aux_classes.py

Auxiliary classes and functions for internal use.

RandomDistibution

Stores a random number generator and distribution parameters make and samples from it.

__init__(self, *args, *, distribution='uniform', lower_limit=None, upper_limit=None, **kwargs) special

Stores a random number generator and distribution parameters make and samples from it.

Parameters:

Name	Type	Description	Default
*args		Arguments to be passed to the distribution on sample.	()
distribution	str	Any distribution from numpy.random. Defaults to 'uniform'.	'uniform'
lower_limit	float	Lower limit for samples. Samples below lower_limit will be replaced by it.	None
upper_limit	float	Upper limit for samples. Samples above upper_limit will be replaced by it.	None
**kwargs		Keyword arguments to be passed to the distribution on sample.	{}

Source code in comorbuss/aux_classes.py

def __init__(
    self,
    *args,
    distribution="uniform",
    lower_limit=None,
    upper_limit=None,
    **kwargs
) -> None:
    """Stores a random number generator and distribution parameters make and samples from it.

    Args:
        *args: Arguments to be passed to the distribution on sample.
        distribution (str, optional): Any distribution from numpy.random. Defaults to 'uniform'.
        lower_limit (float): Lower limit for samples. Samples below lower_limit will be replaced by it.
        upper_limit (float): Upper limit for samples. Samples above upper_limit will be replaced by it.
        **kwargs: Keyword arguments to be passed to the distribution on sample.
    """
    self.dist = distribution
    self.args = args
    self.limits = (lower_limit, upper_limit)
    self.kwargs = kwargs

sample(self, rng, size=1)

Sample values from distribution.

Parameters:

Name	Type	Description	Default
size	int	Size to be sampled. Defaults to 1.	1

Returns:

Type	Description
float	float: Samples.

Source code in comorbuss/aux_classes.py

def sample(self, rng, size: int = 1) -> float:
    """Sample values from distribution.

    Args:
        size (int, optional): Size to be sampled. Defaults to 1.

    Returns:
        float: Samples.
    """
    dist = getattr(rng, self.dist)
    samples = dist(size=size, *self.args, **self.kwargs)

    # Apply limits
    if self.limits[0] != None:
        samples[samples < self.limits[0]] = self.limits[0]
    if self.limits[1] != None:
        samples[samples > self.limits[1]] = self.limits[1]
    # Return values
    if size == 1:
        return samples[0]
    else:
        return samples

circularlist

__getitem__(self, key) special

Get element by index, relative to the current index

Source code in comorbuss/aux_classes.py

def __getitem__(self, key):
    """Get element by index, relative to the current index"""
    if len(self._data) == self.size:
        return self._data[(key + self.index) % self.size]
    else:
        return self._data[key]

__init__(self, size, data=[]) special

Initialization

Source code in comorbuss/aux_classes.py

def __init__(self, size, data=[]):
    """Initialization"""
    self.index = 0
    self.size = size
    self._data = list(data)[-size:]

__repr__(self) special

Return string representation

Source code in comorbuss/aux_classes.py

def __repr__(self):
    """Return string representation"""
    return self._data.__repr__() + " (" + str(len(self._data)) + " items)"

append(self, value)

Append an element

Source code in comorbuss/aux_classes.py

def append(self, value):
    """Append an element"""
    if len(self._data) == self.size:
        self._data[self.index] = value
    else:
        self._data.append(value)
    self.index = (self.index + 1) % self.size

clock

Provides a clock for the simulation.

Attributes:

Name	Type	Description
dt	float	Time step in hours.
time	float	Current time in hours since the start of the simulation.
step	int	Number of steps since the start of the simulation.
tod	float	Time of the day in the simulation.
today	int	Number of days since the start of the simulation.
days	floay	Time since the start of the simulation in days.
dow	int	Current day of the week, varies from 0 to 6, where 0 is sunday and 6 saturday.
day_of_the_week	str	Current day of the week in text.

at_time(self, time)

Returns True at or imediatly after the end time informed.

Parameters:

Name	Type	Description	Default
end	float	Time of the day to test.	required

Returns:

Type	Description
bool	Result of the test.

Source code in comorbuss/aux_classes.py

def at_time(self, time):
    """Returns True at or imediatly after the end time informed.

    Args:
        end (float): Time of the day to test.

    Returns:
        bool: Result of the test.
    """
    return ((self.time - self.dt) < time) and (self.time >= time)

at_time_of_day(self, time)

Returns True at or imediatly after the time of the day informed.

Parameters:

Name	Type	Description	Default
end	float	Time of the day to test.	required

Returns:

Type	Description
bool	Result of the test.

Source code in comorbuss/aux_classes.py

def at_time_of_day(self, time):
    """Returns True at or imediatly after the time of the day informed.

    Args:
        end (float): Time of the day to test.

    Returns:
        bool: Result of the test.
    """
    return ((self.tod - self.dt) < time) and (self.tod >= time)

between_hours(self, start, end)

Returns True if current time of the day is inside interval [start, end).

Parameters:

Name	Type	Description	Default
start	float	Start of the interval.	required
end	float	End of the interval.	required

Returns:

Type	Description
bool	Result of the test.

Source code in comorbuss/aux_classes.py

def between_hours(self, start, end):
    """Returns True if current time of the day is inside interval [start, end).

    Args:
        start (float): Start of the interval.
        end (float): End of the interval.

    Returns:
        bool: Result of the test.
    """
    return (self.tod >= start and self.tod < end and start < end) or (
        (self.tod >= start or self.tod < end) and start > end
    )

tick(self)

Advances internal clock by one time step dt.

Source code in comorbuss/aux_classes.py

def tick(self):
    """Advances internal clock by one time step dt."""
    self.time += self.dt
    self.step += 1
    self.tod = self.time % 24
    self.step_of_the_day = self.time_to_steps(self.tod)
    self.today = int(self.time / 24)
    self.days = self.time / 24
    self.dow = (self.today + self.first_dow) % 7
    self.week = int((self.today + self.first_dow) / 7)
    self.day_of_the_week = DAYS_OF_THE_WEEK[self.dow]

coefficient_container

__getattribute__(self, name) special

Gets an attribute, if it has coefficients applies them.

Parameters:

Name	Type	Description	Default
name	str	Attribute name.	required

Returns:

Type	Description
Any	Any: Attribute value with coefficients applied.

Source code in comorbuss/aux_classes.py

def __getattribute__(self, name: str) -> Any:
    """Gets an attribute, if it has coefficients applies them.

    Args:
        name (str): Attribute name.

    Returns:
        Any: Attribute value with coefficients applied.
    """
    try:
        return super(coefficient_container, self).__getattribute__(
            name + CRRCT_MRKR
        )
    except AttributeError:
        return super(coefficient_container, self).__getattribute__(name)

add_coefficient(self, name, value, identifier)

Adds an attribute coefficient.

Parameters:

Name	Type	Description	Default
name	str	Attribute name.	required
value	ndarray	Coefficient name (needs to have the same shape as the attribute).	required
identifier	str	String identifier for the coefficient.	required

Exceptions:

Type	Description
ValueError	Raises if type of attribute or coefficient is not np.nd.array, or if shapes do not match.

Source code in comorbuss/aux_classes.py

def add_coefficient(self, name: str, value: np.ndarray, identifier: str) -> None:
    """Adds an attribute coefficient.

    Args:
        name (str): Attribute name.
        value (np.ndarray): Coefficient name (needs to have the same shape as the attribute).
        identifier (str): String identifier for the coefficient.

    Raises:
        ValueError: Raises if type of attribute or coefficient is not np.nd.array, or
            if shapes do not match.
    """
    # Gets attribute to check coefficient shape and types
    attribute = getattr(self, name)
    # Check if attribute
    if type(attribute) is not np.ndarray:
        raise RuntimeError(
            "Tried to set an coefficient for {}.{} attribute that is not an np.ndarray.".format(
                self.__repr__(), name
            )
        )
    if type(value) is not np.ndarray:
        raise RuntimeError(
            "Tried to set an coefficient for {}.{} attribute, but coefficient not an np.ndarray.".format(
                self.__repr__(), name
            )
        )
    # Check shape
    if attribute.shape != value.shape:
        raise ValueError(
            "Tried to set a coefficient for {}.{} with shape {}, but coefficient shape is {}.".format(
                self.__repr__(), name, attribute.shape, value.shape
            )
        )

    # Stores coefficient
    if hasattr(self, name + COEFF_MRKR):
        coeff_dict = getattr(self, name + COEFF_MRKR)
    else:
        coeff_dict = {}
    coeff_dict[identifier] = value
    setattr(self, name + COEFF_MRKR, coeff_dict)
    self._update_values(name)

del_coefficient(self, name, identifier)

Deletes an attribute coefficient if it exists.

Parameters:

Name	Type	Description	Default
name	str	Attribute name.	required
identifier	str	String identifier for the coefficient.	required

Source code in comorbuss/aux_classes.py

def del_coefficient(self, name: str, identifier: str) -> None:
    """Deletes an attribute coefficient if it exists.

    Args:
        name (str): Attribute name.
        identifier (str): String identifier for the coefficient.
    """
    if hasattr(self, name + COEFF_MRKR):
        coeff_dict = getattr(self, name + COEFF_MRKR)
        del coeff_dict[identifier]
        setattr(self, name + COEFF_MRKR, coeff_dict)

get_coefficient(self, name, identifier)

Returns a coefficient.

Parameters:

Name	Type	Description	Default
name	str	Attribute name.	required
identifier	str	String identifier for the coefficient.	required

Returns:

Type	Description
ndarray	np.ndarray: Coefficient array.

Source code in comorbuss/aux_classes.py

def get_coefficient(self, name: str, identifier: str) -> np.ndarray:
    """Returns a coefficient.

    Args:
        name (str): Attribute name.
        identifier (str): String identifier for the coefficient.

    Returns:
        np.ndarray: Coefficient array.
    """
    return getattr(self, name + COEFF_MRKR)[identifier]

set_coefficient(self, name, value, identifier)

Sets a coefficient.

Parameters:

Name	Type	Description	Default
name	str	Attribute name.	required
value	ndarray	Coefficient name (needs to have the same shape as the attribute).	required
identifier	str	String identifier for the coefficient.	required

Source code in comorbuss/aux_classes.py

def set_coefficient(self, name: str, value: np.ndarray, identifier: str) -> None:
    """Sets a coefficient.

    Args:
        name (str): Attribute name.
        value (np.ndarray): Coefficient name (needs to have the same shape as the attribute).
        identifier (str): String identifier for the coefficient.
    """
    return self.add_coefficient(name, value, identifier)

empty_module

__init__(self, parameters, comm, name='empty_module') special

Initialization method for a COMORBUSS module.

parameters and comm will be passed to your module at initialization.

Parameters:

Name	Type	Description	Default
parameters	dict	Parameters for this module.	required
comm	comorbuss.community	Community object.	required
name	str	[description]. Defaults to "empty_module".	'empty_module'

Source code in comorbuss/aux_classes.py

def __init__(self, parameters, comm, name="empty_module"):
    """Initialization method for a COMORBUSS module.

    parameters and comm will be passed to your module at initialization.

    Args:
        parameters (dict): Parameters for this module.
        comm (comorbuss.community): Community object.
        name (str, optional): [description]. Defaults to "empty_module".
    """
    self.name = name

    self.comm = comm
    self.pop = comm.pop
    self.clk = comm.clk
    self.event_log = lambda msg, type: comm.event_log(
        "[{}] {}".format(name, msg), type
    )
    self.rng = np.random.default_rng(comm.random_seed)
    self.parameters = parameters

log_results(self)

Logs results related to this module.

Source code in comorbuss/aux_classes.py

def log_results(self):
    """Logs results related to this module."""
    pass

run_after_init(self)

Method to be run at the end of the community's initialization.

Source code in comorbuss/aux_classes.py

def run_after_init(self):
    """Method to be run at the end of the community's initialization."""
    pass