from typing import Union as _Union
from typing import List as _List
from .._network import Network
from .._networks import Networks
__all__ = ["go_isolate"]
_str_or_int = _Union[str, int]
_list_str_or_int = _List[_str_or_int]
_strs_or_ints = _Union[_str_or_int, _list_str_or_int]
[docs]def go_isolate(network: _Union[Network, Networks],
go_from: _strs_or_ints = None,
from_demographic: _strs_or_ints = None,
go_to: _strs_or_ints = None,
to_demographic: _strs_or_ints = None,
self_isolate_stage: _Union[_List[int], int] = 2,
fraction: _Union[_List[float], float] = 1.0,
number: int = None,
**kwargs) -> None:
"""This go function will move individuals from the "from"
demographic(s) to the "to" demographic if they show any
signs of infection (the disease stage is greater or equal
to 'self_isolate_stage'. This can move
a subset of individuals if 'fraction' is less than 1, e.g.
0.5 would move 50% of individuals (chosen using
a random binomial distribution)
This can move a subset of individuals if 'fraction' is less than 1,
e.g. 0.5 would move 50% of individuals (chosen using
a random binomial distribution). You can also specify the
maximum number of individuals to move per ward by
specifying the 'number' parameters
Parameters
----------
go_from: int, str or list of int / str
The ID(s) of the demographic(s) to move from. This is the old
parameter name used to maintain backwards compatibility.
Prefer to use from_demo if you can
go_to: int, str or list of int / str
The ID(s) of the demographic(s) to move to. This is the old
parameter name used to maintain backwards compatibility.
Prefer to use to_demo if you can
from_demographic: int, str or list of int / str
The ID(s) of the demographic(s) to move from. This can be either
a single demographic (identified by an integer ID or string),
a list of demographics, or, if None, then all demographics.
to_demographic: int, str or list of int / str
The ID(s) of the demographic to move to. This can be either
a single demographic (identified by an integer ID or string),
a list of demographics, or, if None, then all demographics.
If this is not set, then it is equal to "from_demo"
self_isolate_stage: int or List[int]
The stage of infection an individual must be at before they
are moved into this demographic. If a list is passed then
this can be multiple stages, e.g. [2, 3] will move at
stages 2 and 3. Multiple stages are needed if only
a fraction of individuals move.
fraction: float or List[float]
The fraction (percentage) of individuals who are moved from
this stage into isolation. If this is a single value then
the same fraction applies to all self_isolation_stages. Otherwise,
the fraction for self_isolate_stage[i] is fraction[i]
number: int
The maximum number of individuals in each ward / ward-link to move.
The fraction is taken from min(number, number_in_ward). By
default all individuals in a ward / ward-link are sampled.
**kwargs:
This calls go_ward, so any options that are acceptible to go_ward
(with the exception of 'generator') can be passed here too
"""
from ._movegenerator import MoveGenerator
from ._go_ward import go_ward
if from_demographic is None:
from_demographic = go_from
if to_demographic is None:
to_demographic = go_to
# first get the base moves...
generator = MoveGenerator(from_demographic=from_demographic,
to_demographic=to_demographic)
# find the largest index of the disease stage
N_INF_CLASSES = 0
for stage in generator.generate(network):
N_INF_CLASSES = max(N_INF_CLASSES, stage[1], stage[3])
if isinstance(self_isolate_stage, list):
stages = [int(stage) for stage in self_isolate_stage]
else:
stages = [int(self_isolate_stage)]
if isinstance(fraction, list):
fractions = [float(frac) for frac in fraction]
else:
fractions = [float(fraction)] * len(stages)
for fraction in fractions:
if fraction < 0 or fraction > 1:
raise ValueError(
f"The move fractions {fractions} should all be 0 to 1")
for stage in stages:
if stage < 1 or stage >= N_INF_CLASSES:
raise ValueError(
f"The stage(s) of self-isolation {stages} "
f"is invalid for a disease with {N_INF_CLASSES} stages")
if len(stages) != len(fractions):
raise ValueError(
f"The number of self isolation stages {stages} must equal "
f"the number of fractions {fractions}")
for stage, fraction in zip(stages, fractions):
from_stage = list(range(stage, N_INF_CLASSES))
to_stage = from_stage
generator = MoveGenerator(from_demographic=from_demographic,
to_demographic=to_demographic,
from_stage=from_stage,
to_stage=to_stage,
fraction=fraction)
go_ward(network=network, generator=generator, **kwargs)