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data registry update

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lrdossan 2024-09-23 16:25:11 +02:00
parent 515c8ef118
commit 33cc378ebe
2 changed files with 52 additions and 38 deletions
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10
caimira/src/caimira/calculator/models/monte_carlo/data.py
View file

@ -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): def symptomatic_vl_frequencies(data_registry):
return param_evaluation(data_registry.virological_data, 'symptomatic_vl_frequencies') return param_evaluation(data_registry.virological_data, 'symptomatic_vl_frequencies')
@ -419,8 +419,8 @@ def expiration_distributions(data_registry):
exp_type: expiration_distribution( exp_type: expiration_distribution(
data_registry=data_registry, data_registry=data_registry,
BLO_factors=BLO_factors, BLO_factors=BLO_factors,
d_min=param_evaluation(data_registry.expiration_particle['long_range_particle_diameter'], 'minimum_diameter'), d_min=param_evaluation(data_registry.expiration_particle['particle_size_range']['long_range'], 'minimum_diameter'),
d_max=param_evaluation(data_registry.expiration_particle['long_range_particle_diameter'], 'maximum_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() 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( exp_type: expiration_distribution(
data_registry=data_registry, data_registry=data_registry,
BLO_factors=BLO_factors, BLO_factors=BLO_factors,
d_min=param_evaluation(data_registry.expiration_particle['short_range_particle_diameter'], 'minimum_diameter'), d_min=param_evaluation(data_registry.expiration_particle['particle_size_range']['short_range'], 'minimum_diameter'),
d_max=param_evaluation(data_registry.expiration_particle['short_range_particle_diameter'], 'maximum_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() for exp_type, BLO_factors in expiration_BLO_factors(data_registry).items()
} }

80
caimira/src/caimira/calculator/store/data_registry.py
View file

@ -7,16 +7,18 @@ class DataRegistry:
version = None version = None
expiration_particle = { expiration_particle = {
"long_range_particle_diameter": { "particle_size_range": {
"minimum_diameter": 0.1, "long_range": {
"maximum_diameter": 30, "minimum_diameter": 0.1,
"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).", "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, "short_range": {
"maximum_diameter": 100, "minimum_diameter": 0.1,
"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).", "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": { "BLOmodel": {
"cn": {"B": 0.06, "L": 0.2, "O": 0.0010008}, "cn": {"B": 0.06, "L": 0.2, "O": 0.0010008},
"mu": {"B": 0.989541, "L": 1.38629, "O": 4.97673}, "mu": {"B": 0.989541, "L": 1.38629, "O": 4.97673},
@ -244,7 +246,7 @@ class DataRegistry:
"viable_to_RNA_ratio": { "viable_to_RNA_ratio": {
"associated_value": "Uniform distribution", "associated_value": "Uniform distribution",
"parameters": {"low": 0.01, "high": 0.6}, "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": { "transmissibility_factor": {
"value": 1, "value": 1,
@ -252,7 +254,7 @@ class DataRegistry:
}, },
"infectiousness_days": { "infectiousness_days": {
"value": 14, "value": 14,
"references": "", "references": "From authorities, only used for incidence rate calculations.",
}, },
}, },
"SARS_CoV_2_ALPHA": { "SARS_CoV_2_ALPHA": {
@ -265,7 +267,7 @@ class DataRegistry:
"viable_to_RNA_ratio": { "viable_to_RNA_ratio": {
"associated_value": "Uniform distribution", "associated_value": "Uniform distribution",
"parameters": {"low": 0.01, "high": 0.6}, "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": { "transmissibility_factor": {
"value": 0.78, "value": 0.78,
@ -273,7 +275,7 @@ class DataRegistry:
}, },
"infectiousness_days": { "infectiousness_days": {
"value": 14, "value": 14,
"references": "", "references": "From authorities, only used for incidence rate calculations.",
}, },
}, },
"SARS_CoV_2_BETA": { "SARS_CoV_2_BETA": {
@ -286,7 +288,7 @@ class DataRegistry:
"viable_to_RNA_ratio": { "viable_to_RNA_ratio": {
"associated_value": "Uniform distribution", "associated_value": "Uniform distribution",
"parameters": {"low": 0.01, "high": 0.6}, "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": { "transmissibility_factor": {
"value": 0.8, "value": 0.8,
@ -294,7 +296,7 @@ class DataRegistry:
}, },
"infectiousness_days": { "infectiousness_days": {
"value": 14, "value": 14,
"references": "", "references": "From authorities, only used for incidence rate calculations.",
}, },
}, },
"SARS_CoV_2_GAMMA": { "SARS_CoV_2_GAMMA": {
@ -307,7 +309,7 @@ class DataRegistry:
"viable_to_RNA_ratio": { "viable_to_RNA_ratio": {
"associated_value": "Uniform distribution", "associated_value": "Uniform distribution",
"parameters": {"low": 0.01, "high": 0.6}, "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": { "transmissibility_factor": {
"value": 0.72, "value": 0.72,
@ -315,7 +317,7 @@ class DataRegistry:
}, },
"infectiousness_days": { "infectiousness_days": {
"value": 14, "value": 14,
"references": "", "references": "From authorities, only used for incidence rate calculations.",
}, },
}, },
"SARS_CoV_2_DELTA": { "SARS_CoV_2_DELTA": {
@ -328,7 +330,7 @@ class DataRegistry:
"viable_to_RNA_ratio": { "viable_to_RNA_ratio": {
"associated_value": "Uniform distribution", "associated_value": "Uniform distribution",
"parameters": {"low": 0.01, "high": 0.6}, "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": { "transmissibility_factor": {
"value": 0.51, "value": 0.51,
@ -336,7 +338,7 @@ class DataRegistry:
}, },
"infectiousness_days": { "infectiousness_days": {
"value": 14, "value": 14,
"references": "", "references": "From authorities, only used for incidence rate calculations.",
}, },
}, },
"SARS_CoV_2_OMICRON": { "SARS_CoV_2_OMICRON": {
@ -349,15 +351,15 @@ class DataRegistry:
"viable_to_RNA_ratio": { "viable_to_RNA_ratio": {
"associated_value": "Uniform distribution", "associated_value": "Uniform distribution",
"parameters": {"low": 0.01, "high": 0.6}, "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": { "transmissibility_factor": {
"value": 0.2, "value": 0.2,
"references": "", "references": "Du et al. (https://www.mdpi.com/1999-4915/14/4/821).",
}, },
"infectiousness_days": { "infectiousness_days": {
"value": 14, "value": 14,
"references": "", "references": "From authorities, only used for incidence rate calculations.",
}, },
}, },
}, },
@ -422,7 +424,7 @@ class DataRegistry:
"inside_temp": 293., "inside_temp": 293.,
"humidity_with_heating": 0.3, "humidity_with_heating": 0.3,
"humidity_without_heating": 0.5, "humidity_without_heating": 0.5,
"references": "", "references": "N/A.",
} }
ventilation = { ventilation = {
@ -438,12 +440,12 @@ class DataRegistry:
concentration_model = { concentration_model = {
"virus_concentration_model": { "virus_concentration_model": {
"min_background_concentration": 0.0, "min_background_concentration": 0.0,
"references": "", "references": "N/A.",
}, },
"CO2_concentration_model": { "CO2_concentration_model": {
"CO2_atmosphere_concentration": 440.44, "CO2_atmosphere_concentration": 440.44,
"CO2_fraction_exhaled": 0.042, "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 = { monte_carlo = {
"sample_size": 250000, "sample_size": 250000,
"references": "", "references": "N/A.",
} }
population_scenario_activity = { 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": { "smallmeeting": {
"placeholder": "Small meeting (<10 occ.)", "placeholder": "Small meeting (<10 occ.)",
"activity": "Seated", "activity": "Seated",
"expiration": {"Speaking": 1}, "expiration": {"Speaking": 1},
"references": "N/A.",
}, },
"largemeeting": { "largemeeting": {
"placeholder": "Large meeting (>= 10 occ.)", "placeholder": "Large meeting (>= 10 occ.)",
"activity": "Standing", "activity": "Standing",
"expiration": {"Speaking": 1, "Breathing": 2}, "expiration": {"Speaking": 1, "Breathing": 2},
"references": "N/A.",
}, },
"callcenter": {"placeholder": "Call Center", "activity": "Seated", "expiration": {"Speaking": 1}}, "callcenter": {"placeholder": "Call Center", "activity": "Seated", "expiration": {"Speaking": 1}},
"controlroom-day": { "controlroom-day": {
"placeholder": "Control Room - Day shift", "placeholder": "Control Room - Day shift",
"activity": "Seated", "activity": "Seated",
"expiration": {"Speaking": 1, "Breathing": 1}, "expiration": {"Speaking": 1, "Breathing": 1},
"references": "N/A.",
}, },
"controlroom-night": { "controlroom-night": {
"placeholder": "Control Room - Night shift", "placeholder": "Control Room - Night shift",
"activity": "Seated", "activity": "Seated",
"expiration": {"Speaking": 1, "Breathing": 9}, "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": { "lab": {
"placeholder": "Lab", "placeholder": "Lab",
"activity": "Light activity", "activity": "Light activity",
"expiration": {"Speaking": 1, "Breathing": 1}, "expiration": {"Speaking": 1, "Breathing": 1},
"references": "N/A.",
}, },
"workshop": { "workshop": {
"placeholder": "Workshop", "placeholder": "Workshop",
"activity": "Moderate activity", "activity": "Moderate activity",
"expiration": {"Speaking": 1, "Breathing": 1}, "expiration": {"Speaking": 1, "Breathing": 1},
"references": "N/A.",
}, },
"training": {"placeholder": "Conference/Training (speaker infected)", "activity": "Standing", "expiration": {"Speaking": 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}}, "training_attendee": {"placeholder": "Conference/Training (attendee infected)", "activity": "Seated", "expiration": {"Breathing": 1}, "references": "N/A."},
"gym": {"placeholder": "Gym", "activity": "Heavy exercise", "expiration": {"Breathing": 1}}, "gym": {"placeholder": "Gym", "activity": "Heavy exercise", "expiration": {"Breathing": 1}, "references": "N/A."},
"household-day": { "household-day": {
"placeholder": "Household (day time)", "placeholder": "Household (day time)",
"activity": "Light activity", "activity": "Light activity",
"expiration": {"Breathing": 5, "Speaking": 5}, "expiration": {"Breathing": 5, "Speaking": 5},
"references": "N/A.",
}, },
"household-night": { "household-night": {
"placeholder": "Household (evening and night time)", "placeholder": "Household (evening and night time)",
"activity": "Seated", "activity": "Seated",
"expiration": {"Breathing": 7, "Speaking": 3}, "expiration": {"Breathing": 7, "Speaking": 3},
"references": "N/A."
}, },
"primary-school": { "primary-school": {
"placeholder": "Primary school", "placeholder": "Primary school",
"activity": "Light activity", "activity": "Light activity",
"expiration": {"Breathing": 5, "Speaking": 5}, "expiration": {"Breathing": 5, "Speaking": 5},
"references": "N/A.",
}, },
"secondary-school": { "secondary-school": {
"placeholder": "Secondary school", "placeholder": "Secondary school",
"activity": "Light activity", "activity": "Light activity",
"expiration": {"Breathing": 7, "Speaking": 3}, "expiration": {"Breathing": 7, "Speaking": 3},
"references": "N/A.",
}, },
"university": { "university": {
"placeholder": "University", "placeholder": "University",
"activity": "Seated", "activity": "Seated",
"expiration": {"Breathing": 9, "Speaking": 1}, "expiration": {"Breathing": 9, "Speaking": 1},
"references": "N/A.",
}, },
"restaurant": { "restaurant": {
"placeholder": "Restaurant", "placeholder": "Restaurant",
"activity": "Seated", "activity": "Seated",
"expiration": {"Breathing": 1, "Speaking": 9}, "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): def to_dict(self):