Thanks for getting back to me so quickly!
I have a ‘quarantined’ vertex property map that maintains who is quarantined
and have set a vertex filter on the graph to filter out quarantined people.
Quarantined people are not supposed to be able to infect others.
Here is a minimum working example where I quarantine all infected people from
the graph but new people are infected in the next time step.
# SETUP
from graph_tool.generation import price_network
from graph_tool.dynamics import SIRSState
g = price_network(20)
model = SIRSState(g, r=0) # make sure there are no spontaneous infections
state = model.get_state()
# Keep track of who is quarantined
quarantined = g.new_vertex_property('bool', False)
# Filter out quarantined nodes from graph
g.set_vertex_filter(quarantined, inverted=True)
# TEST:
print("before quarantining:\n", state.a)
# Quarantine all infected individuals
quarantined.a = (state.a == 1)
# Run model one time step
model.iterate_sync()
# New nodes in the filtered graph are infected (with some probability):
print("filtered state after quarantining:\n", state.fa)
For completeness, here is the complete code of my extended model:
https://gist.github.com/edwinlock/ccece9b82d13383ef50df8b6e5aedf60
Another question: I want to stop quarantined people from infecting others, but
I do want them to recover with the same probability as non-quarantined people.
In this case it makes sense to use an edge filter to remove all edges adjacent
to a quarantined person
instead of filtering the person’s vertex itself, right?
Best,
Edwin
> On 9 Apr 2020, at 22:23, [email protected] wrote:
>
> Date: Thu, 9 Apr 2020 23:23:07 +0200
> From: Tiago de Paula Peixoto <[email protected] <mailto:[email protected]>>
> To: [email protected] <mailto:[email protected]>
> Subject: Re: [graph-tool] Extending SIR epidemic model with a
> quarantined/immunised state
> Message-ID: <[email protected]
> <mailto:[email protected]>>
> Content-Type: text/plain; charset="utf-8"
>
> Am 09.04.20 um 22:24 schrieb Edwin Lock:
>> Initially, I thought I would be able maintain who is quarantined (and for
>> how long) with a vertex property map and filter the quarantined individuals
>> out from the network using a vertex filter. However, I noticed that the
>> iterate_sync() function, which iterates the model by one time step, seems to
>> ignore vertex filters. In particular, if I filter out all infected
>> individuals, it will still infect new people.
>
> Using the epidemic models on filtered graphs should work. Maybe you
> should try explaining in more detail how you are doing it so we can see
> what the problem may be.
>
>> My second idea was to directly edit the vertex property maps that store the
>> state of each individual in the graph (susceptible, infected and recovered),
>> and introduce an additional ?immunised? state (with value 4, say). However,
>> I have noticed that changing the values of instance.s and instance.s_copy
>> does not seem to have any effect on iterate_sync(). In particular, if I mark
>> everyone as susceptible and thus nobody as infected, it still infects new
>> people in the next time step when I call iterate_sync(). So I am assuming
>> that the state is also stored elsewhere?
>
> Indeed this approach will not work so well, as the logic of the dynamics
> only differentiates between three states, not four.
>
>> Any pointers that might help me extend graph-tool?s SIR model to incorporate
>> quarantining/immunising would be greatly appreciated. I have tried
>> implementing my own model from scratch, but it is significantly slower.
>
> As mentioned above, filtered graphs should work. In addition, the SIR
> model allows for different transmission probabilities on each edge, by
> passing an edge property map as the 'beta' parameter, which you can set
> to zero for the edges incident on quarantined nodes. If these change
> over time, don't forget to pass the 'constant_beta=False' option as well.
>
> Best,
> Tiago
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