Calculate node metrics for specific nodes only

Collin

As the title suggests, is this possible?
I have a rather large landscape graph with >30,000 nodes. I attempted to calculate dPC for the entire graph (all nodes) using a HPC with 26 cores and 500 Gb of RAM, but timed out unfinished after 10 days of computation. In truth, I only need dPC for a few specific nodes.

Absent of calculating this manually (creating a new graph without the node(s) in question), is there a way to specify the calculation for specific nodes directly in the graphab_metric() function?

Paul Savary

Dear Collin,
The first answer to your question is no. Unfortunately, I did not include such a functionality in graphab_metric(). This R function only includes some command-line functionalities of Graphab 2.8.
However, I believe that what you are intending to do could find a workaround in the new functionalities of Graphab 3.0, and you could use it with the command-line. The specific nodes you are interested in could be assigned a specific habitat type (type 2 for instance), while all the others would be of habitat type 1. You could then build the graph with all the nodes and all connections, regardless of the node identity. I assume that you could then compute the metric only for the nodes of habitat type 2 while considering all habitat types and connections in the computation. I do not know if it would be compatible with the dPC computation.
Otherwise, some batch functionalities simulating the removal of graph elements might also make your task easier.
I will let my colleagues (@gvuidel ?) confirm that one of these workarounds could work. And if that is the case, I will be happy to help you with the command-lines.
We come back to you ASAP
Thanks again for your interest in Graphab
Best,
Paul Savary

gvuidel

Hi,
You can calculate delta metric for specific nodes only with the Graphab command line.
If you use Graphab 3 the syntax is:
--gmetric PC d=xxxx p=yyy --delta obj=patch sel=id1,id2,...,idn
And for Graphab 2:
--delta PC d=xxxx p=yy beta=1 obj=patch sel=id1,id2,...,idn

where id1,id2,...,idn is the list of the patch/node identifiers.
Best,
Gilles

Collin

Thanks for the reply, glad to hear it is possible via command line. For my specific case, a manual calculation may be easier.