v2: Merge observableTransformation and noiseDistribution
#619
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
dweindl
force-pushed
the
v2_replace_obs_transform
branch
from
36c925a to
e2eccd4
Compare
dilpath
approved these changes
Mar 27, 2025
doc/v2/documentation_data_format.rst
Outdated
Comment on lines
651
to
660
| * ``normal``: Gaussian noise model with standard deviation as specified in | ||
| ``noiseFormula``. | ||
| * ``log-normal``: Log-normal noise model with standard deviation as specified | ||
| in ``noiseFormula``. I.e., the logarithm of the measurements is normally | ||
| distributed. | ||
| * ``laplace``: Laplace noise model with scale parameter as specified in | ||
| ``noiseFormula``. | ||
| * ``log-laplace``: Log-Laplace noise model with scale parameter as specified | ||
| in ``noiseFormula``. I.e., the logarithm of the measurements is Laplace | ||
| distributed. |
Member
There was a problem hiding this comment.
This could be a table like
| noiseDistribution | observableFormula | noiseFormula |
|---|---|---|
| normal | mean | standard deviation |
The table means we lose some descriptive text like "Gaussian noise model", but it's probably unnecessary or could be moved to the v2_noise_distributions section.
dweindl
commented
Mar 28, 2025
FFroehlich
approved these changes
Apr 23, 2025
sebapersson
approved these changes
Apr 23, 2025
Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
dweindl
added a commit
to dweindl/libpetab-python
that referenced
this pull request
Apr 24, 2025
…eDistribution Update to changes in PEtab v2 draft, see PEtab-dev/PEtab#619. Closes PEtab-dev#375.
dweindl
added a commit
to dweindl/libpetab-python
that referenced
this pull request
Apr 25, 2025
…eDistribution Update to changes in PEtab v2 draft, see PEtab-dev/PEtab#619. Closes PEtab-dev#375.
dweindl
added a commit
to PEtab-dev/libpetab-python
that referenced
this pull request
Apr 25, 2025
#376) * v2: handle merged observable.observableTransformation observable.noiseDistribution Update to changes in PEtab v2 draft, see PEtab-dev/PEtab#619. Closes #375. * upconversion
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Merge the
observableTransformationandnoiseDistributioncolumns of the observable table.See also #618 (comment)
👀 https://petab--619.org.readthedocs.build/en/619/v2/documentation_data_format.html#noise-distributions