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Bug in infection times? #53

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afmagee42 opened this issue Dec 20, 2024 · 1 comment · Fixed by #55
Closed

Bug in infection times? #53

afmagee42 opened this issue Dec 20, 2024 · 1 comment · Fixed by #55
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It looks to me like we're missing a infection_times += t_infectious somewhere.

That is, we generate waiting times in generate_infection() but store them as the property self.infections[person]["infection_times"] and add them to the queue as if they were absolute times.
@afmagee42 afmagee42 added the bug Something isn't working label Dec 20, 2024
@swo swo self-assigned this Dec 20, 2024
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swo commented Dec 20, 2024

Good catch. We should probably:

  • rename generate_infection_times -> generation_infection_delays
  • put an assert in the simulation, that the infection times are all between the onset of infectiousness and recovery time

@afmagee42 afmagee42 mentioned this issue Dec 21, 2024
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afmagee42 added a commit that referenced this issue Dec 23, 2024
@afmagee42
cleanup #53
6611577
@afmagee42 afmagee42 mentioned this issue Dec 23, 2024
Merged
@swo swo assigned afmagee42 and unassigned swo Dec 31, 2024
afmagee42 added a commit that referenced this issue Jan 7, 2025
@afmagee42
drafting plotting
733c4f4 
works

rename

use new plot

dropped these

update deps

cleanup #53

use get_person_properties() everywhere

clean up plotting

add matplotlib (#61)

cleanup per @swo #55

bug fix requires test changes

triangles

precommit

let counterfactual show passive detection, remove unused par

put axis back where it belongs, optional gen plotting
@afmagee42 afmagee42 linked a pull request Jan 8, 2025 that will close this issue
Visualize whole tree of infections #55
Merged
@afmagee42 afmagee42 mentioned this issue Jan 10, 2025
Closed
afmagee42 added a commit that referenced this issue Jan 10, 2025
@afmagee42
Visualize whole tree of infections (#55)
e01050b 
* drafting plotting

works

rename

use new plot

dropped these

update deps

cleanup #53

use get_person_properties() everywhere

clean up plotting

add matplotlib (#61)

cleanup per @swo #55

bug fix requires test changes

triangles

precommit

let counterfactual show passive detection, remove unused par

put axis back where it belongs, optional gen plotting

* rebase smuggled in non-precommit-compliance

* legend

* trying to make the triangles perceptually same size... why is it not working?

* new plotting takes longer

* debug statement

* small tweaks
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Visualize whole tree of infections CDCgov/cfa-ring-vax-widget
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