Add helper data PyrenewHEWData class to hold input data to PyrenewHewModels
#283
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## main #283 +/- ##
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- Coverage 15.87% 15.63% -0.25%
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Files 21 22 +1
Lines 1537 1561 +24
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Hits 244 244
- Misses 1293 1317 +24
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| @property | ||
| def last_data_dates(self): |
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Is this better as a dictionary?
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| @property | ||
| def first_data_dates(self): |
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Is this better as a dictionary?
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| @property | ||
| def first_data_date_overall(self): | ||
| return min([x for x in self.first_data_dates if x is not None]) |
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| return min([x for x in self.first_data_dates if x is not None]) | |
| return min(filter(None, self.first_data_dates)) |
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| @property | ||
| def last_data_date_overall(self): | ||
| return max([x for x in self.last_data_dates if x is not None]) |
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| return max([x for x in self.last_data_dates if x is not None]) | |
| return max(filter(None, self.last_data_dates)) |
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Should we prune the data_for_model_fit.json object to only supply the info necessary to create pyrenew_hew_data?
| n_init_days = self.latent_infection_process_rv.infection_initialization_process.infection_init_method.n_timepoints | ||
| first_latent_infection_dow = ( | ||
| data.first_data_date_overall - datetime.timedelta(days=n_init_days) | ||
| ).weekday() | ||
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| sampled_ed_visits, sampled_admissions, sampled_wastewater = ( |
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Slight preference for
| sampled_ed_visits, sampled_admissions, sampled_wastewater = ( | |
| sampled_ed_visits = sampled_admissions = sampled_wastewater = None |
or
| sampled_ed_visits, sampled_admissions, sampled_wastewater = ( | |
| sampled_ed_visits = None | |
| sampled_admissions = None | |
| sampled_wastewater = None |
| self.ihr_rv = ihr_rv | ||
| self.ihr_rel_iedr_rv = ihr_rel_iedr_rv |
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check that at most one of these is not None?
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| hospital_admissions_obs_rv = NegativeBinomialObservation( | ||
| "observed_hospital_admissions", | ||
| concentration_rv=self.hosp_admit_neg_bin_concentration_rv, | ||
| ) | ||
| predicted_admissions = latent_hospital_admissions | ||
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| sampled_admissions = hospital_admissions_obs_rv( |
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| sampled_admissions = hospital_admissions_obs_rv( | |
| observed_hospital_admissions = hospital_admissions_obs_rv( |
and rename in the return
| else: | ||
| ihr = self.ihr_rv() | ||
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| latent_admissions = population_size * ihr * latent_infections |
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Needs a better name. Or just pass latent_incidence=population_size * ihr * latent_infections in to compute_delay_ascertained_incidence
| @@ -227,61 +234,89 @@ def sample( | |||
| concentration_rv=self.ed_neg_bin_concentration_rv, | |||
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| observed_ed_visits = ed_visit_obs_rv( | |||
| sampled_ed_visits = ed_visit_obs_rv( | |||
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| sampled_ed_visits = ed_visit_obs_rv( | |
| observed_ed_visits = ed_visit_obs_rv( |
also change the return
Main change
Add
PyrenewHEWDataThis:
if is Noneconditionals from the mainmodel.sample()code.to_forecast_data()transformation helper for posterior prediction.Additional changes:
create_pyrenew_hew_model_from_stan_data()and hosp_only_ww_model/pyrenew_hew_model.qmd, closing Removecreate_pyrenew_hew_model_from_stan_data? #280