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v2 spec: allow infinite nominal values (erratum E3) #687

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99d0ace
v2 spec: allow infinite nominal values (erratum E3)
dweindl Oct 24, 2026
efc534a
Update doc/v2/errata.rst
dweindl Oct 26, 2026
41f9991
v2 spec: allow infinite placeholder overrides (erratum E3)
dweindl Oct 27, 2026
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69 changes: 42 additions & 27 deletions doc/v2/documentation_data_format.rst
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Expand Up @@ -514,17 +514,17 @@ order:

*(wrapped for readability)*

+-----+----------------------------+----------------------------+
| ... | [observableParameters] | [noiseParameters] |
+=====+============================+============================+
| ... | LIST[parameterId\|NUMERIC] | LIST[parameterId\|NUMERIC] |
+-----+----------------------------+----------------------------+
| ... | | |
+-----+----------------------------+----------------------------+
| ... | | |
+-----+----------------------------+----------------------------+
| ... | ... | ... |
+-----+----------------------------+----------------------------+
+-----+----------------------------------------+----------------------------------------+
| ... | [observableParameters] | [noiseParameters] |
+=====+========================================+========================================+
| ... | LIST[parameterId\|NUMERIC\|inf\|-inf] | LIST[parameterId\|NUMERIC\|inf\|-inf] |
+-----+----------------------------------------+----------------------------------------+
| ... | | |
+-----+----------------------------------------+----------------------------------------+
| ... | | |
+-----+----------------------------------------+----------------------------------------+
| ... | ... | ... |
+-----+----------------------------------------+----------------------------------------+

Additional (non-standard) columns may be added.

Expand Down Expand Up @@ -567,7 +567,8 @@ Detailed field description
the condition change is applied before the observable is evaluated
(see :ref:`v2_reinitialization_semantics` for details).

- ``observableParameters`` [LIST[parameterId, NUMERIC], NULL, OPTIONAL]
- ``observableParameters`` [LIST[parameterId, NUMERIC, ``inf``, ``-inf``],
NULL, OPTIONAL]

Measurement-specific overrides for placeholder parameters in the
`observableFormula` declared in the
Expand All @@ -582,8 +583,12 @@ Detailed field description
observable in the observable table. I.e., if the observable table contains
no observable placeholders for the given observable, this field must be
empty.
The values may be either numeric values or the IDs of parameters from the
:ref:`parameter table <v2_parameter_table>`.
The values may be either numeric values, ``inf``, ``-inf``, or the IDs of
parameters from the :ref:`parameter table <v2_parameter_table>`.

.. note::

Infinite values are valid as per :ref:`erratum E3 <v2_errata_e3>`.

Different measurements for the same ``observableId`` may specify different
values. This may be used to account for condition-specific or
Expand All @@ -592,7 +597,8 @@ Detailed field description
If none of the observables referenced in a given measurement table use any
observable placeholders, this column may be omitted there.

- ``noiseParameters`` [LIST[parameterId, NUMERIC], NULL, OPTIONAL]
- ``noiseParameters`` [LIST[parameterId, NUMERIC, ``inf``, ``-inf``],
NULL, OPTIONAL]

Measurement-specific overrides for placeholder parameters in the
`noiseFormula` declared in the
Expand All @@ -607,8 +613,12 @@ Detailed field description
observable in the observable table. I.e., if the observable table contains
no noise placeholders for the given observable, this field must be
empty.
The values may be either numeric values or the IDs of parameters from the
:ref:`parameter table <v2_parameter_table>`.
The values may be either numeric values, ``inf``, ``-inf``, or the IDs of
parameters from the :ref:`parameter table <v2_parameter_table>`.

.. note::

Infinite values are valid as per :ref:`erratum E3 <v2_errata_e3>`.

Different measurements for the same ``observableId`` may specify different
values. This may be used to account for condition-specific or
Expand Down Expand Up @@ -861,15 +871,15 @@ it *may* include:

One row per parameter with arbitrary order of rows and columns:

+-------------+-----------------+---------------+--------------+--------------+-------------+-----+
| parameterId | [parameterName] | lowerBound | upperBound | nominalValue | estimate | ... |
+=============+=================+===============+==============+==============+=============+=====+
| PETAB_ID | [STRING] | NUMERIC\|-inf | NUMERIC\|inf | NUMERIC | true\|false | ... |
+-------------+-----------------+---------------+--------------+--------------+-------------+-----+
| k1 | | 1e-5 | 1e5 | 100 | true | ... |
+-------------+-----------------+---------------+--------------+--------------+-------------+-----+
| ... | ... | ... | ... | ... | ... | ... |
+-------------+-----------------+---------------+--------------+--------------+-------------+-----+
+-------------+-----------------+---------------+--------------+--------------------+-------------+-----+
| parameterId | [parameterName] | lowerBound | upperBound | nominalValue | estimate | ... |
+=============+=================+===============+==============+====================+=============+=====+
| PETAB_ID | [STRING] | NUMERIC\|-inf | NUMERIC\|inf | NUMERIC\|inf\|-inf | true\|false | ... |
+-------------+-----------------+---------------+--------------+--------------------+-------------+-----+
| k1 | | 1e-5 | 1e5 | 100 | true | ... |
+-------------+-----------------+---------------+--------------+--------------------+-------------+-----+
| ... | ... | ... | ... | ... | ... | ... |
+-------------+-----------------+---------------+--------------+--------------------+-------------+-----+

*(wrapped for readability)*

Expand Down Expand Up @@ -919,12 +929,17 @@ Detailed field description
``inf`` indicates that the parameter is not bounded from above.
Optional, if ``estimate==false``.

- ``nominalValue`` [NUMERIC]
- ``nominalValue`` [NUMERIC or ``inf`` or ``-inf``]

Some parameter value to be used if
the parameter is not subject to estimation (see ``estimate`` below).
Optional, unless ``estimate==false``.

.. note::

Infinite nominal values are valid as per
:ref:`erratum E3 <v2_errata_e3>`.

- ``estimate`` [``true`` | ``false``]

``true`` or ``false`` (case-sensitive), depending on whether the parameter
Expand Down
38 changes: 37 additions & 1 deletion doc/v2/errata.rst
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Expand Up @@ -40,7 +40,7 @@ parameter bounds to the prior's domain (e.g., ``0`` and ``inf`` for

* ``lowerBound`` may be ``-inf``, ``upperBound`` may be ``inf``.
``inf`` as lower bound and ``-inf`` as upper bound remain invalid.
``nominalValue`` remains ``NUMERIC``, i.e., finite.
``nominalValue`` is addressed by :ref:`erratum E3 <v2_errata_e3>`.
* If priors are specified for any parameter, the default
``uniform(lowerBound, upperBound)`` prior for the remaining parameters is
improper for infinite bounds. Therefore, in this case, a proper prior
Expand Down Expand Up @@ -72,3 +72,39 @@ contrast, defines the prior only for the estimated parameters.
* The default ``uniform(lowerBound, upperBound)`` prior applies only to
estimated parameters, and only if priors are specified for any estimated
parameter.

.. _v2_errata_e3:

E3: Infinite parameter values
-----------------------------

:Type: technical
:Affects: :ref:`v2_parameter_table`, :ref:`v2_measurement_table`
:Discussion: `#685 <https://github.com/PEtab-dev/PEtab/issues/685>`__,
`#687 <https://github.com/PEtab-dev/PEtab/pull/687>`__

**Problem:**
``nominalValue`` was specified as ``NUMERIC``, which excludes infinite
values. At the same time, the list of changes from PEtab 1 states that the
effect of the removed ``parameterScale`` column can be obtained by
transforming the model parameters in the model file. This does not hold for
fixed parameters on the boundary of their domain: in PEtab 1, a parameter
``k1`` with ``parameterScale=log`` can be fixed to ``nominalValue=0``
(nominal values are on linear scale). For a model reparameterized in terms of
``log_k1``, the corresponding nominal value is ``-inf``.

The same applies to numeric values in ``observableParameters`` and
``noiseParameters`` in the measurement table, which were specified as
``NUMERIC``. Since these entries may also reference parameters from the
parameter table, an infinite value could be given via a parameter, but not
directly.

**Resolution:**

* ``nominalValue`` may be ``inf`` or ``-inf``. ``NaN`` remains invalid.
* Numeric values in ``observableParameters`` and ``noiseParameters`` may be
``inf`` or ``-inf``. ``NaN`` remains invalid.
* For parameters with ``estimate==false``, infinite nominal values are applied
as specified.
* For parameters with ``estimate==true``, ``nominalValue`` does not affect the
problem definition, so infinite values have no further implications.