atomica.model.TimedLink

class atomica.model.TimedLink(pop, parameter, source, dest)

Bases: Link

A TimedLink connects two TimedCompartments

A TimedLink should be used between two TimedCompartments if it is important to preserve the ‘time until forced removal’ when making the transition. For example, a vaccinated individual with 3 years of protection remaining may need to move to a vaccinated+latent state, for instance. In that case, they would still have 3 years remaining in vaccinated+latent.

The value for the TimedLink corresponds to the number of people in each time bin from the source compartment. If there is a mismatch in durations across the TimedLink endpoints, it is up to the destination compartment to resolve them.

A TimedLink should _not_ be used for the timed outflow of a TimedCompartment as people flowing out of a timed outflow all originate at the same time.

Attributes

name	Variable code name
vals	Link total flow
id	Unique identifier for the integration object
units	The units for the quantity, used for plotting and for validation.
pop	Reference back to the Population containing this object

Methods

create	Create and wire up a new link
plot	Produce a time series plot
preallocate	Preallocate data storage
relink
set_dynamic	Make the variable a dependency
unlink
update	Updated link flow rate

classmethod create(pop, parameter, source, dest)

Create and wire up a new link

This method instantiates a Link (including of derived types) and also wires it up to the population, parameter, source, and destination compartments. This allows the Link constructor to be used without needing the entire population infrastructure

Parameters:

• pop – A Population instance that will contain the new Link

• parameter – A Parameter instance that will supply values for the new Link

• source – A Compartment instance to transfer from

• dest – A Compartment instance to transfer to

Returns:

The newly created Link instance

id

Unique identifier for the integration object

property name: str

Variable code name

This is implemented as a property method because the id of the Variable is a tuple containing the population name and the variable code name, so this property method returns just the variable code name portion. That way, storage does not need to be duplicated.

Returns:

A code name

plot()

Produce a time series plot

This is a quick function to make a basic line plot of this Variable. Mainly intended for debugging. Production-ready plots should be generated using the plotting library functions instead

pop

Reference back to the Population containing this object

preallocate(tvec, dt)

Preallocate data storage

Note that TimedLinks preallocate their internal storage based on the preallocated size of the source TimedCompartment. Therefore, it must be preallocated after the compartments have been preallocated.

Parameters:

• tvec (array) – An array of time values

• dt (float) – Time step size

Return type:

None

set_dynamic(**kwargs)

Make the variable a dependency

For Compartments and Links, this does nothing. For Characteristics and Parameters, it will set the dynamic flag, but in addition, any validation constraints e.g. a Parameter that depends on Links cannot itself be dynamic, will be enforced.

This method generally must be overloaded in derived classes e.g. Parameter.set_dynamic()

Return type:

None

units

The units for the quantity, used for plotting and for validation. Note that the default 'unknown' units are distinct to dimensionless units, which have value ''

update(ti, converted_frac)

Updated link flow rate

For TimedLink instances, we update at all of the time indices

Parameters:

• ti (int) – Time index to update

• converted_frac (float) – The fraction of the source compartment to move (the parent parameter value, converted to timestep fraction)

Return type:

None

property vals: array

Link total flow

This returns link outflow obtained by summing over the people in each time bin at each point in time

Returns:

A numpy array with the link flow rate