laser.cohorts.SEIR
SEIR model component preset.
Assembles the Susceptible, Exposed, Infectious (recovery to R), and Recovered compartments with SE-style transmission for use as a standalone SEIR model.
Exposed(model, r_progression, validating=False)
Exposed (E) compartment component.
Tracks individuals who are infected but not yet infectious. Applies non-disease mortality and progression from E to I each time step. Initial E counts are read from the scenario at setup.
Initialize the Exposed component.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
model
|
Model
|
The parent model instance. |
required |
r_progression
|
ValuesMap
|
Per-tick, per-node rate of progression from E to I. |
required |
validating
|
bool
|
Enable validation checks during simulation. |
False
|
property
properties
Return node properties required by this component.
Returns:
| Type | Description |
|---|---|
list[PropertyType]
|
list[PropertyType]: |
property
states
Return the compartment state names managed by this component.
Returns:
| Type | Description |
|---|---|
list[str]
|
list[str]: |
end_step(tick)
No-op end-of-step hook for the E compartment.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
setup()
Initialize state E at tick 0 from the scenario E column.
start_step(tick)
No-op start-of-step hook; carry-forward is handled by the Model.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
step(tick)
Apply disease progression to exposed individuals.
Draws newly infectious individuals from a binomial using r_progression,
moving them from E to I and recording the flow in nodes.newly_infectious.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
Infectious(model, r_recovery=None, validating=False)
Bases: Infectious
Infectious (I) compartment with recovery to R.
Extends Infectious by drawing newly recovered individuals each tick and
moving them from I to R. Used in SIR and SEIR model configurations.
Initialize the InfectiousToRecovered component.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
model
|
Model
|
The parent model instance. |
required |
r_recovery
|
ValuesMap | None
|
Per-tick, per-node recovery rate (I → R). Defaults to zero if not provided. |
None
|
validating
|
bool
|
Enable validation checks during simulation. |
False
|
property
properties
Return node properties required by this component.
Returns:
| Type | Description |
|---|---|
list[PropertyType]
|
list[PropertyType]: Parent properties plus
|
property
states
Return the compartment state names managed by this component.
Returns:
| Type | Description |
|---|---|
list[str]
|
list[str]: Parent states plus |
step(tick)
Apply recovery (I → R) to infectious individuals.
Draws newly recovered individuals from a binomial using r_recovery, moving
them from I to R and recording the flow in nodes.newly_recovered.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
Recovered(model, validating=False)
Recovered (R) compartment component.
Tracks the recovered population and applies non-disease mortality each time step. Initial R counts are read from the scenario at setup.
Initialize the Recovered component.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
model
|
Model
|
The parent model instance. |
required |
validating
|
bool
|
Enable validation checks during simulation. |
False
|
property
properties
Return node properties required by this component.
Returns:
| Type | Description |
|---|---|
list[PropertyType]
|
list[PropertyType]: Empty list; mortality tracking belongs to
|
property
states
Return the compartment state names managed by this component.
Returns:
| Type | Description |
|---|---|
list[str]
|
list[str]: |
end_step(tick)
No-op end-of-step hook for the R compartment.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
setup()
Initialize state R at tick 0 from the scenario R column.
start_step(tick)
No-op start-of-step hook; carry-forward is handled by the Model.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
step(tick)
No-op step hook for the R compartment.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
Susceptible(model, validating=False)
Susceptible (S) compartment component.
Tracks the susceptible population and applies non-disease mortality each time step. Initial S counts are read from the scenario at setup.
Initialize the Susceptible component.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
model
|
Model
|
The parent model instance. |
required |
validating
|
bool
|
Enable validation checks during simulation. |
False
|
property
properties
Return node properties required by this component.
Returns:
| Type | Description |
|---|---|
list[PropertyType]
|
list[PropertyType]: Empty list; mortality tracking belongs to
|
property
states
Return the compartment state names managed by this component.
Returns:
| Type | Description |
|---|---|
list[str]
|
list[str]: |
end_step(tick)
No-op end-of-step hook for the S compartment.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
setup()
Initialize state S at tick 0 from the scenario S column.
start_step(tick)
No-op start-of-step hook; carry-forward is handled by the Model.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
step(tick)
No-op step hook for the S compartment.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tick
|
int
|
Current simulation tick (0-indexed). |
required |
Transmission(
model, beta, seasonality=None, validating=False
)
Bases: TransmissionCommon
Transmission component that moves individuals from S to E.
Specialises TransmissionCommon for models with an exposed/latent period
(SEI, SEIR, SEIS, SEIRS). Newly infected individuals enter the E
compartment before becoming infectious.
Initialize the S → E transmission component.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
model
|
Model
|
The parent model instance. |
required |
beta
|
ValuesMap
|
Per-tick, per-node transmission rate. |
required |
validating
|
bool
|
Enable validation checks during simulation. |
False
|
property
properties
Return node properties required by this component.
Returns:
| Type | Description |
|---|---|
list[PropertyType]
|
list[PropertyType]: Parent properties plus
|
property
states
Return the compartment state names managed by this component.
Returns:
| Type | Description |
|---|---|
list[str]
|
list[str]: Parent states plus |