fit.petab_v2.gaps¶
What PEtab v2 does not express about an sbmlsim optimization problem.
PEtab describes a parameter estimation problem as tables: a model, the
conditions and experiments it is simulated under, the observables, the
measurements and the parameters. sbmlsim describes more than that, i.e., the
units of everything, what a fit does with a subset of the data and how the
residuals are weighted, and less of it in tables: a SimulationExperiment is
python and its data can be a function of other data.
This module is the catalogue of the differences. Every Gap says what
sbmlsim has, what PEtab v2 offers for it and what the layer does about it,
and gaps_of_problem reports the gaps a given problem actually runs into, so
that what a specific export loses is known before it is written.
Bases: StrEnum
What the layer does about a difference to PEtab v2.
class-attribute
instance-attribute
¶
PEtab has no place for it, the sbmlsim extension of the problem
carries it, so the round trip through sbmlsim is exact. The extension is
required, i.e. a tool which does not know it rejects the problem rather
than reading it without the information; required_extension=False writes
a problem for other tools.
class-attribute
instance-attribute
¶
The information is transformed and the round trip is not exact, i.e., the problem which is read back is not the problem which was written.
class-attribute
instance-attribute
¶
The export raises, there is no representation which keeps the meaning of the fit.
dataclass
¶
A difference between an sbmlsim fit and a PEtab v2 problem.
Attributes:
| Name | Type | Description |
|---|---|---|
id |
str
|
identifier of the gap. |
kind |
GapKind
|
what the layer does about it. |
sbmlsim |
str
|
what |
petab |
str
|
what PEtab v2 offers for it, |
detail |
str
|
what the layer does and what it costs. |
Report the gaps an optimization problem runs into.
The problem must be initialized, i.e., its mappings are resolved; the gaps of the data are only known then.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
problem
|
OptimizationProblem
|
the problem which is exported. |
required |
Returns:
| Type | Description |
|---|---|
list[Gap]
|
The gaps which apply to this problem, in the order of |
Raises:
| Type | Description |
|---|---|
ValueError
|
if the problem is not initialized. |