Fix / refactor parameter mapping (breaking change) #344
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Fixes #342 Parameter value and parameter scale mapping now always done together. Fixed handling of parameter scale for non-estimated scaled parameters.
Codecov Report
@@ Coverage Diff @@
## develop #344 +/- ##
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+ Coverage 76.31% 76.93% +0.62%
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Files 23 23
Lines 1925 2012 +87
Branches 424 446 +22
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+ Hits 1469 1548 +79
- Misses 348 349 +1
- Partials 108 115 +7
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yannikschaelte
approved these changes
Feb 26, 2020
| second for simulation. ``NaN`` is used where no mapping exists. | ||
| Parameter value and parameter scale mapping for all conditions. | ||
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| The length of the returned array is the number of unique combinations |
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Suggested change
| The length of the returned array is the number of unique combinations | |
| The lengths of the returned array are respectively the numbers of unique combinations |
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I'd say it was correct before. It's an array of tuples, not a tuple of arrays.
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of course, you are right!
petab/parameter_mapping.py
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| Parameter value and parameter scale mapping for all conditions. | ||
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| The length of the returned array is the number of unique combinations | ||
| of simulationConditionId and preequilibrationConditionId from the |
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Suggested change
| of simulationConditionId and preequilibrationConditionId from the | |
| of simulationConditionIds and preequilibrationConditionIds from the |
petab/parameter_mapping.py
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| # Replace any leftover mapped parameter coming from condition table | ||
| for key, value in mapping.items(): | ||
| for key, value in par_mapping.items(): |
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use more descriptive than key and value?
| condition_df=condition_df, | ||
| parameter_df=parameter_df, | ||
| sbml_model=model, | ||
| scaled_parameters=True |
This was referenced Feb 27, 2020
Merged
dweindl
added a commit
that referenced
this pull request
Feb 28, 2020
Release 0.1.3 File format: * Updated documentation * Observables table in YAML file now mandatory in schema (was implicitly mandatory before, as observable table was required already) Library: * petablint: * Fix: allow specifying observables file via CLI (Closes #302) * Fix: nominalValue is optional unless estimated!=1 anywhere (Fixes #303) * Fix: handle undefined observables more gracefully (Closes #300) (#351) * Parameter mapping: * Fix / refactor parameter mapping (breaking change) (#344) (now performing parameter value and scale mapping together) * check optional measurement cols in mapping (#350) * allow calculating llhs (#349), chi2 values (#348) and residuals (#345) * Visualization * Basic Scatterplots & lot of bar plot fixes (#270) * Fix incorrect length of bool `bool_preequ` when subsetting with ind_meas (Closes #322) * make libcombine optional (#338)
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Fixes #342
Parameter value and parameter scale mapping now always done together.
Fixed handling of parameter scale for non-estimated scaled parameters.