@saibolla/ada 0.1.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.ada/SYSTEM.md +81 -0
- package/.ada/agents/researcher.md +69 -0
- package/.ada/agents/reviewer.md +92 -0
- package/.ada/agents/verifier.md +45 -0
- package/.ada/agents/writer.md +54 -0
- package/.ada/settings.json +32 -0
- package/.ada/themes/ada.json +85 -0
- package/.env.example +31 -0
- package/AGENTS.md +79 -0
- package/LICENSE +191 -0
- package/README.md +188 -0
- package/bin/ada.js +26 -0
- package/dist/bootstrap/sync.js +143 -0
- package/dist/cli.js +404 -0
- package/dist/config/paths.js +32 -0
- package/dist/index.js +10 -0
- package/dist/model/catalog.js +255 -0
- package/dist/model/commands.js +180 -0
- package/dist/pi/launch.js +33 -0
- package/dist/pi/package-presets.js +55 -0
- package/dist/pi/runtime.js +81 -0
- package/dist/pi/settings.js +108 -0
- package/dist/pi/web-access.js +74 -0
- package/dist/search/commands.js +12 -0
- package/dist/setup/doctor.js +126 -0
- package/dist/setup/preview.js +117 -0
- package/dist/setup/prompts.js +34 -0
- package/dist/setup/setup.js +98 -0
- package/dist/setup/update.js +133 -0
- package/dist/system/executables.js +38 -0
- package/dist/system/node-version.js +31 -0
- package/dist/system/open-url.js +35 -0
- package/dist/system/promise-polyfill.js +12 -0
- package/dist/ui/terminal.js +64 -0
- package/dist/web/launch.js +48 -0
- package/dist/web-search.js +1 -0
- package/extensions/docparser/constants.ts +62 -0
- package/extensions/docparser/deps.ts +584 -0
- package/extensions/docparser/doctor.ts +353 -0
- package/extensions/docparser/index.ts +9 -0
- package/extensions/docparser/input.ts +230 -0
- package/extensions/docparser/request.ts +67 -0
- package/extensions/docparser/schema.ts +82 -0
- package/extensions/docparser/tool.ts +305 -0
- package/extensions/docparser/types.ts +99 -0
- package/extensions/research-tools/alpha.ts +107 -0
- package/extensions/research-tools/header.ts +284 -0
- package/extensions/research-tools/help.ts +93 -0
- package/extensions/research-tools/project-scaffold.ts +64 -0
- package/extensions/research-tools/project.ts +123 -0
- package/extensions/research-tools/shared.ts +16 -0
- package/extensions/research-tools.ts +42 -0
- package/logo.d.mts +3 -0
- package/logo.mjs +14 -0
- package/metadata/commands.d.mts +46 -0
- package/metadata/commands.mjs +133 -0
- package/package.json +80 -0
- package/prompts/audit.md +17 -0
- package/prompts/autoresearch.md +66 -0
- package/prompts/compare.md +18 -0
- package/prompts/deepresearch.md +189 -0
- package/prompts/draft.md +19 -0
- package/prompts/jobs.md +16 -0
- package/prompts/litreview.md +18 -0
- package/prompts/log.md +14 -0
- package/prompts/replicate.md +24 -0
- package/prompts/review.md +18 -0
- package/prompts/watch.md +16 -0
- package/scripts/build-native-bundle.mjs +349 -0
- package/scripts/check-node-version.mjs +35 -0
- package/scripts/patch-embedded-pi.mjs +588 -0
- package/scripts/prepare-runtime-workspace.mjs +162 -0
- package/scripts/prune-runtime-deps.mjs +131 -0
- package/scripts/release.sh +152 -0
- package/skills/adaptyv/SKILL.md +112 -0
- package/skills/adaptyv/reference/api_reference.md +308 -0
- package/skills/adaptyv/reference/examples.md +913 -0
- package/skills/adaptyv/reference/experiments.md +360 -0
- package/skills/adaptyv/reference/protein_optimization.md +637 -0
- package/skills/aeon/SKILL.md +372 -0
- package/skills/aeon/references/anomaly_detection.md +154 -0
- package/skills/aeon/references/classification.md +144 -0
- package/skills/aeon/references/clustering.md +123 -0
- package/skills/aeon/references/datasets_benchmarking.md +387 -0
- package/skills/aeon/references/distances.md +256 -0
- package/skills/aeon/references/forecasting.md +140 -0
- package/skills/aeon/references/networks.md +289 -0
- package/skills/aeon/references/regression.md +118 -0
- package/skills/aeon/references/segmentation.md +163 -0
- package/skills/aeon/references/similarity_search.md +187 -0
- package/skills/aeon/references/transformations.md +246 -0
- package/skills/alpha-research/SKILL.md +42 -0
- package/skills/alpha-vantage/SKILL.md +142 -0
- package/skills/alpha-vantage/references/commodities.md +153 -0
- package/skills/alpha-vantage/references/economic-indicators.md +158 -0
- package/skills/alpha-vantage/references/forex-crypto.md +154 -0
- package/skills/alpha-vantage/references/fundamentals.md +223 -0
- package/skills/alpha-vantage/references/intelligence.md +138 -0
- package/skills/alpha-vantage/references/options.md +93 -0
- package/skills/alpha-vantage/references/technical-indicators.md +374 -0
- package/skills/alpha-vantage/references/time-series.md +157 -0
- package/skills/alphafold-database/SKILL.md +511 -0
- package/skills/alphafold-database/references/api_reference.md +423 -0
- package/skills/anndata/SKILL.md +398 -0
- package/skills/anndata/references/best_practices.md +525 -0
- package/skills/anndata/references/concatenation.md +396 -0
- package/skills/anndata/references/data_structure.md +314 -0
- package/skills/anndata/references/io_operations.md +404 -0
- package/skills/anndata/references/manipulation.md +516 -0
- package/skills/arboreto/SKILL.md +241 -0
- package/skills/arboreto/references/algorithms.md +138 -0
- package/skills/arboreto/references/basic_inference.md +151 -0
- package/skills/arboreto/references/distributed_computing.md +242 -0
- package/skills/arboreto/scripts/basic_grn_inference.py +97 -0
- package/skills/arxiv-database/SKILL.md +362 -0
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- package/skills/arxiv-database/scripts/arxiv_search.py +414 -0
- package/skills/astropy/SKILL.md +329 -0
- package/skills/astropy/references/coordinates.md +273 -0
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- package/skills/autoresearch/SKILL.md +12 -0
- package/skills/benchling-integration/SKILL.md +478 -0
- package/skills/benchling-integration/references/api_endpoints.md +883 -0
- package/skills/benchling-integration/references/authentication.md +379 -0
- package/skills/benchling-integration/references/sdk_reference.md +774 -0
- package/skills/bgpt-paper-search/SKILL.md +81 -0
- package/skills/bindingdb-database/SKILL.md +332 -0
- package/skills/bindingdb-database/references/affinity_queries.md +178 -0
- package/skills/biopython/SKILL.md +441 -0
- package/skills/biopython/references/advanced.md +577 -0
- package/skills/biopython/references/alignment.md +362 -0
- package/skills/biopython/references/blast.md +455 -0
- package/skills/biopython/references/databases.md +484 -0
- package/skills/biopython/references/phylogenetics.md +566 -0
- package/skills/biopython/references/sequence_io.md +285 -0
- package/skills/biopython/references/structure.md +564 -0
- package/skills/biorxiv-database/SKILL.md +481 -0
- package/skills/biorxiv-database/references/api_reference.md +280 -0
- package/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
- package/skills/bioservices/SKILL.md +359 -0
- package/skills/bioservices/references/identifier_mapping.md +685 -0
- package/skills/bioservices/references/services_reference.md +636 -0
- package/skills/bioservices/references/workflow_patterns.md +811 -0
- package/skills/bioservices/scripts/batch_id_converter.py +347 -0
- package/skills/bioservices/scripts/compound_cross_reference.py +378 -0
- package/skills/bioservices/scripts/pathway_analysis.py +309 -0
- package/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
- package/skills/brenda-database/SKILL.md +717 -0
- package/skills/brenda-database/references/api_reference.md +537 -0
- package/skills/brenda-database/scripts/brenda_queries.py +844 -0
- package/skills/brenda-database/scripts/brenda_visualization.py +772 -0
- package/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
- package/skills/cbioportal-database/SKILL.md +367 -0
- package/skills/cbioportal-database/references/study_exploration.md +128 -0
- package/skills/cellxgene-census/SKILL.md +509 -0
- package/skills/cellxgene-census/references/census_schema.md +182 -0
- package/skills/cellxgene-census/references/common_patterns.md +351 -0
- package/skills/chembl-database/SKILL.md +387 -0
- package/skills/chembl-database/references/api_reference.md +272 -0
- package/skills/chembl-database/scripts/example_queries.py +278 -0
- package/skills/cirq/SKILL.md +344 -0
- package/skills/cirq/references/building.md +307 -0
- package/skills/cirq/references/experiments.md +572 -0
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- package/skills/cirq/references/transformation.md +416 -0
- package/skills/citation-management/SKILL.md +1113 -0
- package/skills/citation-management/assets/bibtex_template.bib +264 -0
- package/skills/citation-management/assets/citation_checklist.md +386 -0
- package/skills/citation-management/references/bibtex_formatting.md +908 -0
- package/skills/citation-management/references/citation_validation.md +794 -0
- package/skills/citation-management/references/google_scholar_search.md +725 -0
- package/skills/citation-management/references/metadata_extraction.md +870 -0
- package/skills/citation-management/references/pubmed_search.md +839 -0
- package/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
- package/skills/citation-management/scripts/extract_metadata.py +569 -0
- package/skills/citation-management/scripts/format_bibtex.py +349 -0
- package/skills/citation-management/scripts/search_google_scholar.py +282 -0
- package/skills/citation-management/scripts/search_pubmed.py +398 -0
- package/skills/citation-management/scripts/validate_citations.py +497 -0
- package/skills/clinical-decision-support/SKILL.md +510 -0
- package/skills/clinical-decision-support/assets/biomarker_report_template.tex +380 -0
- package/skills/clinical-decision-support/assets/clinical_pathway_template.tex +222 -0
- package/skills/clinical-decision-support/assets/cohort_analysis_template.tex +359 -0
- package/skills/clinical-decision-support/assets/color_schemes.tex +149 -0
- package/skills/clinical-decision-support/assets/example_gbm_cohort.md +208 -0
- package/skills/clinical-decision-support/assets/recommendation_strength_guide.md +328 -0
- package/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +529 -0
- package/skills/clinical-decision-support/references/README.md +129 -0
- package/skills/clinical-decision-support/references/biomarker_classification.md +719 -0
- package/skills/clinical-decision-support/references/clinical_decision_algorithms.md +604 -0
- package/skills/clinical-decision-support/references/evidence_synthesis.md +840 -0
- package/skills/clinical-decision-support/references/outcome_analysis.md +640 -0
- package/skills/clinical-decision-support/references/patient_cohort_analysis.md +427 -0
- package/skills/clinical-decision-support/references/treatment_recommendations.md +521 -0
- package/skills/clinical-decision-support/scripts/biomarker_classifier.py +384 -0
- package/skills/clinical-decision-support/scripts/build_decision_tree.py +447 -0
- package/skills/clinical-decision-support/scripts/create_cohort_tables.py +524 -0
- package/skills/clinical-decision-support/scripts/generate_survival_analysis.py +422 -0
- package/skills/clinical-decision-support/scripts/validate_cds_document.py +335 -0
- package/skills/clinical-reports/SKILL.md +1131 -0
- package/skills/clinical-reports/assets/case_report_template.md +352 -0
- package/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
- package/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
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- package/skills/clinical-reports/assets/pathology_report_template.md +249 -0
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- package/skills/clinical-reports/scripts/check_deidentification.py +346 -0
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- package/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
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- package/skills/clinical-reports/scripts/generate_report_template.py +163 -0
- package/skills/clinical-reports/scripts/terminology_validator.py +133 -0
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- package/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
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- package/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
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- package/skills/vaex/references/core_dataframes.md +367 -0
- package/skills/vaex/references/data_processing.md +555 -0
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- package/skills/vaex/references/machine_learning.md +728 -0
- package/skills/vaex/references/performance.md +571 -0
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- package/skills/venue-templates/SKILL.md +688 -0
- package/skills/venue-templates/assets/examples/cell_summary_example.md +247 -0
- package/skills/venue-templates/assets/examples/medical_structured_abstract.md +313 -0
- package/skills/venue-templates/assets/examples/nature_abstract_examples.md +213 -0
- package/skills/venue-templates/assets/examples/neurips_introduction_example.md +245 -0
- package/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
- package/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
- package/skills/venue-templates/assets/journals/nature_article.tex +171 -0
- package/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
- package/skills/venue-templates/assets/journals/plos_one.tex +317 -0
- package/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
- package/skills/venue-templates/references/cell_press_style.md +483 -0
- package/skills/venue-templates/references/conferences_formatting.md +564 -0
- package/skills/venue-templates/references/cs_conference_style.md +463 -0
- package/skills/venue-templates/references/grants_requirements.md +787 -0
- package/skills/venue-templates/references/journals_formatting.md +486 -0
- package/skills/venue-templates/references/medical_journal_styles.md +535 -0
- package/skills/venue-templates/references/ml_conference_style.md +556 -0
- package/skills/venue-templates/references/nature_science_style.md +405 -0
- package/skills/venue-templates/references/posters_guidelines.md +628 -0
- package/skills/venue-templates/references/reviewer_expectations.md +417 -0
- package/skills/venue-templates/references/venue_writing_styles.md +321 -0
- package/skills/venue-templates/scripts/customize_template.py +206 -0
- package/skills/venue-templates/scripts/query_template.py +260 -0
- package/skills/venue-templates/scripts/validate_format.py +255 -0
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- package/skills/what-if-oracle/references/scenario-templates.md +137 -0
- package/skills/writing/SKILL.md +414 -0
- package/skills/xlsx/LICENSE.txt +30 -0
- package/skills/xlsx/SKILL.md +292 -0
- package/skills/xlsx/scripts/office/helpers/__init__.py +0 -0
- package/skills/xlsx/scripts/office/helpers/merge_runs.py +199 -0
- package/skills/xlsx/scripts/office/helpers/simplify_redlines.py +197 -0
- package/skills/xlsx/scripts/office/pack.py +159 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
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- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
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- package/skills/xlsx/scripts/office/schemas/mce/mc.xsd +75 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
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- package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/skills/xlsx/scripts/office/soffice.py +183 -0
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- package/skills/xlsx/scripts/office/validators/base.py +847 -0
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- package/skills/xlsx/scripts/office/validators/redlining.py +247 -0
- package/skills/xlsx/scripts/recalc.py +184 -0
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# Statistical Tests and Diagnostics Reference
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This document provides comprehensive guidance on statistical tests, diagnostics, and tools available in statsmodels.
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## Overview
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Statsmodels provides extensive statistical testing capabilities:
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- Residual diagnostics and specification tests
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- Hypothesis testing (parametric and non-parametric)
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- Goodness-of-fit tests
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- Multiple comparisons and post-hoc tests
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- Power and sample size calculations
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- Robust covariance matrices
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- Influence and outlier detection
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## Residual Diagnostics
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### Autocorrelation Tests
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**Ljung-Box Test**: Tests for autocorrelation in residuals
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```python
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from statsmodels.stats.diagnostic import acorr_ljungbox
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# Test residuals for autocorrelation
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lb_test = acorr_ljungbox(residuals, lags=10, return_df=True)
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print(lb_test)
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# H0: No autocorrelation up to lag k
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# If p-value < 0.05, reject H0 (autocorrelation present)
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```
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**Durbin-Watson Test**: Tests for first-order autocorrelation
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```python
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from statsmodels.stats.stattools import durbin_watson
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dw_stat = durbin_watson(residuals)
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print(f"Durbin-Watson: {dw_stat:.4f}")
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# DW ≈ 2: no autocorrelation
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# DW < 2: positive autocorrelation
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# DW > 2: negative autocorrelation
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# Exact critical values depend on n and k
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```
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**Breusch-Godfrey Test**: More general test for autocorrelation
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```python
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from statsmodels.stats.diagnostic import acorr_breusch_godfrey
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bg_test = acorr_breusch_godfrey(results, nlags=5)
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lm_stat, lm_pval, f_stat, f_pval = bg_test
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print(f"LM statistic: {lm_stat:.4f}, p-value: {lm_pval:.4f}")
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# H0: No autocorrelation up to lag k
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```
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### Heteroskedasticity Tests
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**Breusch-Pagan Test**: Tests for heteroskedasticity
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```python
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from statsmodels.stats.diagnostic import het_breuschpagan
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bp_test = het_breuschpagan(residuals, exog)
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lm_stat, lm_pval, f_stat, f_pval = bp_test
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print(f"Breusch-Pagan test p-value: {lm_pval:.4f}")
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# H0: Homoskedasticity (constant variance)
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# If p-value < 0.05, reject H0 (heteroskedasticity present)
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```
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**White Test**: More general test for heteroskedasticity
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```python
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from statsmodels.stats.diagnostic import het_white
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white_test = het_white(residuals, exog)
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lm_stat, lm_pval, f_stat, f_pval = white_test
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print(f"White test p-value: {lm_pval:.4f}")
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# H0: Homoskedasticity
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```
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**ARCH Test**: Tests for autoregressive conditional heteroskedasticity
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```python
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from statsmodels.stats.diagnostic import het_arch
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arch_test = het_arch(residuals, nlags=5)
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lm_stat, lm_pval, f_stat, f_pval = arch_test
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print(f"ARCH test p-value: {lm_pval:.4f}")
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# H0: No ARCH effects
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# If significant, consider GARCH model
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```
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### Normality Tests
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**Jarque-Bera Test**: Tests for normality using skewness and kurtosis
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```python
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from statsmodels.stats.stattools import jarque_bera
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jb_stat, jb_pval, skew, kurtosis = jarque_bera(residuals)
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print(f"Jarque-Bera statistic: {jb_stat:.4f}")
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print(f"p-value: {jb_pval:.4f}")
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print(f"Skewness: {skew:.4f}")
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print(f"Kurtosis: {kurtosis:.4f}")
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# H0: Residuals are normally distributed
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# Normal: skewness ≈ 0, kurtosis ≈ 3
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```
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**Omnibus Test**: Another normality test (also based on skewness/kurtosis)
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```python
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from statsmodels.stats.stattools import omni_normtest
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omni_stat, omni_pval = omni_normtest(residuals)
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print(f"Omnibus test p-value: {omni_pval:.4f}")
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# H0: Normality
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```
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**Anderson-Darling Test**: Distribution fit test
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```python
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from statsmodels.stats.diagnostic import normal_ad
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ad_stat, ad_pval = normal_ad(residuals)
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print(f"Anderson-Darling test p-value: {ad_pval:.4f}")
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```
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**Lilliefors Test**: Modified Kolmogorov-Smirnov test
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```python
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from statsmodels.stats.diagnostic import lilliefors
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lf_stat, lf_pval = lilliefors(residuals, dist='norm')
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print(f"Lilliefors test p-value: {lf_pval:.4f}")
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```
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### Linearity and Specification Tests
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**Ramsey RESET Test**: Tests for functional form misspecification
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```python
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from statsmodels.stats.diagnostic import linear_reset
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reset_test = linear_reset(results, power=2)
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f_stat, f_pval = reset_test
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print(f"RESET test p-value: {f_pval:.4f}")
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# H0: Model is correctly specified (linear)
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# If rejected, may need polynomial terms or transformations
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```
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**Harvey-Collier Test**: Tests for linearity
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```python
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from statsmodels.stats.diagnostic import linear_harvey_collier
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hc_stat, hc_pval = linear_harvey_collier(results)
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print(f"Harvey-Collier test p-value: {hc_pval:.4f}")
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# H0: Linear specification is correct
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```
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## Multicollinearity Detection
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**Variance Inflation Factor (VIF)**:
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```python
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from statsmodels.stats.outliers_influence import variance_inflation_factor
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import pandas as pd
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# Calculate VIF for each variable
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vif_data = pd.DataFrame()
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180
|
+
vif_data["Variable"] = X.columns
|
|
181
|
+
vif_data["VIF"] = [variance_inflation_factor(X.values, i)
|
|
182
|
+
for i in range(X.shape[1])]
|
|
183
|
+
|
|
184
|
+
print(vif_data.sort_values('VIF', ascending=False))
|
|
185
|
+
|
|
186
|
+
# Interpretation:
|
|
187
|
+
# VIF = 1: No correlation with other predictors
|
|
188
|
+
# VIF > 5: Moderate multicollinearity
|
|
189
|
+
# VIF > 10: Serious multicollinearity problem
|
|
190
|
+
# VIF > 20: Severe multicollinearity (consider removing variable)
|
|
191
|
+
```
|
|
192
|
+
|
|
193
|
+
**Condition Number**: From regression results
|
|
194
|
+
|
|
195
|
+
```python
|
|
196
|
+
print(f"Condition number: {results.condition_number:.2f}")
|
|
197
|
+
|
|
198
|
+
# Interpretation:
|
|
199
|
+
# < 10: No multicollinearity concern
|
|
200
|
+
# 10-30: Moderate multicollinearity
|
|
201
|
+
# > 30: Strong multicollinearity
|
|
202
|
+
# > 100: Severe multicollinearity
|
|
203
|
+
```
|
|
204
|
+
|
|
205
|
+
## Influence and Outlier Detection
|
|
206
|
+
|
|
207
|
+
### Leverage
|
|
208
|
+
|
|
209
|
+
High leverage points have extreme predictor values.
|
|
210
|
+
|
|
211
|
+
```python
|
|
212
|
+
from statsmodels.stats.outliers_influence import OLSInfluence
|
|
213
|
+
|
|
214
|
+
influence = results.get_influence()
|
|
215
|
+
|
|
216
|
+
# Hat values (leverage)
|
|
217
|
+
leverage = influence.hat_matrix_diag
|
|
218
|
+
|
|
219
|
+
# Rule of thumb: leverage > 2*p/n or 3*p/n is high
|
|
220
|
+
# p = number of parameters, n = sample size
|
|
221
|
+
threshold = 2 * len(results.params) / len(y)
|
|
222
|
+
high_leverage = np.where(leverage > threshold)[0]
|
|
223
|
+
|
|
224
|
+
print(f"High leverage observations: {high_leverage}")
|
|
225
|
+
```
|
|
226
|
+
|
|
227
|
+
### Cook's Distance
|
|
228
|
+
|
|
229
|
+
Measures overall influence of each observation.
|
|
230
|
+
|
|
231
|
+
```python
|
|
232
|
+
# Cook's distance
|
|
233
|
+
cooks_d = influence.cooks_distance[0]
|
|
234
|
+
|
|
235
|
+
# Rule of thumb: Cook's D > 4/n is influential
|
|
236
|
+
threshold = 4 / len(y)
|
|
237
|
+
influential = np.where(cooks_d > threshold)[0]
|
|
238
|
+
|
|
239
|
+
print(f"Influential observations (Cook's D): {influential}")
|
|
240
|
+
|
|
241
|
+
# Plot
|
|
242
|
+
import matplotlib.pyplot as plt
|
|
243
|
+
plt.stem(range(len(cooks_d)), cooks_d)
|
|
244
|
+
plt.axhline(y=threshold, color='r', linestyle='--', label=f'Threshold (4/n)')
|
|
245
|
+
plt.xlabel('Observation')
|
|
246
|
+
plt.ylabel("Cook's Distance")
|
|
247
|
+
plt.legend()
|
|
248
|
+
plt.show()
|
|
249
|
+
```
|
|
250
|
+
|
|
251
|
+
### DFFITS
|
|
252
|
+
|
|
253
|
+
Measures influence on fitted value.
|
|
254
|
+
|
|
255
|
+
```python
|
|
256
|
+
# DFFITS
|
|
257
|
+
dffits = influence.dffits[0]
|
|
258
|
+
|
|
259
|
+
# Rule of thumb: |DFFITS| > 2*sqrt(p/n) is influential
|
|
260
|
+
p = len(results.params)
|
|
261
|
+
n = len(y)
|
|
262
|
+
threshold = 2 * np.sqrt(p / n)
|
|
263
|
+
|
|
264
|
+
influential_dffits = np.where(np.abs(dffits) > threshold)[0]
|
|
265
|
+
print(f"Influential observations (DFFITS): {influential_dffits}")
|
|
266
|
+
```
|
|
267
|
+
|
|
268
|
+
### DFBETAs
|
|
269
|
+
|
|
270
|
+
Measures influence on each coefficient.
|
|
271
|
+
|
|
272
|
+
```python
|
|
273
|
+
# DFBETAs (one for each parameter)
|
|
274
|
+
dfbetas = influence.dfbetas
|
|
275
|
+
|
|
276
|
+
# Rule of thumb: |DFBETA| > 2/sqrt(n)
|
|
277
|
+
threshold = 2 / np.sqrt(n)
|
|
278
|
+
|
|
279
|
+
for i, param_name in enumerate(results.params.index):
|
|
280
|
+
influential = np.where(np.abs(dfbetas[:, i]) > threshold)[0]
|
|
281
|
+
if len(influential) > 0:
|
|
282
|
+
print(f"Influential for {param_name}: {influential}")
|
|
283
|
+
```
|
|
284
|
+
|
|
285
|
+
### Influence Plot
|
|
286
|
+
|
|
287
|
+
```python
|
|
288
|
+
from statsmodels.graphics.regressionplots import influence_plot
|
|
289
|
+
|
|
290
|
+
fig, ax = plt.subplots(figsize=(12, 8))
|
|
291
|
+
influence_plot(results, ax=ax, criterion='cooks')
|
|
292
|
+
plt.show()
|
|
293
|
+
|
|
294
|
+
# Combines leverage, residuals, and Cook's distance
|
|
295
|
+
# Large bubbles = high Cook's distance
|
|
296
|
+
# Far from x=0 = high leverage
|
|
297
|
+
# Far from y=0 = large residual
|
|
298
|
+
```
|
|
299
|
+
|
|
300
|
+
### Studentized Residuals
|
|
301
|
+
|
|
302
|
+
```python
|
|
303
|
+
# Studentized residuals (outliers)
|
|
304
|
+
student_resid = influence.resid_studentized_internal
|
|
305
|
+
|
|
306
|
+
# External studentized residuals (more conservative)
|
|
307
|
+
student_resid_external = influence.resid_studentized_external
|
|
308
|
+
|
|
309
|
+
# Outliers: |studentized residual| > 3 (or > 2.5)
|
|
310
|
+
outliers = np.where(np.abs(student_resid_external) > 3)[0]
|
|
311
|
+
print(f"Outliers: {outliers}")
|
|
312
|
+
```
|
|
313
|
+
|
|
314
|
+
## Hypothesis Testing
|
|
315
|
+
|
|
316
|
+
### t-tests
|
|
317
|
+
|
|
318
|
+
**One-sample t-test**: Test if mean equals specific value
|
|
319
|
+
|
|
320
|
+
```python
|
|
321
|
+
from scipy import stats
|
|
322
|
+
|
|
323
|
+
# H0: population mean = mu_0
|
|
324
|
+
t_stat, p_value = stats.ttest_1samp(data, popmean=mu_0)
|
|
325
|
+
|
|
326
|
+
print(f"t-statistic: {t_stat:.4f}")
|
|
327
|
+
print(f"p-value: {p_value:.4f}")
|
|
328
|
+
```
|
|
329
|
+
|
|
330
|
+
**Two-sample t-test**: Compare means of two groups
|
|
331
|
+
|
|
332
|
+
```python
|
|
333
|
+
# H0: mean1 = mean2 (equal variances)
|
|
334
|
+
t_stat, p_value = stats.ttest_ind(group1, group2)
|
|
335
|
+
|
|
336
|
+
# Welch's t-test (unequal variances)
|
|
337
|
+
t_stat, p_value = stats.ttest_ind(group1, group2, equal_var=False)
|
|
338
|
+
|
|
339
|
+
print(f"t-statistic: {t_stat:.4f}")
|
|
340
|
+
print(f"p-value: {p_value:.4f}")
|
|
341
|
+
```
|
|
342
|
+
|
|
343
|
+
**Paired t-test**: Compare paired observations
|
|
344
|
+
|
|
345
|
+
```python
|
|
346
|
+
# H0: mean difference = 0
|
|
347
|
+
t_stat, p_value = stats.ttest_rel(before, after)
|
|
348
|
+
|
|
349
|
+
print(f"t-statistic: {t_stat:.4f}")
|
|
350
|
+
print(f"p-value: {p_value:.4f}")
|
|
351
|
+
```
|
|
352
|
+
|
|
353
|
+
### Proportion Tests
|
|
354
|
+
|
|
355
|
+
**One-proportion test**:
|
|
356
|
+
|
|
357
|
+
```python
|
|
358
|
+
from statsmodels.stats.proportion import proportions_ztest
|
|
359
|
+
|
|
360
|
+
# H0: proportion = p0
|
|
361
|
+
count = 45 # successes
|
|
362
|
+
nobs = 100 # total observations
|
|
363
|
+
p0 = 0.5 # hypothesized proportion
|
|
364
|
+
|
|
365
|
+
z_stat, p_value = proportions_ztest(count, nobs, value=p0)
|
|
366
|
+
|
|
367
|
+
print(f"z-statistic: {z_stat:.4f}")
|
|
368
|
+
print(f"p-value: {p_value:.4f}")
|
|
369
|
+
```
|
|
370
|
+
|
|
371
|
+
**Two-proportion test**:
|
|
372
|
+
|
|
373
|
+
```python
|
|
374
|
+
# H0: proportion1 = proportion2
|
|
375
|
+
counts = [45, 60]
|
|
376
|
+
nobs = [100, 120]
|
|
377
|
+
|
|
378
|
+
z_stat, p_value = proportions_ztest(counts, nobs)
|
|
379
|
+
print(f"z-statistic: {z_stat:.4f}")
|
|
380
|
+
print(f"p-value: {p_value:.4f}")
|
|
381
|
+
```
|
|
382
|
+
|
|
383
|
+
### Chi-square Tests
|
|
384
|
+
|
|
385
|
+
**Chi-square test of independence**:
|
|
386
|
+
|
|
387
|
+
```python
|
|
388
|
+
from scipy.stats import chi2_contingency
|
|
389
|
+
|
|
390
|
+
# Contingency table
|
|
391
|
+
contingency_table = pd.crosstab(variable1, variable2)
|
|
392
|
+
|
|
393
|
+
chi2, p_value, dof, expected = chi2_contingency(contingency_table)
|
|
394
|
+
|
|
395
|
+
print(f"Chi-square statistic: {chi2:.4f}")
|
|
396
|
+
print(f"p-value: {p_value:.4f}")
|
|
397
|
+
print(f"Degrees of freedom: {dof}")
|
|
398
|
+
|
|
399
|
+
# H0: Variables are independent
|
|
400
|
+
```
|
|
401
|
+
|
|
402
|
+
**Chi-square goodness-of-fit**:
|
|
403
|
+
|
|
404
|
+
```python
|
|
405
|
+
from scipy.stats import chisquare
|
|
406
|
+
|
|
407
|
+
# Observed frequencies
|
|
408
|
+
observed = [20, 30, 25, 25]
|
|
409
|
+
|
|
410
|
+
# Expected frequencies (equal by default)
|
|
411
|
+
expected = [25, 25, 25, 25]
|
|
412
|
+
|
|
413
|
+
chi2, p_value = chisquare(observed, expected)
|
|
414
|
+
|
|
415
|
+
print(f"Chi-square statistic: {chi2:.4f}")
|
|
416
|
+
print(f"p-value: {p_value:.4f}")
|
|
417
|
+
|
|
418
|
+
# H0: Data follow the expected distribution
|
|
419
|
+
```
|
|
420
|
+
|
|
421
|
+
### Non-parametric Tests
|
|
422
|
+
|
|
423
|
+
**Mann-Whitney U test** (independent samples):
|
|
424
|
+
|
|
425
|
+
```python
|
|
426
|
+
from scipy.stats import mannwhitneyu
|
|
427
|
+
|
|
428
|
+
# H0: Distributions are equal
|
|
429
|
+
u_stat, p_value = mannwhitneyu(group1, group2, alternative='two-sided')
|
|
430
|
+
|
|
431
|
+
print(f"U statistic: {u_stat:.4f}")
|
|
432
|
+
print(f"p-value: {p_value:.4f}")
|
|
433
|
+
```
|
|
434
|
+
|
|
435
|
+
**Wilcoxon signed-rank test** (paired samples):
|
|
436
|
+
|
|
437
|
+
```python
|
|
438
|
+
from scipy.stats import wilcoxon
|
|
439
|
+
|
|
440
|
+
# H0: Median difference = 0
|
|
441
|
+
w_stat, p_value = wilcoxon(before, after)
|
|
442
|
+
|
|
443
|
+
print(f"W statistic: {w_stat:.4f}")
|
|
444
|
+
print(f"p-value: {p_value:.4f}")
|
|
445
|
+
```
|
|
446
|
+
|
|
447
|
+
**Kruskal-Wallis H test** (>2 groups):
|
|
448
|
+
|
|
449
|
+
```python
|
|
450
|
+
from scipy.stats import kruskal
|
|
451
|
+
|
|
452
|
+
# H0: All groups have same distribution
|
|
453
|
+
h_stat, p_value = kruskal(group1, group2, group3)
|
|
454
|
+
|
|
455
|
+
print(f"H statistic: {h_stat:.4f}")
|
|
456
|
+
print(f"p-value: {p_value:.4f}")
|
|
457
|
+
```
|
|
458
|
+
|
|
459
|
+
**Sign test**:
|
|
460
|
+
|
|
461
|
+
```python
|
|
462
|
+
from statsmodels.stats.descriptivestats import sign_test
|
|
463
|
+
|
|
464
|
+
# H0: Median = m0
|
|
465
|
+
result = sign_test(data, m0=0)
|
|
466
|
+
print(result)
|
|
467
|
+
```
|
|
468
|
+
|
|
469
|
+
### ANOVA
|
|
470
|
+
|
|
471
|
+
**One-way ANOVA**:
|
|
472
|
+
|
|
473
|
+
```python
|
|
474
|
+
from scipy.stats import f_oneway
|
|
475
|
+
|
|
476
|
+
# H0: All group means are equal
|
|
477
|
+
f_stat, p_value = f_oneway(group1, group2, group3)
|
|
478
|
+
|
|
479
|
+
print(f"F-statistic: {f_stat:.4f}")
|
|
480
|
+
print(f"p-value: {p_value:.4f}")
|
|
481
|
+
```
|
|
482
|
+
|
|
483
|
+
**Two-way ANOVA** (with statsmodels):
|
|
484
|
+
|
|
485
|
+
```python
|
|
486
|
+
from statsmodels.formula.api import ols
|
|
487
|
+
from statsmodels.stats.anova import anova_lm
|
|
488
|
+
|
|
489
|
+
# Fit model
|
|
490
|
+
model = ols('response ~ C(factor1) + C(factor2) + C(factor1):C(factor2)',
|
|
491
|
+
data=df).fit()
|
|
492
|
+
|
|
493
|
+
# ANOVA table
|
|
494
|
+
anova_table = anova_lm(model, typ=2)
|
|
495
|
+
print(anova_table)
|
|
496
|
+
```
|
|
497
|
+
|
|
498
|
+
**Repeated measures ANOVA**:
|
|
499
|
+
|
|
500
|
+
```python
|
|
501
|
+
from statsmodels.stats.anova import AnovaRM
|
|
502
|
+
|
|
503
|
+
# Requires long-format data
|
|
504
|
+
aovrm = AnovaRM(df, depvar='score', subject='subject_id', within=['time'])
|
|
505
|
+
results = aovrm.fit()
|
|
506
|
+
|
|
507
|
+
print(results.summary())
|
|
508
|
+
```
|
|
509
|
+
|
|
510
|
+
## Multiple Comparisons
|
|
511
|
+
|
|
512
|
+
### Post-hoc Tests
|
|
513
|
+
|
|
514
|
+
**Tukey's HSD** (Honest Significant Difference):
|
|
515
|
+
|
|
516
|
+
```python
|
|
517
|
+
from statsmodels.stats.multicomp import pairwise_tukeyhsd
|
|
518
|
+
|
|
519
|
+
# Perform Tukey HSD test
|
|
520
|
+
tukey = pairwise_tukeyhsd(data, groups, alpha=0.05)
|
|
521
|
+
|
|
522
|
+
print(tukey.summary())
|
|
523
|
+
|
|
524
|
+
# Plot confidence intervals
|
|
525
|
+
tukey.plot_simultaneous()
|
|
526
|
+
plt.show()
|
|
527
|
+
```
|
|
528
|
+
|
|
529
|
+
**Bonferroni correction**:
|
|
530
|
+
|
|
531
|
+
```python
|
|
532
|
+
from statsmodels.stats.multitest import multipletests
|
|
533
|
+
|
|
534
|
+
# P-values from multiple tests
|
|
535
|
+
p_values = [0.01, 0.03, 0.04, 0.15, 0.001]
|
|
536
|
+
|
|
537
|
+
# Apply correction
|
|
538
|
+
reject, pvals_corrected, alphac_sidak, alphac_bonf = multipletests(
|
|
539
|
+
p_values,
|
|
540
|
+
alpha=0.05,
|
|
541
|
+
method='bonferroni'
|
|
542
|
+
)
|
|
543
|
+
|
|
544
|
+
print("Rejected:", reject)
|
|
545
|
+
print("Corrected p-values:", pvals_corrected)
|
|
546
|
+
```
|
|
547
|
+
|
|
548
|
+
**False Discovery Rate (FDR)**:
|
|
549
|
+
|
|
550
|
+
```python
|
|
551
|
+
# FDR correction (less conservative than Bonferroni)
|
|
552
|
+
reject, pvals_corrected, alphac_sidak, alphac_bonf = multipletests(
|
|
553
|
+
p_values,
|
|
554
|
+
alpha=0.05,
|
|
555
|
+
method='fdr_bh' # Benjamini-Hochberg
|
|
556
|
+
)
|
|
557
|
+
|
|
558
|
+
print("Rejected:", reject)
|
|
559
|
+
print("Corrected p-values:", pvals_corrected)
|
|
560
|
+
```
|
|
561
|
+
|
|
562
|
+
## Robust Covariance Matrices
|
|
563
|
+
|
|
564
|
+
### Heteroskedasticity-Consistent (HC) Standard Errors
|
|
565
|
+
|
|
566
|
+
```python
|
|
567
|
+
# After fitting OLS
|
|
568
|
+
results = sm.OLS(y, X).fit()
|
|
569
|
+
|
|
570
|
+
# HC0 (White's heteroskedasticity-consistent SEs)
|
|
571
|
+
results_hc0 = results.get_robustcov_results(cov_type='HC0')
|
|
572
|
+
|
|
573
|
+
# HC1 (degrees of freedom adjustment)
|
|
574
|
+
results_hc1 = results.get_robustcov_results(cov_type='HC1')
|
|
575
|
+
|
|
576
|
+
# HC2 (leverage adjustment)
|
|
577
|
+
results_hc2 = results.get_robustcov_results(cov_type='HC2')
|
|
578
|
+
|
|
579
|
+
# HC3 (most conservative, recommended for small samples)
|
|
580
|
+
results_hc3 = results.get_robustcov_results(cov_type='HC3')
|
|
581
|
+
|
|
582
|
+
print("Standard OLS SEs:", results.bse)
|
|
583
|
+
print("Robust HC3 SEs:", results_hc3.bse)
|
|
584
|
+
```
|
|
585
|
+
|
|
586
|
+
### HAC (Heteroskedasticity and Autocorrelation Consistent)
|
|
587
|
+
|
|
588
|
+
**Newey-West standard errors**:
|
|
589
|
+
|
|
590
|
+
```python
|
|
591
|
+
# For time series with autocorrelation and heteroskedasticity
|
|
592
|
+
results_hac = results.get_robustcov_results(cov_type='HAC', maxlags=4)
|
|
593
|
+
|
|
594
|
+
print("HAC (Newey-West) SEs:", results_hac.bse)
|
|
595
|
+
print(results_hac.summary())
|
|
596
|
+
```
|
|
597
|
+
|
|
598
|
+
### Cluster-Robust Standard Errors
|
|
599
|
+
|
|
600
|
+
```python
|
|
601
|
+
# For clustered/grouped data
|
|
602
|
+
results_cluster = results.get_robustcov_results(
|
|
603
|
+
cov_type='cluster',
|
|
604
|
+
groups=cluster_ids
|
|
605
|
+
)
|
|
606
|
+
|
|
607
|
+
print("Cluster-robust SEs:", results_cluster.bse)
|
|
608
|
+
```
|
|
609
|
+
|
|
610
|
+
## Descriptive Statistics
|
|
611
|
+
|
|
612
|
+
**Basic descriptive statistics**:
|
|
613
|
+
|
|
614
|
+
```python
|
|
615
|
+
from statsmodels.stats.api import DescrStatsW
|
|
616
|
+
|
|
617
|
+
# Comprehensive descriptive stats
|
|
618
|
+
desc = DescrStatsW(data)
|
|
619
|
+
|
|
620
|
+
print("Mean:", desc.mean)
|
|
621
|
+
print("Std Dev:", desc.std)
|
|
622
|
+
print("Variance:", desc.var)
|
|
623
|
+
print("Confidence interval:", desc.tconfint_mean())
|
|
624
|
+
|
|
625
|
+
# Quantiles
|
|
626
|
+
print("Median:", desc.quantile(0.5))
|
|
627
|
+
print("IQR:", desc.quantile([0.25, 0.75]))
|
|
628
|
+
```
|
|
629
|
+
|
|
630
|
+
**Weighted statistics**:
|
|
631
|
+
|
|
632
|
+
```python
|
|
633
|
+
# With weights
|
|
634
|
+
desc_weighted = DescrStatsW(data, weights=weights)
|
|
635
|
+
|
|
636
|
+
print("Weighted mean:", desc_weighted.mean)
|
|
637
|
+
print("Weighted std:", desc_weighted.std)
|
|
638
|
+
```
|
|
639
|
+
|
|
640
|
+
**Compare two groups**:
|
|
641
|
+
|
|
642
|
+
```python
|
|
643
|
+
from statsmodels.stats.weightstats import CompareMeans
|
|
644
|
+
|
|
645
|
+
# Create comparison object
|
|
646
|
+
cm = CompareMeans(DescrStatsW(group1), DescrStatsW(group2))
|
|
647
|
+
|
|
648
|
+
# t-test
|
|
649
|
+
print("t-test:", cm.ttest_ind())
|
|
650
|
+
|
|
651
|
+
# Confidence interval for difference
|
|
652
|
+
print("CI for difference:", cm.tconfint_diff())
|
|
653
|
+
|
|
654
|
+
# Test for equal variances
|
|
655
|
+
print("Equal variance test:", cm.test_equal_var())
|
|
656
|
+
```
|
|
657
|
+
|
|
658
|
+
## Power Analysis and Sample Size
|
|
659
|
+
|
|
660
|
+
**Power for t-test**:
|
|
661
|
+
|
|
662
|
+
```python
|
|
663
|
+
from statsmodels.stats.power import tt_ind_solve_power
|
|
664
|
+
|
|
665
|
+
# Solve for sample size
|
|
666
|
+
effect_size = 0.5 # Cohen's d
|
|
667
|
+
alpha = 0.05
|
|
668
|
+
power = 0.8
|
|
669
|
+
|
|
670
|
+
n = tt_ind_solve_power(effect_size=effect_size,
|
|
671
|
+
alpha=alpha,
|
|
672
|
+
power=power,
|
|
673
|
+
alternative='two-sided')
|
|
674
|
+
|
|
675
|
+
print(f"Required sample size per group: {n:.0f}")
|
|
676
|
+
|
|
677
|
+
# Solve for power given n
|
|
678
|
+
power = tt_ind_solve_power(effect_size=0.5,
|
|
679
|
+
nobs1=50,
|
|
680
|
+
alpha=0.05,
|
|
681
|
+
alternative='two-sided')
|
|
682
|
+
|
|
683
|
+
print(f"Power: {power:.4f}")
|
|
684
|
+
```
|
|
685
|
+
|
|
686
|
+
**Power for proportion test**:
|
|
687
|
+
|
|
688
|
+
```python
|
|
689
|
+
from statsmodels.stats.power import zt_ind_solve_power
|
|
690
|
+
|
|
691
|
+
# For proportion tests (z-test)
|
|
692
|
+
effect_size = 0.3 # Difference in proportions
|
|
693
|
+
alpha = 0.05
|
|
694
|
+
power = 0.8
|
|
695
|
+
|
|
696
|
+
n = zt_ind_solve_power(effect_size=effect_size,
|
|
697
|
+
alpha=alpha,
|
|
698
|
+
power=power,
|
|
699
|
+
alternative='two-sided')
|
|
700
|
+
|
|
701
|
+
print(f"Required sample size per group: {n:.0f}")
|
|
702
|
+
```
|
|
703
|
+
|
|
704
|
+
**Power curves**:
|
|
705
|
+
|
|
706
|
+
```python
|
|
707
|
+
from statsmodels.stats.power import TTestIndPower
|
|
708
|
+
import matplotlib.pyplot as plt
|
|
709
|
+
|
|
710
|
+
# Create power analysis object
|
|
711
|
+
analysis = TTestIndPower()
|
|
712
|
+
|
|
713
|
+
# Plot power curves for different sample sizes
|
|
714
|
+
sample_sizes = range(10, 200, 10)
|
|
715
|
+
effect_sizes = [0.2, 0.5, 0.8] # Small, medium, large
|
|
716
|
+
|
|
717
|
+
fig, ax = plt.subplots(figsize=(10, 6))
|
|
718
|
+
|
|
719
|
+
for es in effect_sizes:
|
|
720
|
+
power = [analysis.solve_power(effect_size=es, nobs1=n, alpha=0.05)
|
|
721
|
+
for n in sample_sizes]
|
|
722
|
+
ax.plot(sample_sizes, power, label=f'Effect size = {es}')
|
|
723
|
+
|
|
724
|
+
ax.axhline(y=0.8, color='r', linestyle='--', label='Power = 0.8')
|
|
725
|
+
ax.set_xlabel('Sample size per group')
|
|
726
|
+
ax.set_ylabel('Power')
|
|
727
|
+
ax.set_title('Power Curves for Two-Sample t-test')
|
|
728
|
+
ax.legend()
|
|
729
|
+
ax.grid(True, alpha=0.3)
|
|
730
|
+
plt.show()
|
|
731
|
+
```
|
|
732
|
+
|
|
733
|
+
## Effect Sizes
|
|
734
|
+
|
|
735
|
+
**Cohen's d** (standardized mean difference):
|
|
736
|
+
|
|
737
|
+
```python
|
|
738
|
+
def cohens_d(group1, group2):
|
|
739
|
+
\"\"\"Calculate Cohen's d for independent samples\"\"\"
|
|
740
|
+
n1, n2 = len(group1), len(group2)
|
|
741
|
+
var1, var2 = np.var(group1, ddof=1), np.var(group2, ddof=1)
|
|
742
|
+
|
|
743
|
+
# Pooled standard deviation
|
|
744
|
+
pooled_std = np.sqrt(((n1-1)*var1 + (n2-1)*var2) / (n1+n2-2))
|
|
745
|
+
|
|
746
|
+
# Cohen's d
|
|
747
|
+
d = (np.mean(group1) - np.mean(group2)) / pooled_std
|
|
748
|
+
|
|
749
|
+
return d
|
|
750
|
+
|
|
751
|
+
d = cohens_d(group1, group2)
|
|
752
|
+
print(f"Cohen's d: {d:.4f}")
|
|
753
|
+
|
|
754
|
+
# Interpretation:
|
|
755
|
+
# |d| < 0.2: negligible
|
|
756
|
+
# |d| ~ 0.2: small
|
|
757
|
+
# |d| ~ 0.5: medium
|
|
758
|
+
# |d| ~ 0.8: large
|
|
759
|
+
```
|
|
760
|
+
|
|
761
|
+
**Eta-squared** (for ANOVA):
|
|
762
|
+
|
|
763
|
+
```python
|
|
764
|
+
# From ANOVA table
|
|
765
|
+
# η² = SS_between / SS_total
|
|
766
|
+
|
|
767
|
+
def eta_squared(anova_table):
|
|
768
|
+
return anova_table['sum_sq'][0] / anova_table['sum_sq'].sum()
|
|
769
|
+
|
|
770
|
+
# After running ANOVA
|
|
771
|
+
eta_sq = eta_squared(anova_table)
|
|
772
|
+
print(f"Eta-squared: {eta_sq:.4f}")
|
|
773
|
+
|
|
774
|
+
# Interpretation:
|
|
775
|
+
# 0.01: small effect
|
|
776
|
+
# 0.06: medium effect
|
|
777
|
+
# 0.14: large effect
|
|
778
|
+
```
|
|
779
|
+
|
|
780
|
+
## Contingency Tables and Association
|
|
781
|
+
|
|
782
|
+
**McNemar's test** (paired binary data):
|
|
783
|
+
|
|
784
|
+
```python
|
|
785
|
+
from statsmodels.stats.contingency_tables import mcnemar
|
|
786
|
+
|
|
787
|
+
# 2x2 contingency table
|
|
788
|
+
table = [[a, b],
|
|
789
|
+
[c, d]]
|
|
790
|
+
|
|
791
|
+
result = mcnemar(table, exact=True) # or exact=False for large samples
|
|
792
|
+
print(f"p-value: {result.pvalue:.4f}")
|
|
793
|
+
|
|
794
|
+
# H0: Marginal probabilities are equal
|
|
795
|
+
```
|
|
796
|
+
|
|
797
|
+
**Cochran-Mantel-Haenszel test**:
|
|
798
|
+
|
|
799
|
+
```python
|
|
800
|
+
from statsmodels.stats.contingency_tables import StratifiedTable
|
|
801
|
+
|
|
802
|
+
# For stratified 2x2 tables
|
|
803
|
+
strat_table = StratifiedTable(tables_list)
|
|
804
|
+
result = strat_table.test_null_odds()
|
|
805
|
+
|
|
806
|
+
print(f"p-value: {result.pvalue:.4f}")
|
|
807
|
+
```
|
|
808
|
+
|
|
809
|
+
## Treatment Effects and Causal Inference
|
|
810
|
+
|
|
811
|
+
**Propensity score matching**:
|
|
812
|
+
|
|
813
|
+
```python
|
|
814
|
+
from statsmodels.treatment import propensity_score
|
|
815
|
+
|
|
816
|
+
# Estimate propensity scores
|
|
817
|
+
ps_model = sm.Logit(treatment, X).fit()
|
|
818
|
+
propensity_scores = ps_model.predict(X)
|
|
819
|
+
|
|
820
|
+
# Use for matching or weighting
|
|
821
|
+
# (manual implementation of matching needed)
|
|
822
|
+
```
|
|
823
|
+
|
|
824
|
+
**Difference-in-differences**:
|
|
825
|
+
|
|
826
|
+
```python
|
|
827
|
+
# Did formula: outcome ~ treatment * post
|
|
828
|
+
model = ols('outcome ~ treatment + post + treatment:post', data=df).fit()
|
|
829
|
+
|
|
830
|
+
# DiD estimate is the interaction coefficient
|
|
831
|
+
did_estimate = model.params['treatment:post']
|
|
832
|
+
print(f"DiD estimate: {did_estimate:.4f}")
|
|
833
|
+
```
|
|
834
|
+
|
|
835
|
+
## Best Practices
|
|
836
|
+
|
|
837
|
+
1. **Always check assumptions**: Test before interpreting results
|
|
838
|
+
2. **Report effect sizes**: Not just p-values
|
|
839
|
+
3. **Use appropriate tests**: Match test to data type and distribution
|
|
840
|
+
4. **Correct for multiple comparisons**: When conducting many tests
|
|
841
|
+
5. **Check sample size**: Ensure adequate power
|
|
842
|
+
6. **Visual inspection**: Plot data before testing
|
|
843
|
+
7. **Report confidence intervals**: Along with point estimates
|
|
844
|
+
8. **Consider alternatives**: Non-parametric when assumptions violated
|
|
845
|
+
9. **Robust standard errors**: Use when heteroskedasticity/autocorrelation present
|
|
846
|
+
10. **Document decisions**: Note which tests used and why
|
|
847
|
+
|
|
848
|
+
## Common Pitfalls
|
|
849
|
+
|
|
850
|
+
1. **Not checking test assumptions**: May invalidate results
|
|
851
|
+
2. **Multiple testing without correction**: Inflated Type I error
|
|
852
|
+
3. **Using parametric tests on non-normal data**: Consider non-parametric
|
|
853
|
+
4. **Ignoring heteroskedasticity**: Use robust SEs
|
|
854
|
+
5. **Confusing statistical and practical significance**: Check effect sizes
|
|
855
|
+
6. **Not reporting confidence intervals**: Only p-values insufficient
|
|
856
|
+
7. **Using wrong test**: Match test to research question
|
|
857
|
+
8. **Insufficient power**: Risk of Type II error (false negatives)
|
|
858
|
+
9. **p-hacking**: Testing many specifications until significant
|
|
859
|
+
10. **Overinterpreting p-values**: Remember limitations of NHST
|