june.infection.trajectory_maker¶
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class
june.infection.trajectory_maker.
BetaCompletionTime
(a, b, loc=0.0, scale=1.0)¶ -
__init__
(a, b, loc=0.0, scale=1.0)¶ Initialize self. See help(type(self)) for accurate signature.
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static
class_for_type
(type_string: str) → type¶ Get a CompletionTime class from a string in configuration
- type_string
The type of CompletionTime e.g. constant/exponential/beta
The corresponding class
- AssertionError
If the type string is not recognised
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classmethod
from_dict
(variation_type_dict)¶
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_abc_impl
= <_abc_data object>¶
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property
distribution
¶
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class
june.infection.trajectory_maker.
CompletionTime
¶ -
static
class_for_type
(type_string: str) → type¶ Get a CompletionTime class from a string in configuration
- type_string
The type of CompletionTime e.g. constant/exponential/beta
The corresponding class
- AssertionError
If the type string is not recognised
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classmethod
from_dict
(variation_type_dict)¶
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_abc_impl
= <_abc_data object>¶
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static
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class
june.infection.trajectory_maker.
ConstantCompletionTime
(value: float)¶ -
__init__
(value: float)¶ Initialize self. See help(type(self)) for accurate signature.
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static
class_for_type
(type_string: str) → type¶ Get a CompletionTime class from a string in configuration
- type_string
The type of CompletionTime e.g. constant/exponential/beta
The corresponding class
- AssertionError
If the type string is not recognised
-
classmethod
from_dict
(variation_type_dict)¶
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_abc_impl
= <_abc_data object>¶
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-
class
june.infection.trajectory_maker.
DistributionCompletionTime
(distribution, *args, **kwargs)¶ -
__init__
(distribution, *args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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static
class_for_type
(type_string: str) → type¶ Get a CompletionTime class from a string in configuration
- type_string
The type of CompletionTime e.g. constant/exponential/beta
The corresponding class
- AssertionError
If the type string is not recognised
-
classmethod
from_dict
(variation_type_dict)¶
-
_abc_impl
= <_abc_data object>¶
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property
distribution
¶
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class
june.infection.trajectory_maker.
ExponentialCompletionTime
(loc: float, scale)¶ -
__init__
(loc: float, scale)¶ Initialize self. See help(type(self)) for accurate signature.
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static
class_for_type
(type_string: str) → type¶ Get a CompletionTime class from a string in configuration
- type_string
The type of CompletionTime e.g. constant/exponential/beta
The corresponding class
- AssertionError
If the type string is not recognised
-
classmethod
from_dict
(variation_type_dict)¶
-
_abc_impl
= <_abc_data object>¶
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property
distribution
¶
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-
class
june.infection.trajectory_maker.
ExponweibCompletionTime
(a, c, loc=0.0, scale=1.0)¶ -
__init__
(a, c, loc=0.0, scale=1.0)¶ Initialize self. See help(type(self)) for accurate signature.
-
static
class_for_type
(type_string: str) → type¶ Get a CompletionTime class from a string in configuration
- type_string
The type of CompletionTime e.g. constant/exponential/beta
The corresponding class
- AssertionError
If the type string is not recognised
-
classmethod
from_dict
(variation_type_dict)¶
-
_abc_impl
= <_abc_data object>¶
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property
distribution
¶
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class
june.infection.trajectory_maker.
LognormalCompletionTime
(s, loc=0.0, scale=1.0)¶ -
__init__
(s, loc=0.0, scale=1.0)¶ Initialize self. See help(type(self)) for accurate signature.
-
static
class_for_type
(type_string: str) → type¶ Get a CompletionTime class from a string in configuration
- type_string
The type of CompletionTime e.g. constant/exponential/beta
The corresponding class
- AssertionError
If the type string is not recognised
-
classmethod
from_dict
(variation_type_dict)¶
-
_abc_impl
= <_abc_data object>¶
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property
distribution
¶
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class
june.infection.trajectory_maker.
NormalCompletionTime
(loc, scale)¶ -
__init__
(loc, scale)¶ Initialize self. See help(type(self)) for accurate signature.
-
static
class_for_type
(type_string: str) → type¶ Get a CompletionTime class from a string in configuration
- type_string
The type of CompletionTime e.g. constant/exponential/beta
The corresponding class
- AssertionError
If the type string is not recognised
-
classmethod
from_dict
(variation_type_dict)¶
-
_abc_impl
= <_abc_data object>¶
-
property
distribution
¶
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class
june.infection.trajectory_maker.
Stage
(*, symptoms_tag: june.infection.symptom_tag.SymptomTag, completion_time: june.infection.trajectory_maker.CompletionTime = <class 'june.infection.trajectory_maker.ConstantCompletionTime'>)¶ A stage on an illness,
- symptoms_tag
What symptoms does the person have at this stage?
- completion_time
Function that returns value for how long this stage takes to complete.
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__init__
(*, symptoms_tag: june.infection.symptom_tag.SymptomTag, completion_time: june.infection.trajectory_maker.CompletionTime = <class 'june.infection.trajectory_maker.ConstantCompletionTime'>)¶ A stage on an illness,
- symptoms_tag
What symptoms does the person have at this stage?
- completion_time
Function that returns value for how long this stage takes to complete.
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classmethod
from_dict
(stage_dict)¶
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class
june.infection.trajectory_maker.
TrajectoryMaker
(*stages)¶ Generate trajectories of a particular kind.
This defines how a given person moves through a series of symptoms.
- stages
A list of stages through which the person progresses
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__init__
(*stages)¶ Generate trajectories of a particular kind.
This defines how a given person moves through a series of symptoms.
- stages
A list of stages through which the person progresses
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classmethod
from_dict
(trajectory_dict)¶
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generate_trajectory
() → List[Tuple[float, june.infection.symptom_tag.SymptomTag]]¶ Generate a trajectory for a person. This is a list of tuples describing what symptoms the person should display at a given time.
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property
most_severe_symptoms
¶ The most severe symptoms experienced at any stage in this trajectory
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class
june.infection.trajectory_maker.
TrajectoryMakers
(trajectories: List[june.infection.trajectory_maker.TrajectoryMaker])¶ The various trajectories should depend on external data, and may depend on age & gender of the patient. This would lead to a table of tons of trajectories, with lots of mean values/deviations and an instruction on how to vary them. For this first simple implementation I will choose everything to be fixed (constant)
The trajectories will count “backwards” with zero time being the moment of infection.
Trajectories and their stages should be parsed from configuration. I’ve removed params for now as they weren’t being used but it will be trivial to reintroduce them when we are ready for configurable trajectories.
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__init__
(trajectories: List[june.infection.trajectory_maker.TrajectoryMaker])¶ Trajectories and their stages should be parsed from configuration. I’ve removed params for now as they weren’t being used but it will be trivial to reintroduce them when we are ready for configurable trajectories.
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classmethod
from_file
(config_path: str = PosixPath('/home/sadie/JUNE/configs/defaults/symptoms/trajectories.yaml')) → june.infection.trajectory_maker.TrajectoryMakers¶ Currently this doesn’t do what it says it does.
By setting an instance on the class we can make the trajectory maker something like a singleton. However, if it were being loaded from configurations we’d need to be careful as this could give unexpected effects.
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classmethod
from_list
(trajectory_dicts)¶
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