laser.cohorts.vitaldynamics
Vital dynamics components for cohort-based simulation.
Provides NonDiseaseMortality, a component that applies background (non-disease) mortality to one or more compartment states each simulation tick.
ConstantPopBirths(model)
Constant-population birth component.
Reads the per-node death count recorded by NonDiseaseMortality at each
tick and adds the same number of individuals back into the S compartment,
keeping the total population constant across ticks.
Must be ordered after NonDiseaseMortality in the component list so
that non_disease_mortality is populated before births are applied.
Example
ndm = NonDiseaseMortality(model, r_mortality=1/365/70) cpb = ConstantPopBirths(model) model.components = [Susceptible(model), ndm, cpb]
Initialize the ConstantPopBirths component.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
model
|
Model
|
The parent model instance. |
required |
property
properties
Return the node properties required by this component.
Returns:
| Type | Description |
|---|---|
list[PropertyType]
|
list[PropertyType]: |
property
states
Return the compartment states used by this component.
Returns:
| Type | Description |
|---|---|
list[str]
|
list[str]: |
end_step(tick)
No-op end-of-step hook.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
setup()
No-op setup hook.
start_step(tick)
No-op start-of-step hook.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
step(tick)
Add births equal to deaths recorded this tick into the S compartment.
Reads nodes.non_disease_mortality[tick] — the deaths accumulated by
NonDiseaseMortality during the current tick — and adds that count
to states.S[tick+1], replacing every death with one new susceptible.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
NonDiseaseMortality(model, r_mortality, states=None)
Background (non-disease) mortality component.
Applies a binomial mortality draw each tick to the specified compartment
states, removing individuals and recording the deaths in
nodes.non_disease_mortality.
By default acts on every state in model.states. Passing states
restricts mortality to only the named compartments, creating an implicit
mask over the state axis.
Example
ndm = NonDiseaseMortality(model, r_mortality=1/365/70) # ~70-year life expectancy ndm_s_only = NonDiseaseMortality(model, r_mortality=1/365/70, states=["S"])
Initialize the NonDiseaseMortality component.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
model
|
Model
|
The parent model instance. |
required |
r_mortality
|
int | float | ValuesMap | ndarray
|
Per-tick, per-node
crude mortality rate. A scalar is broadcast to all ticks and nodes
via |
required |
states
|
Iterable[str] | None
|
Names of compartment states to apply
mortality to. Accepts any iterable (list, tuple, set, generator,
etc.). |
None
|
property
properties
Return the node properties required by this component.
Returns:
| Type | Description |
|---|---|
list[PropertyType]
|
list[PropertyType]: |
property
states
Return the compartment states created by this component.
Returns:
| Type | Description |
|---|---|
list[str]
|
list[str]: Empty list; this component acts on existing states but does not create any new ones. |
end_step(tick)
No-op end-of-step hook.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
setup()
Build a boolean state mask for the target compartment states.
Resolves which states to apply mortality to — all states when
states was None, or the requested subset — then builds a
boolean mask over the state axis using get_state_index so that
step can select all target states in one vectorised operation.
start_step(tick)
No-op start-of-step hook.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
step(tick)
Apply binomial mortality draws to all target states in one operation.
Selects all target compartments at tick+1 via the boolean state
mask, draws deaths from a binomial distribution for all of them at
once, subtracts the deaths back via boolean-index assignment, and
accumulates per-node totals in nodes.non_disease_mortality.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |