From b8b346f765b3708747c7c855e691236cc72f6f3b Mon Sep 17 00:00:00 2001 From: Romain Ragonnet Date: Thu, 7 Sep 2023 14:35:00 +1000 Subject: [PATCH] Update params following Angus's review --- autumn/models/sm_covid2/params.yml | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/autumn/models/sm_covid2/params.yml b/autumn/models/sm_covid2/params.yml index 4477f2251..97abfe8aa 100644 --- a/autumn/models/sm_covid2/params.yml +++ b/autumn/models/sm_covid2/params.yml @@ -38,8 +38,8 @@ infectious_seed_time: 60 seed_duration: 7 sojourns: - latent: 6.57 # Pooled estimate from Wu et al. doi:10.1001/jamanetworkopen.2022.28008 - active: 8. + latent: 6.65 # wild-type + active: 6.5 mobility: region: null @@ -150,9 +150,9 @@ is_dynamic_mixing_matrix: true # parameters related to immunity stratification (two strata: unvaccinated / vaccinated) vaccine_effects: - ve_infection: .5 #FIXME: dummy data - ve_hospitalisation: .9 #FIXME: dummy data - ve_death: .9 #FIXME: dummy data + ve_infection: .7 + ve_hospitalisation: .9 + ve_death: .9 # voc_emergence: null voc_emergence: @@ -176,11 +176,11 @@ voc_emergence: new_voc_seed: time_from_gisaid_report: 0. seed_duration: 10. - contact_rate_multiplier: 1.38 # DOI: 10.1503/cmaj.211248 + contact_rate_multiplier: 1.5 incubation_overwrite_value: 4.41 # Wu et al. doi:10.1001/jamanetworkopen.2022.28008 - vacc_immune_escape: .32 # DOI: 10.1503/cmaj.211248 - hosp_risk_adjuster: 2.1 # Fisman et al. doi: 10.1503/cmaj.211248 - death_risk_adjuster: 2.3 # Fisman et al. doi: 10.1503/cmaj.211248 + vacc_immune_escape: .3 + hosp_risk_adjuster: 2.0 + death_risk_adjuster: 2.3 icu_risk_adjuster: 3.4 # Fisman et al. doi: 10.1503/cmaj.211248 cross_protection: wild_type: 1. @@ -192,11 +192,11 @@ voc_emergence: new_voc_seed: time_from_gisaid_report: 0. seed_duration: 10. - contact_rate_multiplier: 1.92 # DOI: 10.1503/cmaj.211248 + contact_rate_multiplier: 2. # DOI: 10.1503/cmaj.211248 incubation_overwrite_value: 3.42 # Wu et al. doi:10.1001/jamanetworkopen.2022.28008 - vacc_immune_escape: .55 # DOI: 10.1503/cmaj.211248 - hosp_risk_adjuster: 0.861 # 2.1 * .41 using HR of Omicron vs Delta (Nyberg doi.org/10.1016/S0140-6736(22)00462-7) - death_risk_adjuster: 0.713 # 2.3 * 0.31 using HR of Omicron vs Delta (Nyberg doi.org/10.1016/S0140-6736(22)00462-7) + vacc_immune_escape: .6 # DOI: 10.1503/cmaj.211248 + hosp_risk_adjuster: 0.82 # Multiply Nyberg by Fisman = 0.41*2 = 0.82 + death_risk_adjuster: 0.71 # Multiply Nyberg by Fisman =0.31*2.3=0.713 icu_risk_adjuster: 1. # FIXME dummy value for now but not used at the moment cross_protection: wild_type: 1. @@ -207,7 +207,7 @@ time_from_onset_to_event: # using time of symptom onset as reference hospitalisation: distribution: gamma shape: 5. - mean: 7.7 # Estimates taken from ISARIC report 4th Oct 2020 (Mendeley citation key Pritchard2020} + mean: 3. icu_admission: # using time of hospitalisation as reference distribution: gamma shape: 5. @@ -223,7 +223,7 @@ hospital_stay: hospital_all: distribution: gamma shape: 5. - mean: 12.8 # Estimates taken from ISARIC report 4th Oct 2020 (Mendeley citation key Pritchard2020} + mean: 9 icu: distribution: gamma