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Advanced settings in version 2.0 #57
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Hi and sorry for late reply. I'm currently busy with other projects but will catch up on this project as soon as possible. Some of the advanced options are experimental and everything should be cleaned up and explained more in the app, but some quick answers on your questions for now: Variable Markov time and Markov time Details are explained here: https://arxiv.org/abs/2211.04287. It has a section on the effect in Infomap Bioregions. State network Patch sparse cells Render data while zooming Hope this helps, and please reply if you have more questions. I will try to reply quicker. |
Thank you very much! Actually I do: 1 - I am having some problems obtaining neat results, but part of it may be because of the data quality. I want to use global marine data to calculate bioregions. However, I cannot get enough flexibility. If I set the very high resolution (markov time a bit lower, but dumping higher) I get better resolution at the coasts and more realistic bioregion boundaries. However, the pelagic realm (most of the oceans) becomes all messy and with hundreds of realms. It seems like to get enough resolution in some areas, the algorithm collapses for the other areas, and gives me one realm per cell. This happens even if I set the dumping to 3.0. Any idea why this could be? 2 - Also, to be able to track all my tests, I now tried to use the Python API. I managed to run the algorithm, by downloading the network from Infomaps and using it as the input for Python Infomp. Here the problem is that I am not achieving the same results as in Infomap, although I get similar ones. Are the default parameters in the webpage (https://www.mapequation.org/bioregions2/) the original default values described in GitHub? (https://mapequation.github.io/infomap/python/infomap.html#infomap.Infomap) Thank you and all the best!! |
Interesting questions.
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Thank you, this is such a big help! The results are already looking so much better :). May I ask another question? The "summary" output, with the 10 most representative species in each cluster, how could I derive it from the Python function Infomap()? |
Hello and thanks for such a cool tool.
Is there a source for understanding all the advanced parameters? What does the variable markov time do? I have a lot of noise in my results and I am playing with several parameters, but for some of them I don't know what I am doing. I would like to understand better:
Thanks a lot!
Best,
Cesc
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