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config: remove Ref: config parsing

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Nicola Tarocco 2023-12-08 13:56:55 +01:00 committed by Luis Aleixo
parent bb51eaa360
commit 2abdd130cf
4 changed files with 96 additions and 77 deletions
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13
caimira/enums.py Normal file
View file

@ -0,0 +1,13 @@
from enum import Enum
class ViralLoads(Enum):
COVID_OVERALL = "COVID overall"
SYMPTOMATIC_FREQUENCIES = "Symptomatic frequencies"
class InfectiousDoses(Enum):
DISTRIBUTION = "Distribution"
class ViableToRNARatios(Enum):
DISTRIBUTION = "Distribution"

109
caimira/monte_carlo/data.py
View file

@ -1,3 +1,5 @@
from __future__ import annotations
from dataclasses import dataclass
import typing
@ -5,10 +7,37 @@ import numpy as np
from scipy import special as sp
from scipy.stats import weibull_min
import caimira.monte_carlo as mc
from caimira.enums import ViralLoads, InfectiousDoses, ViableToRNARatios
import caimira.monte_carlo.models as mc
from caimira.monte_carlo.sampleable import LogCustom, LogNormal, Normal, LogCustomKernel, CustomKernel, Uniform, Custom
from caimira.store.data_registry import DataRegistry
def evaluate_vl(value, data_registry: DataRegistry):
if value == ViralLoads.COVID_OVERALL:
return covid_overal_vl_data(data_registry)
elif value == ViralLoads.COVID_OVERALL:
return symptomatic_vl_frequencies
else:
raise ValueError(f"Invalid ViralLoads value {value}")
def evaluate_infectd(value, data_registry: DataRegistry):
if value == InfectiousDoses.DISTRIBUTION:
return infectious_dose_distribution(data_registry)
else:
raise ValueError(f"Invalid InfectiousDoses value {value}")
def evaluate_vtrr(value, data_registry: DataRegistry):
"""."""
if value == ViableToRNARatios.DISTRIBUTION:
return viable_to_RNA_ratio_distribution(data_registry)
else:
raise ValueError(f"Invalid ViableToRNARatios value {value}")
sqrt2pi = np.sqrt(2.*np.pi)
sqrt2 = np.sqrt(2.)
@ -94,10 +123,7 @@ def param_evaluation(root: typing.Dict, param: typing.Union[str, typing.Any]) ->
value = root.get(param)
if isinstance(value, str):
if value.startswith('Ref:'):
reference_variable = value.split(' - ')[1].strip()
return evaluate_reference(reference_variable)
elif value == 'Custom':
if value == 'Custom':
custom_distribution: typing.Dict = custom_distribution_lookup(
root, 'custom distribution')
for d, p in custom_distribution.items():
@ -286,66 +312,43 @@ def infectious_dose_distribution(data_registry):
# From https://doi.org/10.1101/2021.10.14.21264988 and references therein
def virus_distributions(data_registry):
vd = data_registry.virus_distributions
return {
'SARS_CoV_2': mc.SARSCoV2(
viral_load_in_sputum=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2'], 'viral_load_in_sputum'),
infectious_dose=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2'], 'infectious_dose'),
viable_to_RNA_ratio=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2'], 'viable_to_RNA_ratio'),
transmissibility_factor=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2'], 'transmissibility_factor'),
viral_load_in_sputum=evaluate_vl(vd['SARS_CoV_2']['viral_load_in_sputum'], data_registry),
infectious_dose=evaluate_infectd(vd['SARS_CoV_2']['infectious_dose'], data_registry),
viable_to_RNA_ratio=evaluate_vtrr(vd['SARS_CoV_2']['viable_to_RNA_ratio'], data_registry),
transmissibility_factor=vd['SARS_CoV_2']['transmissibility_factor'],
),
'SARS_CoV_2_ALPHA': mc.SARSCoV2(
viral_load_in_sputum=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_ALPHA'], 'viral_load_in_sputum'),
infectious_dose=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_ALPHA'], 'infectious_dose'),
viable_to_RNA_ratio=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_ALPHA'], 'viable_to_RNA_ratio'),
transmissibility_factor=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_ALPHA'], 'transmissibility_factor'),
viral_load_in_sputum=evaluate_vl(vd['SARS_CoV_2_ALPHA']['viral_load_in_sputum'], data_registry),
infectious_dose=evaluate_infectd(vd['SARS_CoV_2_ALPHA']['infectious_dose'], data_registry),
viable_to_RNA_ratio=evaluate_vtrr(vd['SARS_CoV_2_ALPHA']['viable_to_RNA_ratio'], data_registry),
transmissibility_factor=vd['SARS_CoV_2_ALPHA']['transmissibility_factor'],
),
'SARS_CoV_2_BETA': mc.SARSCoV2(
viral_load_in_sputum=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_BETA'], 'viral_load_in_sputum'),
infectious_dose=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_BETA'], 'infectious_dose'),
viable_to_RNA_ratio=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_BETA'], 'viable_to_RNA_ratio'),
transmissibility_factor=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_BETA'], 'transmissibility_factor'),
viral_load_in_sputum=evaluate_vl(vd['SARS_CoV_2_BETA']['viral_load_in_sputum'], data_registry),
infectious_dose=evaluate_infectd(vd['SARS_CoV_2_BETA']['infectious_dose'], data_registry),
viable_to_RNA_ratio=evaluate_vtrr(vd['SARS_CoV_2_BETA']['viable_to_RNA_ratio'], data_registry),
transmissibility_factor=vd['SARS_CoV_2_BETA']['transmissibility_factor'],
),
'SARS_CoV_2_GAMMA': mc.SARSCoV2(
viral_load_in_sputum=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_GAMMA'], 'viral_load_in_sputum'),
infectious_dose=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_GAMMA'], 'infectious_dose'),
viable_to_RNA_ratio=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_GAMMA'], 'viable_to_RNA_ratio'),
transmissibility_factor=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_GAMMA'], 'transmissibility_factor'),
viral_load_in_sputum=evaluate_vl(vd['SARS_CoV_2_GAMMA']['viral_load_in_sputum'], data_registry),
infectious_dose=evaluate_infectd(vd['SARS_CoV_2_GAMMA']['infectious_dose'], data_registry),
viable_to_RNA_ratio=evaluate_vtrr(vd['SARS_CoV_2_GAMMA']['viable_to_RNA_ratio'], data_registry),
transmissibility_factor=vd['SARS_CoV_2_GAMMA']['transmissibility_factor'],
),
'SARS_CoV_2_DELTA': mc.SARSCoV2(
viral_load_in_sputum=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_DELTA'], 'viral_load_in_sputum'),
infectious_dose=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_DELTA'], 'infectious_dose'),
viable_to_RNA_ratio=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_DELTA'], 'viable_to_RNA_ratio'),
transmissibility_factor=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_DELTA'], 'transmissibility_factor'),
viral_load_in_sputum=evaluate_vl(vd['SARS_CoV_2_DELTA']['viral_load_in_sputum'], data_registry),
infectious_dose=evaluate_infectd(vd['SARS_CoV_2_DELTA']['infectious_dose'], data_registry),
viable_to_RNA_ratio=evaluate_vtrr(vd['SARS_CoV_2_DELTA']['viable_to_RNA_ratio'], data_registry),
transmissibility_factor=vd['SARS_CoV_2_DELTA']['transmissibility_factor'],
),
'SARS_CoV_2_OMICRON': mc.SARSCoV2(
viral_load_in_sputum=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_OMICRON'], 'viral_load_in_sputum'),
infectious_dose=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_OMICRON'], 'infectious_dose'),
viable_to_RNA_ratio=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_OMICRON'], 'viable_to_RNA_ratio'),
transmissibility_factor=param_evaluation(
data_registry.virus_distributions['SARS_CoV_2_OMICRON'], 'transmissibility_factor'),
viral_load_in_sputum=evaluate_vl(vd['SARS_CoV_2_OMICRON']['viral_load_in_sputum'], data_registry),
infectious_dose=evaluate_infectd(vd['SARS_CoV_2_OMICRON']['infectious_dose'], data_registry),
viable_to_RNA_ratio=evaluate_vtrr(vd['SARS_CoV_2_OMICRON']['viable_to_RNA_ratio'], data_registry),
transmissibility_factor=vd['SARS_CoV_2_OMICRON']['transmissibility_factor'],
),
}

6
caimira/monte_carlo/sampleable.py
View file

@ -62,7 +62,7 @@ class Custom(SampleableDistribution):
Defines a distribution which follows a custom curve vs. the random
variable. Uses a simple algorithm. This is appropriate for a smooth
distribution function.
Note: in max_function, a value slightly above the maximum of the distribution
Note: in max_function, a value slightly above the maximum of the distribution
function should be provided.
"""
def __init__(self, bounds: typing.Tuple[float, float],
@ -87,8 +87,8 @@ class LogCustom(SampleableDistribution):
"""
Defines a distribution which follows a custom curve vs. the log (in base 10)
of the random variable. Uses a simple algorithm. This is appropriate for a smooth
distribution function.
Note: in max_function, a value slightly above the maximum of the distribution
distribution function.
Note: in max_function, a value slightly above the maximum of the distribution
function should be provided.
"""
def __init__(self, bounds: typing.Tuple[float, float],

45
caimira/store/data_registry.py
View file

@ -1,3 +1,6 @@
from caimira.enums import ViralLoads, InfectiousDoses, ViableToRNARatios
class DataRegistry:
"""Registry to hold data values."""
@ -207,51 +210,51 @@ class DataRegistry:
}
virus_distributions = {
"SARS_CoV_2": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"transmissibility_factor": 1,
"infectiousness_days": 14,
},
"SARS_CoV_2_ALPHA": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"transmissibility_factor": 0.78,
"infectiousness_days": 14,
},
"SARS_CoV_2_BETA": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"transmissibility_factor": 0.8,
"infectiousness_days": 14,
},
"SARS_CoV_2_GAMMA": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"transmissibility_factor": 0.72,
"infectiousness_days": 14,
},
"SARS_CoV_2_DELTA": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"transmissibility_factor": 0.51,
"infectiousness_days": 14,
},
"SARS_CoV_2_OMICRON": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"transmissibility_factor": 0.2,
"infectiousness_days": 14,
},
"SARS_CoV_2_Other": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"viral_load_in_sputum": ViralLoads.COVID_OVERALL,
"infectious_dose": InfectiousDoses.DISTRIBUTION,
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION,
"transmissibility_factor": 0.1,
"infectiousness_days": 14,
},