From 33cc378ebee4d5ed8d97bbd4635c431bdcdb2cd3 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Mon, 23 Sep 2024 16:25:11 +0200 Subject: [PATCH 1/2] data registry update --- .../calculator/models/monte_carlo/data.py | 10 +-- .../caimira/calculator/store/data_registry.py | 80 +++++++++++-------- 2 files changed, 52 insertions(+), 38 deletions(-) diff --git a/caimira/src/caimira/calculator/models/monte_carlo/data.py b/caimira/src/caimira/calculator/models/monte_carlo/data.py index 7b503cb0..88e7898e 100644 --- a/caimira/src/caimira/calculator/models/monte_carlo/data.py +++ b/caimira/src/caimira/calculator/models/monte_carlo/data.py @@ -224,7 +224,7 @@ def activity_distributions(data_registry): } -# From https://doi.org/10.1101/2021.10.14.21264988 and references therein +# From https://doi.org/10.1098/rsfs.2021.0076 and references therein def symptomatic_vl_frequencies(data_registry): return param_evaluation(data_registry.virological_data, 'symptomatic_vl_frequencies') @@ -419,8 +419,8 @@ def expiration_distributions(data_registry): exp_type: expiration_distribution( data_registry=data_registry, BLO_factors=BLO_factors, - d_min=param_evaluation(data_registry.expiration_particle['long_range_particle_diameter'], 'minimum_diameter'), - d_max=param_evaluation(data_registry.expiration_particle['long_range_particle_diameter'], 'maximum_diameter') + d_min=param_evaluation(data_registry.expiration_particle['particle_size_range']['long_range'], 'minimum_diameter'), + d_max=param_evaluation(data_registry.expiration_particle['particle_size_range']['long_range'], 'maximum_diameter') ) for exp_type, BLO_factors in expiration_BLO_factors(data_registry).items() } @@ -431,8 +431,8 @@ def short_range_expiration_distributions(data_registry): exp_type: expiration_distribution( data_registry=data_registry, BLO_factors=BLO_factors, - d_min=param_evaluation(data_registry.expiration_particle['short_range_particle_diameter'], 'minimum_diameter'), - d_max=param_evaluation(data_registry.expiration_particle['short_range_particle_diameter'], 'maximum_diameter') + d_min=param_evaluation(data_registry.expiration_particle['particle_size_range']['short_range'], 'minimum_diameter'), + d_max=param_evaluation(data_registry.expiration_particle['particle_size_range']['short_range'], 'maximum_diameter') ) for exp_type, BLO_factors in expiration_BLO_factors(data_registry).items() } diff --git a/caimira/src/caimira/calculator/store/data_registry.py b/caimira/src/caimira/calculator/store/data_registry.py index 5b549858..4b6f1380 100644 --- a/caimira/src/caimira/calculator/store/data_registry.py +++ b/caimira/src/caimira/calculator/store/data_registry.py @@ -7,16 +7,18 @@ class DataRegistry: version = None expiration_particle = { - "long_range_particle_diameter": { - "minimum_diameter": 0.1, - "maximum_diameter": 30, - "references": "Morawska et al. (https://doi.org/10.1016/j.jaerosci.2008.11.002); Johnson et al. (https://doi.org/10.1016/j.jaerosci.2011.07.009).", - }, - "short_range_particle_diameter": { - "minimum_diameter": 0.1, - "maximum_diameter": 100, - "references": "Morawska et al. (https://doi.org/10.1016/j.jaerosci.2008.11.002); Johnson et al. (https://doi.org/10.1016/j.jaerosci.2011.07.009).", - }, + "particle_size_range": { + "long_range": { + "minimum_diameter": 0.1, + "maximum_diameter": 30, + "references": "Morawska et al. (https://doi.org/10.1016/j.jaerosci.2008.11.002); Johnson et al. (https://doi.org/10.1016/j.jaerosci.2011.07.009).", + }, + "short_range": { + "minimum_diameter": 0.1, + "maximum_diameter": 100, + "references": "Morawska et al. (https://doi.org/10.1016/j.jaerosci.2008.11.002); Johnson et al. (https://doi.org/10.1016/j.jaerosci.2011.07.009).", + }, + }, "BLOmodel": { "cn": {"B": 0.06, "L": 0.2, "O": 0.0010008}, "mu": {"B": 0.989541, "L": 1.38629, "O": 4.97673}, @@ -244,7 +246,7 @@ class DataRegistry: "viable_to_RNA_ratio": { "associated_value": "Uniform distribution", "parameters": {"low": 0.01, "high": 0.6}, - "references": "", + "references": "Henriques et al. (https://doi.org/10.1098/rsfs.2021.0076) and references therein.", }, "transmissibility_factor": { "value": 1, @@ -252,7 +254,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "", + "references": "From authorities, only used for incidence rate calculations.", }, }, "SARS_CoV_2_ALPHA": { @@ -265,7 +267,7 @@ class DataRegistry: "viable_to_RNA_ratio": { "associated_value": "Uniform distribution", "parameters": {"low": 0.01, "high": 0.6}, - "references": "", + "references": "Henriques et al. (https://doi.org/10.1098/rsfs.2021.0076) and references therein.", }, "transmissibility_factor": { "value": 0.78, @@ -273,7 +275,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "", + "references": "From authorities, only used for incidence rate calculations.", }, }, "SARS_CoV_2_BETA": { @@ -286,7 +288,7 @@ class DataRegistry: "viable_to_RNA_ratio": { "associated_value": "Uniform distribution", "parameters": {"low": 0.01, "high": 0.6}, - "references": "", + "references": "Henriques et al. (https://doi.org/10.1098/rsfs.2021.0076) and references therein.", }, "transmissibility_factor": { "value": 0.8, @@ -294,7 +296,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "", + "references": "From authorities, only used for incidence rate calculations.", }, }, "SARS_CoV_2_GAMMA": { @@ -307,7 +309,7 @@ class DataRegistry: "viable_to_RNA_ratio": { "associated_value": "Uniform distribution", "parameters": {"low": 0.01, "high": 0.6}, - "references": "", + "references": "Henriques et al. (https://doi.org/10.1098/rsfs.2021.0076) and references therein.", }, "transmissibility_factor": { "value": 0.72, @@ -315,7 +317,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "", + "references": "From authorities, only used for incidence rate calculations.", }, }, "SARS_CoV_2_DELTA": { @@ -328,7 +330,7 @@ class DataRegistry: "viable_to_RNA_ratio": { "associated_value": "Uniform distribution", "parameters": {"low": 0.01, "high": 0.6}, - "references": "", + "references": "Henriques et al. (https://doi.org/10.1098/rsfs.2021.0076) and references therein.", }, "transmissibility_factor": { "value": 0.51, @@ -336,7 +338,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "", + "references": "From authorities, only used for incidence rate calculations.", }, }, "SARS_CoV_2_OMICRON": { @@ -349,15 +351,15 @@ class DataRegistry: "viable_to_RNA_ratio": { "associated_value": "Uniform distribution", "parameters": {"low": 0.01, "high": 0.6}, - "references": "", + "references": "Henriques et al. (https://doi.org/10.1098/rsfs.2021.0076) and references therein.", }, "transmissibility_factor": { "value": 0.2, - "references": "", + "references": "Du et al. (https://www.mdpi.com/1999-4915/14/4/821).", }, "infectiousness_days": { "value": 14, - "references": "", + "references": "From authorities, only used for incidence rate calculations.", }, }, }, @@ -422,7 +424,7 @@ class DataRegistry: "inside_temp": 293., "humidity_with_heating": 0.3, "humidity_without_heating": 0.5, - "references": "", + "references": "N/A.", } ventilation = { @@ -438,12 +440,12 @@ class DataRegistry: concentration_model = { "virus_concentration_model": { "min_background_concentration": 0.0, - "references": "", + "references": "N/A.", }, "CO2_concentration_model": { "CO2_atmosphere_concentration": 440.44, "CO2_fraction_exhaled": 0.042, - "references": "", + "references": "ECMWF - https://charts.ecmwf.int/products/carbon-dioxide-forecasts; Zhang et al. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7127751/).", }, } @@ -468,77 +470,89 @@ class DataRegistry: monte_carlo = { "sample_size": 250000, - "references": "", + "references": "N/A.", } population_scenario_activity = { - "office": {"placeholder": "Office", "activity": "Seated", "expiration": {"Speaking": 1, "Breathing": 2}}, + "office": {"placeholder": "Office", "activity": "Seated", "expiration": {"Speaking": 1, "Breathing": 2}, "references": "N/A."}, "smallmeeting": { "placeholder": "Small meeting (<10 occ.)", "activity": "Seated", "expiration": {"Speaking": 1}, + "references": "N/A.", }, "largemeeting": { "placeholder": "Large meeting (>= 10 occ.)", "activity": "Standing", "expiration": {"Speaking": 1, "Breathing": 2}, + "references": "N/A.", }, "callcenter": {"placeholder": "Call Center", "activity": "Seated", "expiration": {"Speaking": 1}}, "controlroom-day": { "placeholder": "Control Room - Day shift", "activity": "Seated", "expiration": {"Speaking": 1, "Breathing": 1}, + "references": "N/A.", }, "controlroom-night": { "placeholder": "Control Room - Night shift", "activity": "Seated", "expiration": {"Speaking": 1, "Breathing": 9}, + "references": "N/A.", }, - "library": {"placeholder": "Library", "activity": "Seated", "expiration": {"Breathing": 1}}, + "library": {"placeholder": "Library", "activity": "Seated", "expiration": {"Breathing": 1}, "references": "N/A."}, "lab": { "placeholder": "Lab", "activity": "Light activity", "expiration": {"Speaking": 1, "Breathing": 1}, + "references": "N/A.", }, "workshop": { "placeholder": "Workshop", "activity": "Moderate activity", "expiration": {"Speaking": 1, "Breathing": 1}, + "references": "N/A.", }, - "training": {"placeholder": "Conference/Training (speaker infected)", "activity": "Standing", "expiration": {"Speaking": 1}}, - "training_attendee": {"placeholder": "Conference/Training (attendee infected)", "activity": "Seated", "expiration": {"Breathing": 1}}, - "gym": {"placeholder": "Gym", "activity": "Heavy exercise", "expiration": {"Breathing": 1}}, + "training": {"placeholder": "Conference/Training (speaker infected)", "activity": "Standing", "expiration": {"Speaking": 1}, "references": "N/A."}, + "training_attendee": {"placeholder": "Conference/Training (attendee infected)", "activity": "Seated", "expiration": {"Breathing": 1}, "references": "N/A."}, + "gym": {"placeholder": "Gym", "activity": "Heavy exercise", "expiration": {"Breathing": 1}, "references": "N/A."}, "household-day": { "placeholder": "Household (day time)", "activity": "Light activity", "expiration": {"Breathing": 5, "Speaking": 5}, + "references": "N/A.", }, "household-night": { "placeholder": "Household (evening and night time)", "activity": "Seated", "expiration": {"Breathing": 7, "Speaking": 3}, + "references": "N/A." }, "primary-school": { "placeholder": "Primary school", "activity": "Light activity", "expiration": {"Breathing": 5, "Speaking": 5}, + "references": "N/A.", }, "secondary-school": { "placeholder": "Secondary school", "activity": "Light activity", "expiration": {"Breathing": 7, "Speaking": 3}, + "references": "N/A.", }, "university": { "placeholder": "University", "activity": "Seated", "expiration": {"Breathing": 9, "Speaking": 1}, + "references": "N/A.", }, "restaurant": { "placeholder": "Restaurant", "activity": "Seated", "expiration": {"Breathing": 1, "Speaking": 9}, + "references": "N/A.", }, - "precise": {"placeholder": "Precise", "activity": "", "expiration": {}}, + "precise": {"placeholder": "Precise", "activity": "", "expiration": {}, "references": "N/A."}, } def to_dict(self): From 78286ec2a9840459cff1158a5205d7568a508c6c Mon Sep 17 00:00:00 2001 From: lrdossan Date: Thu, 21 Nov 2024 16:30:04 +0100 Subject: [PATCH 2/2] adapted infectiousness_days reference --- .../src/caimira/calculator/store/data_registry.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/caimira/src/caimira/calculator/store/data_registry.py b/caimira/src/caimira/calculator/store/data_registry.py index 4b6f1380..2a0e8ae9 100644 --- a/caimira/src/caimira/calculator/store/data_registry.py +++ b/caimira/src/caimira/calculator/store/data_registry.py @@ -254,7 +254,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "From authorities, only used for incidence rate calculations.", + "references": "From French and Swiss guidelines (2021), supported by WHO (https://iris.who.int/bitstream/handle/10665/342004/WHO-2019-nCoV-IHR-Quarantine-2021.1-eng.pdf). Only used for incidence rate calculations.", }, }, "SARS_CoV_2_ALPHA": { @@ -275,7 +275,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "From authorities, only used for incidence rate calculations.", + "references": "From French and Swiss guidelines (2021), supported by WHO (https://iris.who.int/bitstream/handle/10665/342004/WHO-2019-nCoV-IHR-Quarantine-2021.1-eng.pdf). Only used for incidence rate calculations.", }, }, "SARS_CoV_2_BETA": { @@ -296,7 +296,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "From authorities, only used for incidence rate calculations.", + "references": "From French and Swiss guidelines (2021), supported by WHO (https://iris.who.int/bitstream/handle/10665/342004/WHO-2019-nCoV-IHR-Quarantine-2021.1-eng.pdf). Only used for incidence rate calculations.", }, }, "SARS_CoV_2_GAMMA": { @@ -317,7 +317,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "From authorities, only used for incidence rate calculations.", + "references": "From French and Swiss guidelines (2021), supported by WHO (https://iris.who.int/bitstream/handle/10665/342004/WHO-2019-nCoV-IHR-Quarantine-2021.1-eng.pdf). Only used for incidence rate calculations.", }, }, "SARS_CoV_2_DELTA": { @@ -338,7 +338,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "From authorities, only used for incidence rate calculations.", + "references": "From French and Swiss guidelines (2021), supported by WHO (https://iris.who.int/bitstream/handle/10665/342004/WHO-2019-nCoV-IHR-Quarantine-2021.1-eng.pdf). Only used for incidence rate calculations.", }, }, "SARS_CoV_2_OMICRON": { @@ -359,7 +359,7 @@ class DataRegistry: }, "infectiousness_days": { "value": 14, - "references": "From authorities, only used for incidence rate calculations.", + "references": "From French and Swiss guidelines (2021), supported by WHO (https://iris.who.int/bitstream/handle/10665/342004/WHO-2019-nCoV-IHR-Quarantine-2021.1-eng.pdf). Only used for incidence rate calculations.", }, }, },