metawards.Disease

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

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: main
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__(name: Optional[str] = None, stage: Optional[List[str]] = None, mapping: Optional[List[str]] = None, beta: Optional[List[float]] = None, progress: Optional[List[float]] = None, too_ill_to_move: Optional[List[float]] = None, contrib_foi: Optional[List[float]] = None, start_symptom: Optional[int] = None, _version: Optional[str] = None, _authors: Optional[str] = None, _contacts: Optional[str] = None, _references: Optional[str] = None, _filename: Optional[str] = None, _repository: Optional[str] = None, _repository_version: Optional[str] = None, _repository_branch: Optional[str] = None) → None

Methods

N_INF_CLASSES()	Return the number of stages of the disease
__init__(name, stage, mapping, beta, …)
add(name, mapping, beta, progress, …)	Add a new stage to the disease.
from_data(data)	Return a new Disease constructed from the passed data dictionary (e.g.
from_json(s)	Return the Disease constructed from the passed json.
get_index(idx)	Return the index of disease stage ‘idx’ in this disease
get_mapping_to(other)	Return the mapping from stage index i of this disease to stage index j other the passed other disease.
insert(index, name, mapping, beta, progress, …)	Insert a new stage into the disease.
load(disease, repository, folder, filename)	Load the disease parameters for the specified disease.
to_data()	Return a data dictionary version of this disease, suitable for serialising to, e.g., json
to_json(filename, indent, auto_bzip)	Serialise the Disease to JSON.

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
mapping	Mapping label, e.g.
name	Name of the disease
progress	Progress parameter for each stage of the disease
stage	Name of the stage, e.g.
start_symptom	Index of the first symptomatic stage
too_ill_to_move	TooIllToMove parameter for each stage of the disease

N_INF_CLASSES()

Return the number of stages of the disease

__eq__(other)

Return self==value.

__getitem__(index: int) → Dict[str, Union[str, float, bool]]

Return the values of parameters of the stage as specified index

__repr__()

Return repr(self).

__setitem__(index: int, value: Dict[str, Union[str, float, bool]]) → None

Set the value of parameters at this index. The keys in the dictionary (and their values) match the arguments to the “insert” or “add” functions

__str__()

Return str(self).

add(name: str, mapping: Optional[str] = None, beta: Optional[float] = None, progress: Optional[float] = None, too_ill_to_move: Optional[float] = None, contrib_foi: Optional[float] = None, is_start_symptom: Optional[bool] = None) → None

Add a new stage to the disease. This will append a new stage onto the list of stages.

Parameters:

• name (str) – The name of the stage, e.g. “E”, “I”, “R” etc.
• mapping (str) – Which main stage this stage should map to (if this is a sub-stage). This will be derived automatically if not set.
• beta (float) – The beta (infectivity) parameter. This should be between 0.0 amd 1.0. If not set, then this will be set automatically.
• progress (float) – The fraction of individuals at this stage who will move to the next stage. This should be between 0.0 amd 1.0. If this is not set, then this will be set automatically.
• too_ill_to_move (float) – The proportion of workers at this stage who do not travel to work. This should be between 0.0 and 1.0. If this is not set, then this will be set automatically.
• contrib_foi (float) – The contribution of individuals in this stage to the force-of-infection (foi) of the wards they visit. This should normally be 1.0 and will be set automatically if not set.
• is_start_symptom (bool) – Whether this is the start symptom of the disease. This normally doesn’t need to be set as this will be worked out automatically by the code.

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 from_data(data) → metawards._disease.Disease

Return a new Disease constructed from the passed data dictionary (e.g. deserialised from json)

static from_json(s: str) → metawards._disease.Disease

Return the Disease constructed from the passed json. This will either load from a passed json string, or from json loaded from the passed file

get_index(idx)

Return the index of disease stage ‘idx’ in this disease

get_mapping_to(other)

Return the mapping from stage index i of this disease to stage index j other the passed other disease. This returns ‘None’ if there is no need to map because the stages are the same.

The mapping will map the states according to their label, matching the ith labelled X state in this disease to the ith labelled X state in other (or to the highest labelled X state if we have more of these states than other).

Thus, is we have;

self = [“*”, “E”, “I”, “I”, “R”] other = [“*”, “E”, “I”, “I”, “I”, “R”]

then

self.get_mapping_to(other) = [0, 1, 2, 3, 5] other.get_mapping_to(self) = [0, 1, 2, 3, 3, 4]

If we can’t map a state, then we will try to map to “I”. If we still can’t map, then this is an error.

insert(index: int, name: str, mapping: Optional[str] = None, beta: Optional[float] = None, progress: Optional[float] = None, too_ill_to_move: Optional[float] = None, contrib_foi: Optional[float] = None, is_start_symptom: Optional[bool] = None) → None

Insert a new stage into the disease. This will insert a new stage into the list of stages at index ‘index’

Parameters:

• index (str) – The index at which to insert the new stage
• name (str) – The name of the stage, e.g. “E”, “I”, “R” etc.
• mapping (str) – Which main stage this stage should map to (if this is a sub-stage). This will be derived automatically if not set.
• beta (float) – The beta (infectivity) parameter. This should be between 0.0 amd 1.0. If not set, then this will be set automatically.
• progress (float) – The fraction of individuals at this stage who will move to the next stage. This should be between 0.0 amd 1.0. If this is not set, then this will be set automatically.
• too_ill_to_move (float) – The proportion of workers at this stage who do not travel to work. This should be between 0.0 and 1.0. If this is not set, then this will be set automatically.
• contrib_foi (float) – The contribution of individuals in this stage to the force-of-infection (foi) of the wards they visit. This should normally be 1.0 and will be set automatically if not set.
• is_start_symptom (bool) – Whether this is the start symptom of the disease. This normally doesn’t need to be set as this will be worked out automatically by the code.

static load(disease: Optional[str] = None, repository: Optional[str] = None, folder: Optional[str] = None, filename: Optional[str] = None)

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

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

mapping = None

Mapping label, e.g. “*”, “E”, “I” or “R”

name = None

Name of the disease

progress = None

Progress parameter for each stage of the disease

stage = None

Name of the stage, e.g. “H1”, “I2”, “E1” etc.

start_symptom = None

Index of the first symptomatic stage

to_data() → Dict[str, any]

Return a data dictionary version of this disease, suitable for serialising to, e.g., json

to_json(filename: Optional[str] = None, indent: Optional[int] = None, auto_bzip: bool = True) → str

Serialise the Disease to JSON. This will write to a file if filename is set, otherwise it will return a JSON string.

Parameters:

• filename (str) – The name of the file to write the JSON to. The absolute path to the written file will be returned. If filename is None then this will serialise to a JSON string which will be returned.
• indent (int) – The number of spaces of indent to use when writing the json
• auto_bzip (bool) – Whether or not to automatically bzip2 the written json file

Returns:

Returns either the absolute path to the written file, or the json-serialised string

Return type:

str

too_ill_to_move = None

TooIllToMove parameter for each stage of the disease