, out-degree or total as degree type. What does this do to the equation? If I choose, say, "in", will that mean the algorithm will look at edges connecting nodes of indegree x to those of indegree y? If so, is there a way for me to find the assortativity as per the definition in the paper? Best, Philipp -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
Hi, Could I follow up on this again for clarification? I have also come across this paper "Assortative mixing in directed biological networks", M. Piraveenan et al., DOI: 10.1109/TCBB.2010.80 which describes an assortativity coefficient which would perhaps match the description in the manual. Any clarification would be much appreciated! Best, Philipp -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
Hi Tiago, I am sorry to keep bringing this up but could you help me with the definition/source here please? Best, Philipp -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 16.12.2016 16:43, P-M wrote:
If I choose, say, "in", will that mean the algorithm will look at edges connecting nodes of indegree x to those of indegree y?
Yes.
If so, is there a way for me to find the assortativity as per the definition in the paper?
You can write your own loop... It is pretty simple. But if you want the function to be generalized, open an issue in the website, and I will address it when I find the time. -- Tiago de Paula Peixoto <tiago@skewed.de>
Hi Tiago, I am quite happy with the current implementation though can file a feature request if you would like me to. What I am mostly after is the definition of the actual equation used so I can cite it as the paper cited in the manual doesn't contain the equation that seems to be used as far as I can tell. Hence my question if it comes from dx.doi.org/10.1109/TCBB.2010.80 which seems to use an equation that does what you are describing. Best, Philipp -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 19.01.2017 15:26, P-M wrote:
Hi Tiago,
I am quite happy with the current implementation though can file a feature request if you would like me to. What I am mostly after is the definition of the actual equation used so I can cite it as the paper cited in the manual doesn't contain the equation that seems to be used as far as I can tell. Hence my question if it comes from dx.doi.org/10.1109/TCBB.2010.80 which seems to use an equation that does what you are describing.
The documentation describes _exactly_ the equation that is being used: https://graph-tool.skewed.de/static/doc/correlations.html#graph_tool.correla... -- Tiago de Paula Peixoto <tiago@skewed.de>
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