Function for replacing objectivePrior* by observables/measurements#309
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dweindl merged 9 commits intoPEtab-dev:developfrom Oct 15, 2024
Merged
Function for replacing objectivePrior* by observables/measurements#309dweindl merged 9 commits intoPEtab-dev:developfrom
objectivePrior* by observables/measurements#309dweindl merged 9 commits intoPEtab-dev:developfrom
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Reformulate the given PEtab problem such that the objective priors are converted to measurements. This is done by adding a new observable for each prior and adding a corresponding measurement to the measurement table. The resulting optimization problem will be equivalent to the original problem. This is meant to be used for tools that do not support priors. Closes PEtab-dev#307
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## develop #309 +/- ##
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+ Coverage 72.86% 74.95% +2.09%
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Files 51 52 +1
Lines 4842 4896 +54
Branches 826 838 +12
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+ Hits 3528 3670 +142
+ Misses 1018 921 -97
- Partials 296 305 +9 ☔ View full report in Codecov by Sentry. |
dilpath
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Oct 14, 2024
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Overall, looks great, thanks!
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| prior_contrib += norm.logpdf( | ||
| petab_problem_priors.x_nominal_free_scaled[ | ||
| petab_problem_priors.x_free_ids.index(parameter_id) | ||
| ], | ||
| loc=prior_pars[0], | ||
| scale=prior_pars[1], | ||
| ) |
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Looks useful, could be moved to some calculate_posterior_for_table method like calculate_llh_for_table
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Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
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Reformulate the given PEtab problem such that the objective priors are converted to measurements. This is done by adding a new observable for each prior and adding a corresponding measurement to the measurement table. The resulting optimization problem will be equivalent to the original problem. This is meant to be used for tools that do not support priors.
Closes #307