Allow the user to prescribe mitigation date #418
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
… won't change when the model does
PhilMiller
changed the title
PhilMiller
changed the title
|
Documentation and input description wording probably need work. As implemented, without #340 taken into account, the date given needs to be when effects of distancing or other mitigation were/will be seen, not the date a policy was enacted. |
|
Playing with things more, I realize that the fit could potentially have three points where the given census crosses the curve in the allowed time before the forecast maximum |
jlubken
reviewed
Apr 2, 2020
|
Heh, I was actually thinking about how we ought to make n_days go away as
well.
I agree on the passing a list of pairs, and of not making that class state.
I was trying to get the feature built with minimal other disruption, but if
you want the further refactoring, I'm onboard to do it.
…On Wed, Apr 1, 2020, 22:22 Jason ***@***.***> wrote:
***@***.**** commented on this pull request.
------------------------------
In src/penn_chime/models.py
<#418 (comment)>:
> @@ -147,17 +147,29 @@ def __init__(self, p: Parameters):
self.daily_growth_rate_t = get_growth_rate(self.doubling_time_t)
def run_projection(self, p):
I might pass the (beta, n_day) pairs into run_projection(p, *args),
instead of using state. The call site knows better if it is pre or post
fit, and how many of these pairs are needed.
If I was going to use state, then I would store the pairs as in a list:
self.policies = [beta1, n_days1, beta2, n_days2, beta3, n_days3, beta4, n_days4...]
...
self.raw_df = sim_sir_df(
self.susceptible,
self.infected,
p.recovered,
self.gamma,
-self.i_day,
*self.policies)
... to avoid having to rewire run_projection when extending the ui to
allow multiple (social_distancing, date) pairs.
Ideally, the n_days input from the UI input would be merely a UI setting
for the graphs, and gen_sir would simply run until i < 0.5. This would
avoid complicating the model total days computations
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#418 (review)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAA64ABEP5E634KY7SAKNSTRKPZHHANCNFSM4LZQ3SNA>
.
|
…puts are compatible
PhilMiller
commented
Apr 2, 2020
|
Is the new |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This is on top of various cleanup and refactoring in #415, so probably review that first.
There's a potential edge case if distancing is strong enough to cause a dip in the census curve, that prescribed-doubling fitting of first-hospitalization might align to a point on either side of the dip.
I've tested this manually and it seems to behave as expected, but I don't have a great handle on how to really validate it.
Fixes #407