scales
The typical magnitudes of the states of a model, which scale their absolute tolerances.
An absolute tolerance relative to the scale of every state
(AbsoluteTolerance(relative=..., scales=...), see
sbmlsim.model.tolerances) gives a small state the same relative accuracy as
a large one (#435). The initial value of a state is its scale when no scale
is given, which leaves a state which starts at 0, e.g. a drug before its
dose, at the tolerance of its kind. typical_scales gives the largest
magnitude of every state in test simulations, e.g. the standard doses of a
model, which includes its initial value:
scales = typical_scales(simulator, model, [oral_dose, iv_dose])
tolerance = AbsoluteTolerance(relative=1e-10, scales=scales)
The scales are computed once and stored with the model, e.g. in the settings
of the simulator of its project as JSON (AbsoluteTolerance.to_dict), so
that the tolerances of a simulation never depend on its own scenario. Fixed
scales of a standard dose keep the relative accuracy of the states within
about 1e-7 from a hundredth to a hundred times the dose, see #435.
Get the largest magnitude of every state of a model in test simulations.
The states are the ones roadrunner integrates, the targets of the rate
rules and the independent floating species, whose scale is their
amount, as the tolerances of AbsoluteTolerance are amounts. Every
simulation, or every point of a scan, is simulated with the simulator in
the steps of the integrator, and the scale of a state is the largest
absolute value it takes in any of them, the start included.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
simulator
|
Simulator
|
the simulator, of any engine. |
required |
model
|
ModelLike
|
the model. |
required |
simulations
|
Simulation | Scan | Iterable[Simulation | Scan]
|
the test simulations, a simulation or a scan or several. |
required |
Returns:
| Type | Description |
|---|---|
dict[str, float]
|
The scale of every state which is not 0 in all simulations, by id, in |
dict[str, float]
|
the order of the states. |
Raises:
| Type | Description |
|---|---|
ValueError
|
without a simulation. |