Added BCA confidence intervals #552
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WalkthroughThe recent updates to the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant FitFunction
participant Bootstrap
participant ConfidenceInterval
User->>FitFunction: Call fit()
FitFunction->>Bootstrap: Generate bootstrap samples using n_p_b
Bootstrap-->>FitFunction: Return resampled data
FitFunction->>ConfidenceInterval: Calculate confidence intervals
ConfidenceInterval-->>FitFunction: Return confidence intervals
FitFunction-->>User: Return results
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- python/python/bystro/parent_of_origin/parent_of_origin.py (3 hunks)
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python/python/bystro/parent_of_origin/parent_of_origin.py (7)
331-332: Introduce a new variable for readabilityThe introduction of
n_p_bforself.n_permutations_bootstrapimproves readability.
334-335: Initialize confidence interval storageThe initialization of
ci_eigenvectorfor storing confidence intervals is necessary for the subsequent calculations.
335-339: Initialize bootstrap samples storageThe initialization of
bootstrap_samples_for storing bootstrap samples is necessary for the resampling process.
340-347: Resampling logic usingX_het_whitenedThe resampling logic has been updated to use
X_het_whitened, which likely improves the statistical properties of the samples generated.
366-368: Define alpha values for confidence intervalsThe definition of
alpha,alpha1, andalpha2is necessary for the computation of the confidence intervals.
369-415: Compute BCA confidence intervalsThe computation of BCA confidence intervals is a significant enhancement that adds robustness to the confidence interval estimation.
417-417: Store computed confidence intervalsThe computed confidence intervals are stored in
self.confidence_interval_, replacing the previous method of storing bootstrap samples and quantiles.
| jackknife_mean_vector_component = ( | ||
| j_values_vector_component.mean() | ||
| ) | ||
| a_vector_component = np.sum( |
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Could you explain the constants here (** 3, 6.0 * np.sum, **1.5, etc) or reference the equation?
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Referenced the equation, it requires a whole chapter to explain basically.
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Files selected for processing (1)
- python/python/bystro/parent_of_origin/parent_of_origin.py (3 hunks)
Files skipped from review as they are similar to previous changes (1)
- python/python/bystro/parent_of_origin/parent_of_origin.py
This uses the BCA algorithm from the bootstrap to compute confidence intervals on the POE estimates.
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