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Allow using observable IDs in observableFormula and noiseFormula #562

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merged 4 commits into from
Jun 26, 2024
Merged

Allow using observable IDs in observableFormula and noiseFormula #562

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1ac7623
Allow using observable IDs in `observableFormula` and `noiseFormula`
dweindl Jun 27, 2023
669cbcf
Merge branch 'release/2.0.0' into petab2_observable_in_noise
dweindl Jun 27, 2023
e6be74b
Merge branch 'release/2.0.0' into petab2_observable_in_noise
dweindl Jun 26, 2024
05a374b
Update doc/documentation_data_format.rst
dweindl Jun 26, 2024
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12 changes: 9 additions & 3 deletions doc/documentation_data_format.rst
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Expand Up @@ -340,7 +340,9 @@ Detailed field description
Observation function as plain text formula expression.
May contain any symbol defined in the SBML model (including model time ``time``)
or parameter table. In the simplest case just an SBML species ID
or an ``AssignmentRule`` target.
or an ``AssignmentRule`` target. Additionally, any observable ID
introduced in the observable table may be referenced, but circular definitions
must be avoided.

May introduce new parameters of the form ``observableParameter${n}_${observableId}``,
which are overridden by ``observableParameters`` in the measurement table
Expand All @@ -362,10 +364,14 @@ Detailed field description
observable.

Alternatively, some formula expression can be provided to specify
more complex noise models. A noise model which accounts for relative and
more complex noise models. The formula may reference any uniquely identifiable
model entity with PEtab-compatible identifier or any observable ID
specified in the observable table.

A noise model which accounts for relative and
absolute contributions could, e.g., be defined as::

noiseParameter1_observable_pErk + noiseParameter2_observable_pErk*pErk
noiseParameter1_observable_pErk + noiseParameter2_observable_pErk * observable_pErk

with ``noiseParameter1_observable_pErk`` denoting the absolute and
``noiseParameter2_observable_pErk`` the relative contribution for the
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