metawards.Disease¶

class metawards.Disease(beta: List[float] = None, progress: List[float] = None, too_ill_to_move: List[float] = None, contrib_foi: List[float] = None, start_symptom: int = None, _name: str = None, _version: str = None, _authors: str = None, _contacts: str = None, _references: str = None, _filename: str = None, _repository: str = None, _repository_version: str = None, _repository_branch: str = None)[source]¶

This class holds the parameters about a single disease

A disease is characterised as a serious of stages, each with their own values of the beta, progress, too_ill_to_move and contrib_foi parameters. To load a disease use the Disease.load function, e.g.

Examples

>>> disease = Disease.load("ncov")
>>> print(disease)
Disease ncov
repository: https://github.com/metawards/MetaWardsData
repository_branch: master
repository_version: 0.2.0
beta = [0.0, 0.0, 0.95, 0.95, 0.0]
progress = [1.0, 0.1923, 0.909091, 0.909091, 0.0]
too_ill_to_move = [0.0, 0.0, 0.0, 0.0, 0.0]
contrib_foi = [1.0, 1.0, 1.0, 1.0, 0.0]

__init__(beta: List[float] = None, progress: List[float] = None, too_ill_to_move: List[float] = None, contrib_foi: List[float] = None, start_symptom: int = None, _name: str = None, _version: str = None, _authors: str = None, _contacts: str = None, _references: str = None, _filename: str = None, _repository: str = None, _repository_version: str = None, _repository_branch: str = None) → None¶

Methods

`N_INF_CLASSES`()	Return the number of stages of the disease
`__init__`(beta, progress, too_ill_to_move, …)
`load`(disease, repository, folder, filename)	Load the disease parameters for the specified disease.

Attributes

`beta`	Beta parameter for each stage of the disease
`contrib_foi`	Contribution to the Force of Infection (FOI) parameter for each stage of the disease
`progress`	Progress parameter for each stage of the disease
`start_symptom`	Index of the first symptomatic stage
`too_ill_to_move`	TooIllToMove parameter for each stage of the disease

N_INF_CLASSES()[source]¶: Return the number of stages of the disease

beta = None¶: Beta parameter for each stage of the disease

contrib_foi = None¶: Contribution to the Force of Infection (FOI) parameter for each stage of the disease

static load(disease: str = 'ncov', repository: str = None, folder: str = 'diseases', filename: str = None)[source]¶

Load the disease parameters for the specified disease. This will look for a file called f”{disease}.json” in the directory f”{repository}/{disease}/{disease}.ncon”

By default this will load the ncov (SARS-Cov-2) parameters from $HOME/GitHub/model_data/2011Data/diseases/ncov.json

Alternatively you can provide the full path to the json file via the “filename” argument

Parameters:	disease (str) – The name of the disease to load. This is the name that will be searched for in the METAWARDSDATA diseases directory repository (str) – The location of the cloned METAWARDSDATA repository folder (str) – The name of the folder within the METAWARDSDATA repository that contains the diseases filename (str) – The name of the file to load the disease from - this directly loads this file without searching through the METAWARDSDATA repository
Returns:	disease – The constructed and validated disease
Return type:	Disease

progress = None¶: Progress parameter for each stage of the disease

start_symptom = None¶: Index of the first symptomatic stage

too_ill_to_move = None¶: TooIllToMove parameter for each stage of the disease