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Re: [stem-dev] stem-dev Digest, Vol 116, Issue 6

Hi Emily,
The current logger allows you to select which compartments to log but it does not do integration over the spacial nodes. STEM used to have this feature (it was called an integrating disease model) but it was removed for  few reasons.
In order to integrated (eg) level 3 nodes up to level 0 (country) nodes it is necessary to form a graph with all hierarchical admin levels and connect them by containment edges. The containment edges still exist in STEM so this feature could be reimplemented but it has several issues.
1) It adds a lot more nodes and edges to your graph
2) it adds a lot of computational overhead
3) You need to rethink decoration of the graphs itself. You don't want to propagate the disease at all levels - just aggregate above the lowest node. But what if the graph is not uniform in depth. Computing this adds to overhead as well.

We decided it was best to keep things simple. The aggregation feature caused uses to make too many errors in composing their graph. As an alternative you might consider changing the log time interval if the logs are too big. The log time interval is not dependant on your integration time interval.

From:        stem-dev-request@xxxxxxxxxxx
To:        stem-dev@xxxxxxxxxxx
Date:        12/20/2018 03:58 AM
Subject:        stem-dev Digest, Vol 116, Issue 6
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Today's Topics:

  1. Request for a new way of outputting data from STEM (Emily Nixon)


Message: 1
Date: Thu, 20 Dec 2018 11:58:01 +0000
From: Emily Nixon <emily.nixon@xxxxxxxxxxxxx>
To: developer mailing list STEM <stem-dev@xxxxxxxxxxx>
Subject: [stem-dev] Request for a new way of outputting data from STEM
Content-Type: text/plain; charset="iso-8859-1"

Hi all,

As some of you may know, I am running scenarios on STEM that contain graphs with thousands of nodes and edges.

Therefore, the output csv files I get for each compartment of the disease are all very large which makes them difficult to work with and they take up a lot of space.

I am trying to develop ways in R to summarise this data so that I have some meaningful results, however, my supervisor thought that it might be worth checking with STEM developers about whether it is possible to have a new logger, or an option on an existing logger which means that only summary data is output. I know you are very busy at the moment, but she thought that it might not take too long, depending on how the logger code is currently written, and that it could be useful for other people too. Perhaps it could be a new feature on STEM4?

Specifically, what I would like to have is something like the following for the Incidence and I_0 csv files:


*Or the equivalent for I_0

However, if this summary data would be too difficult, then alternatively, having the normal output in a different format would help me a lot with producing this summary data myself in R.


So instead of having a column for every node, having nodeID as a column and then having the node names in this column. This would make the list have more rows but less columns, which would make it much easier to work with.

If anyone has any thoughts or suggestions, if anyone else would find this useful or if anyone thinks they could help with implementing this in STEM, then I would greatly appreciate it!

Best wishes,


Emily Nixon
PhD Student


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Tel +44 (0)117 394 1389
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