diff --git a/cara/monte_carlo/data.py b/cara/monte_carlo/data.py index 63c83084..d043f688 100644 --- a/cara/monte_carlo/data.py +++ b/cara/monte_carlo/data.py @@ -110,7 +110,7 @@ viral_load = np.linspace(weibull_min.ppf(0.01, c=3.47, scale=7.01), weibull_min.ppf(0.99, c=3.47, scale=7.01), 30) frequencies_pdf = weibull_min.pdf(viral_load, c=3.47, scale=7.01) covid_overal_vl_data = LogCustom(bounds=(2, 10), - function=lambda d: np.interp(d, viral_load, frequencies_pdf, right=0., left=0.), + function=lambda d: np.interp(d, viral_load, frequencies_pdf, left=0., right=0.), max_function=0.2) @@ -156,7 +156,7 @@ virus_distributions = { transmissibility_factor=0.51, ), 'SARS_CoV_2_OMICRON': mc.SARSCoV2( - viral_load_in_sputum=symptomatic_vl_frequencies, + viral_load_in_sputum=covid_overal_vl_data, infectious_dose=infectious_dose_distribution, viable_to_RNA_ratio=viable_to_RNA_ratio_distribution, transmissibility_factor=0.2, diff --git a/cara/tests/test_monte_carlo_full_models.py b/cara/tests/test_monte_carlo_full_models.py index 2272948d..93ebd459 100644 --- a/cara/tests/test_monte_carlo_full_models.py +++ b/cara/tests/test_monte_carlo_full_models.py @@ -308,17 +308,17 @@ def waiting_room_mc(): ) -@retry() +@retry(tries=10) @pytest.mark.parametrize( "mc_model, expected_pi, expected_new_cases, expected_dose, expected_ER", [ - ["shared_office_mc", 5.55, 0.17, 2.699, 809], - ["classroom_mc", 9.58, 1.82, 9.034, 5624], - ["ski_cabin_mc", 16.0, 0.47, 17.315, 7966], + ["shared_office_mc", 5.38, 0.16, 3.350, 1056], + ["classroom_mc", 8.21, 1.56, 11.356, 7416], + ["ski_cabin_mc", 12.92, 0.39, 21.796, 10231], ["skagit_chorale_mc",61.01, 36.53, 84.730, 190422], - ["bus_ride_mc", 10.59, 7.06, 6.65, 5419], - ["gym_mc", 0.43, 0.12, 0.197, 1145], - ["waiting_room_mc", 1.34, 0.18, 0.670, 737], + ["bus_ride_mc", 10.59, 7.06, 6.650, 5419], + ["gym_mc", 0.52, 0.14, 0.249, 1450], + ["waiting_room_mc", 1.53, 0.21, 0.844, 929], ] ) def test_report_models(mc_model, expected_pi, expected_new_cases, @@ -339,10 +339,10 @@ 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", 8.46, 8.113, 809], - ["Type I", "Jul", 1.44, 0.727, 149], - ["FFP2", "Jul", 0.43, 0.197, 149], - ["Type I", "Feb", 0.54, 0.253, 149], + ["No mask", "Jul", 7.689, 10.050, 1034.435], + ["Type I", "Jul", 1.663, 0.938, 193.52], + ["FFP2", "Jul", 0.523, 0.253, 193.52], + ["Type I", "Feb", 0.659, 0.325, 193.52], ], ) def test_small_shared_office_Geneva(mask_type, month, expected_pi, diff --git a/cara/tests/test_predefined_distributions.py b/cara/tests/test_predefined_distributions.py index b576b7e3..db8c8c4b 100644 --- a/cara/tests/test_predefined_distributions.py +++ b/cara/tests/test_predefined_distributions.py @@ -34,11 +34,11 @@ def test_activity_distributions(distribution, mean, std): # - with a refined precision on the values @pytest.mark.parametrize( "distribution, mean, std",[ - ['SARS_CoV_2', 6.59, 1.74], + ['SARS_CoV_2', 6.22, 1.80], - ['SARS_CoV_2_ALPHA', 6.59, 1.74], + ['SARS_CoV_2_ALPHA', 6.22, 1.80], - ['SARS_CoV_2_GAMMA', 6.59, 1.74], + ['SARS_CoV_2_GAMMA', 6.22, 1.80], ] ) def test_viral_load_logdistribution(distribution, mean, std):