pingu_98/cara
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Merge branch 'feature/dist_halflife' into 'feature/scientific_model_update'

Browse source 
New r_inf distribution min and max and new halflife value

See merge request cara/cara!304
This commit is contained in:
Andre Henriques 2021-12-06 15:50:14 +01:00
commit 2df636d556
3 changed files with 11 additions and 8 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

4
cara/models.py
View file

@ -459,7 +459,9 @@ class SARSCoV2(Virus):
CERN-OPEN-2021-004, DOI: 10.17181/CERN.1GDQ.5Y75)
"""
halflife = np.empty_like(humidity)
halflife[humidity <= 0.4] = 3.8
# Taken from Morris et al (https://doi.org/10.7554/eLife.65902) data at T = 22°C and RH = 40 %.
halflife[humidity <= 0.4] = 6.43
# Taken from Doremalen et al (https://www.nejm.org/doi/10.1056/NEJMc2004973).
halflife[humidity > 0.4] = 1.1
return halflife

5
cara/monte_carlo/data.py
View file

@ -99,8 +99,9 @@ symptomatic_vl_frequencies = LogCustomKernel(
kernel_bandwidth=0.1
)
# From https://doi.org/10.1093/cid/ciaa1579
viable_to_RNA_ratio_distribution = Uniform(0.15, 0.45)
# Derived from data in doi.org/10.1016/j.ijid.2020.09.025 and
# https://iosh.com/media/8432/aerosol-infection-risk-hospital-patient-care-full-report.pdf (page 60)
viable_to_RNA_ratio_distribution = Uniform(0.01, 0.6)
# From discussion with virologists
infectious_dose_distribution = Uniform(10., 100.)

10
cara/tests/test_monte_carlo_full_models.py
View file

@ -282,9 +282,9 @@ def waiting_room_mc():
"mc_model, expected_pi, expected_new_cases, expected_dose, expected_ER",
[
["shared_office_mc", 6.03, 0.18, 24.55, 809],
["classroom_mc", 10.0, 2.0, 79.98, 5624],
["ski_cabin_mc", 17.0, 0.5, 40.25, 7966],
["skagit_chorale_mc",70, 42.5, 241.28, 190422],
["classroom_mc", 10.0, 1.85, 79.98, 5624],
["ski_cabin_mc", 16.0, 0.5, 40.25, 7966],
["skagit_chorale_mc",65.7, 40.0, 241.28, 190422],
["bus_ride_mc", 12.0, 8.0, 63.79, 5419],
["gym_mc", 0.45, 0.13, 0.4852, 1145],
["waiting_room_mc", 1.59, 0.22, 7.23, 737],
@ -308,10 +308,10 @@ def test_report_models(mc_model, expected_pi, expected_new_cases,
@pytest.mark.parametrize(
"mask_type, month, expected_pi, expected_dose, expected_ER",
[
["No mask", "Jul", 10.02, 84.54, 809],
["No mask", "Jul", 9.52, 84.54, 809],
["Type I", "Jul", 1.7, 15.64, 149],
["FFP2", "Jul", 0.51, 15.64, 149],
["Type I", "Feb", 0.57, 4.59, 149],
["Type I", "Feb", 0.57, 4.59, 162],
],
)
def test_small_shared_office_Geneva(mask_type, month, expected_pi,