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allow calculating llhs #349

Merged
merged 12 commits into from
Feb 27, 2020
Merged

allow calculating llhs #349

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08328f8
allow to compute chi2 values
yannikschaelte Feb 27, 2020
bac290d
add docs
yannikschaelte Feb 27, 2020
020a343
init llh
yannikschaelte Feb 27, 2020
28ba529
fix w602 errors
yannikschaelte Feb 27, 2020
e38cf46
fix docstring coverage
yannikschaelte Feb 27, 2020
1272adc
fix codacy warnings
yannikschaelte Feb 27, 2020
c87dd30
Merge branch 'feature_llh' into feature_llh2
yannikschaelte Feb 27, 2020
b5932f1
allow calculating likelihoods
yannikschaelte Feb 27, 2020
2ab869d
Merge remote-tracking branch 'origin/develop' into feature_llh2
yannikschaelte Feb 27, 2020
ebde39f
fixup
yannikschaelte Feb 27, 2020
146ccf0
add documentation
yannikschaelte Feb 27, 2020
43b356e
fix codacy
yannikschaelte Feb 27, 2020
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init llh
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@yannikschaelte
yannikschaelte committed Feb 27, 2020
commit 020a343b855026807f8f59737b0358c7a430b987
14 changes: 14 additions & 0 deletions petab/calculate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -229,3 +229,17 @@ def calculate_chi2_for_table_from_residuals(
residual_df: pd.DataFrame) -> float:
"""Compute chi2 value for a single residual table."""
return (np.array(residual_df[RESIDUAL])**2).sum()


def calculate_llh(
measurement_dfs: Union[List[pd.DataFrame], pd.DataFrame],
simulation_dfs: Union[List[pd.DataFrame], pd.DataFrame],
observable_dfs: Union[List[pd.DataFrame], pd.DataFrame],
parameter_dfs: Union[List[pd.DataFrame], pd.DataFrame],
normalize: bool = True,
scale: bool = True
) -> float:
residual_dfs = calculate_residuals(
measurement_dfs, simulation_dfs, observable_dfs, parameter_dfs,
normalize, scale)
llhs = [calculate_llh_for_table_from_residuals(residual_df,