Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Allow using observables in noiseFormula #543

Open
dweindl opened this issue May 20, 2022 · 2 comments · May be fixed by #562
Open

Allow using observables in noiseFormula #543

dweindl opened this issue May 20, 2022 · 2 comments · May be fixed by #562
Labels
specification change
Milestone
PEtab 2.0.0

Comments

@dweindl
Copy link
Member

dweindl commented May 20, 2022

Currently it is not allowed to use observable IDs in noiseFormula in the observables table (#368). It would be great to allow that.

This would convenient for specifying relative errors. Although the observableFormula could be copied to the noiseFormula, it would be more readable and less error prone if one could simply use the respective observableId.

Also, some tools do not support state variables, but only observables in noise models, so this would be convenient there too.

Opinions?
@dweindl dweindl added this to the PEtab 2.0.0 milestone May 20, 2022
@dweindl dweindl mentioned this issue Feb 28, 2023
Open
@eraimundez
Copy link

There seems to be something around that maybe could be used / adapted?
https://help.juliahub.com/pumasqsp/dev/example/petabimport/ (see first green box when scrolling down)

@dweindl
Copy link
Member Author

dweindl commented Jun 19, 2023

There seems to be something around that maybe could be used / adapted? https://help.juliahub.com/pumasqsp/dev/example/petabimport/ (see first green box when scrolling down)

This doesn't really require much adaptation. It's mostly about making a decision whether we want to allow that. (I think we should.)
Thanks for the reminder, I'll bring that up again in the next PEtab editor meeting (ping @PEtab-dev/petab-editors).

dweindl added a commit that referenced this issue Jun 27, 2023
@dweindl
Allow using observable IDs in observableFormula and noiseFormula
1ac7623 
Following up on #543 and the discussion during the last PEtab editor meeting:
There was general consent to allow using observableIDs in the `noiseFormula` column in the observables table.

What was not discussed explicitly:
* Should all observable IDs be allowed, or only the current one?
* If so, should it be allowed to use observable IDs inside `observableFormula`?

CC @PEtab-dev/petab-editors

Closes ##543
@dweindl dweindl linked a pull request Jun 27, 2023 that will close this issue
Open
@dweindl dweindl linked a pull request Jun 27, 2023 that will close this issue
Allow using observable IDs in observableFormula and noiseFormula #562
Open
@dweindl dweindl mentioned this issue Apr 21, 2024
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
specification change
Projects
None yet
Milestone
PEtab 2.0.0
Development

Successfully merging a pull request may close this issue.

Allow using observable IDs in observableFormula and noiseFormula PEtab-dev/PEtab
2 participants
@dweindl @eraimundez