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

["James Kaufman" <jhkauf@xxxxxxxxxx>]

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:      
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To:      
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Date:      
 12/20/2018 03:58 AM
Subject:    
   stem-dev Digest,
Vol 116, Issue 6
Sent by:    
   stem-dev-bounces@xxxxxxxxxxx

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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
Message-ID:
                
<VI1PR0601MB2352EDD4E8CA3D4513E36CD1BFBF0@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>
                
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:

[cid:39028d43-8521-4236-a1d9-543cd4cf57dd]

*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.

[cid:4a931012-09e8-42f4-8110-fcb26a17f0c8]

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











Emily Nixon
PhD Student

Demonstrator


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389
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