@pikaa-ai/pikaa 0.3.1 → 0.3.4
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/dist/cli.js +1169 -601
- package/dist/index.js +525 -204
- package/package.json +5 -3
- package/skills/adaptyv/references/api-endpoints.md +0 -690
- package/skills/aeon/references/anomaly_detection.md +0 -154
- package/skills/aeon/references/classification.md +0 -144
- package/skills/aeon/references/clustering.md +0 -123
- package/skills/aeon/references/datasets_benchmarking.md +0 -392
- package/skills/aeon/references/distances.md +0 -256
- package/skills/aeon/references/forecasting.md +0 -109
- package/skills/aeon/references/networks.md +0 -289
- package/skills/aeon/references/regression.md +0 -118
- package/skills/aeon/references/segmentation.md +0 -163
- package/skills/aeon/references/similarity_search.md +0 -187
- package/skills/aeon/references/transformations.md +0 -246
- package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
- package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
- package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
- package/skills/analytical-method-validation/references/framework-selection.md +0 -87
- package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
- package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
- package/skills/analytical-method-validation/references/source-ledger.md +0 -125
- package/skills/analytical-method-validation/references/statistics.md +0 -209
- package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
- package/skills/analytical-method-validation/scripts/_common.py +0 -955
- package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
- package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
- package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
- package/skills/analytical-method-validation/scripts/check_response.py +0 -243
- package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
- package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
- package/skills/anndata/references/best_practices.md +0 -532
- package/skills/anndata/references/concatenation.md +0 -399
- package/skills/anndata/references/data_structure.md +0 -314
- package/skills/anndata/references/io_operations.md +0 -466
- package/skills/anndata/references/manipulation.md +0 -516
- package/skills/arbor/references/arbor-upstream.md +0 -91
- package/skills/arbor/references/executor-brief.md +0 -68
- package/skills/arbor/references/htr-methodology.md +0 -177
- package/skills/arbor/references/report-template.md +0 -39
- package/skills/arbor/scripts/tree.py +0 -564
- package/skills/arboreto/references/algorithms.md +0 -152
- package/skills/arboreto/references/basic_inference.md +0 -181
- package/skills/arboreto/references/distributed_computing.md +0 -242
- package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
- package/skills/astropy/references/coordinates.md +0 -280
- package/skills/astropy/references/cosmology.md +0 -309
- package/skills/astropy/references/fits.md +0 -398
- package/skills/astropy/references/tables.md +0 -495
- package/skills/astropy/references/time.md +0 -412
- package/skills/astropy/references/units.md +0 -178
- package/skills/astropy/references/wcs_and_other_modules.md +0 -377
- package/skills/autoskill/config.yaml +0 -53
- package/skills/autoskill/references/https-proxy.md +0 -62
- package/skills/autoskill/references/screenpipe-config.yaml +0 -61
- package/skills/autoskill/scripts/autoskill.py +0 -35
- package/skills/autoskill/scripts/backends.py +0 -116
- package/skills/autoskill/scripts/cluster.py +0 -54
- package/skills/autoskill/scripts/doctor.py +0 -108
- package/skills/autoskill/scripts/fetch_window.py +0 -33
- package/skills/autoskill/scripts/match_skills.py +0 -46
- package/skills/autoskill/scripts/promote.py +0 -58
- package/skills/autoskill/scripts/redact.py +0 -40
- package/skills/autoskill/scripts/run.py +0 -194
- package/skills/autoskill/scripts/synthesize.py +0 -72
- package/skills/benchling-integration/references/api_endpoints.md +0 -883
- package/skills/benchling-integration/references/authentication.md +0 -390
- package/skills/benchling-integration/references/core_capabilities.md +0 -355
- package/skills/benchling-integration/references/eventbridge.md +0 -255
- package/skills/benchling-integration/references/sdk_reference.md +0 -772
- package/skills/bids/references/beps.yml +0 -637
- package/skills/bids/references/bids_schema.json +0 -21015
- package/skills/bids/references/bids_specification.md +0 -165
- package/skills/bids/references/conversion_tools.md +0 -475
- package/skills/bids/references/core_workflows.md +0 -552
- package/skills/bids/references/metadata_fields.md +0 -365
- package/skills/bids/scripts/update_schema.py +0 -89
- package/skills/biopython/references/advanced.md +0 -580
- package/skills/biopython/references/alignment.md +0 -377
- package/skills/biopython/references/blast.md +0 -463
- package/skills/biopython/references/databases.md +0 -492
- package/skills/biopython/references/phylogenetics.md +0 -566
- package/skills/biopython/references/sequence_io.md +0 -289
- package/skills/biopython/references/structure.md +0 -564
- package/skills/bioservices/references/identifier_mapping.md +0 -685
- package/skills/bioservices/references/services_reference.md +0 -638
- package/skills/bioservices/references/workflow_patterns.md +0 -813
- package/skills/bioservices/scripts/batch_id_converter.py +0 -347
- package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
- package/skills/bioservices/scripts/pathway_analysis.py +0 -309
- package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
- package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
- package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
- package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
- package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
- package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
- package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
- package/skills/cellxgene-census/references/census_schema.md +0 -218
- package/skills/cellxgene-census/references/common_patterns.md +0 -368
- package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
- package/skills/cirq/references/building.md +0 -307
- package/skills/cirq/references/experiments.md +0 -572
- package/skills/cirq/references/hardware.md +0 -527
- package/skills/cirq/references/noise.md +0 -514
- package/skills/cirq/references/simulation.md +0 -353
- package/skills/cirq/references/transformation.md +0 -416
- package/skills/citation-management/assets/bibtex_template.bib +0 -264
- package/skills/citation-management/assets/citation_checklist.md +0 -386
- package/skills/citation-management/references/best_practices.md +0 -91
- package/skills/citation-management/references/bibtex_formatting.md +0 -908
- package/skills/citation-management/references/citation_validation.md +0 -835
- package/skills/citation-management/references/core_workflow.md +0 -569
- package/skills/citation-management/references/example_workflows.md +0 -126
- package/skills/citation-management/references/google_scholar_search.md +0 -732
- package/skills/citation-management/references/metadata_extraction.md +0 -870
- package/skills/citation-management/references/pubmed_search.md +0 -839
- package/skills/citation-management/references/script_reference.md +0 -250
- package/skills/citation-management/references/search_strategies.md +0 -110
- package/skills/citation-management/scripts/_common.py +0 -331
- package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
- package/skills/citation-management/scripts/extract_metadata.py +0 -690
- package/skills/citation-management/scripts/format_bibtex.py +0 -356
- package/skills/citation-management/scripts/search_google_scholar.py +0 -268
- package/skills/citation-management/scripts/search_openalex.py +0 -297
- package/skills/citation-management/scripts/search_pubmed.py +0 -419
- package/skills/citation-management/scripts/validate_citations.py +0 -688
- package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
- package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
- package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
- package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
- package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
- package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
- package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
- package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
- package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
- package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
- package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
- package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
- package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
- package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
- package/skills/clinical-decision-support/references/security_validation.md +0 -60
- package/skills/clinical-decision-support/references/sources.md +0 -119
- package/skills/clinical-decision-support/references/study_reporting.md +0 -134
- package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
- package/skills/clinical-decision-support/scripts/_common.py +0 -223
- package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
- package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
- package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
- package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
- package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
- package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
- package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
- package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
- package/skills/clinical-reports/assets/case_report_template.json +0 -43
- package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
- package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
- package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
- package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
- package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
- package/skills/clinical-reports/assets/lab_report_template.json +0 -36
- package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
- package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
- package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
- package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
- package/skills/clinical-reports/assets/research_summary_template.json +0 -36
- package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
- package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
- package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
- package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
- package/skills/clinical-reports/references/data_presentation.md +0 -92
- package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
- package/skills/clinical-reports/references/medical_terminology.md +0 -84
- package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
- package/skills/clinical-reports/references/professional_review.md +0 -78
- package/skills/clinical-reports/references/report_type_routing.md +0 -57
- package/skills/clinical-reports/references/safety_reporting.md +0 -109
- package/skills/clinical-reports/references/sources.md +0 -75
- package/skills/clinical-reports/scripts/_common.py +0 -263
- package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
- package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
- package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
- package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
- package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
- package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
- package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
- package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
- package/skills/cobrapy/references/api_quick_reference.md +0 -665
- package/skills/cobrapy/references/workflows.md +0 -600
- package/skills/consciousness-council/references/advanced-configurations.md +0 -96
- package/skills/dask/references/arrays.md +0 -495
- package/skills/dask/references/bags.md +0 -468
- package/skills/dask/references/best-practices.md +0 -277
- package/skills/dask/references/dataframes.md +0 -370
- package/skills/dask/references/futures.md +0 -541
- package/skills/dask/references/schedulers.md +0 -517
- package/skills/database-lookup/references/addgene.md +0 -38
- package/skills/database-lookup/references/alphafold.md +0 -52
- package/skills/database-lookup/references/alphavantage.md +0 -261
- package/skills/database-lookup/references/bea.md +0 -409
- package/skills/database-lookup/references/bindingdb.md +0 -85
- package/skills/database-lookup/references/biogrid.md +0 -110
- package/skills/database-lookup/references/bls.md +0 -235
- package/skills/database-lookup/references/brenda.md +0 -71
- package/skills/database-lookup/references/cbioportal.md +0 -206
- package/skills/database-lookup/references/census.md +0 -251
- package/skills/database-lookup/references/chebi.md +0 -103
- package/skills/database-lookup/references/chembl.md +0 -80
- package/skills/database-lookup/references/clinicaltrials.md +0 -86
- package/skills/database-lookup/references/clinpgx.md +0 -64
- package/skills/database-lookup/references/clinvar.md +0 -91
- package/skills/database-lookup/references/cod.md +0 -121
- package/skills/database-lookup/references/cosmic.md +0 -59
- package/skills/database-lookup/references/dailymed.md +0 -65
- package/skills/database-lookup/references/database_selection_guide.md +0 -166
- package/skills/database-lookup/references/datacommons.md +0 -237
- package/skills/database-lookup/references/dbsnp.md +0 -143
- package/skills/database-lookup/references/disgenet.md +0 -52
- package/skills/database-lookup/references/drugbank.md +0 -54
- package/skills/database-lookup/references/ecb.md +0 -191
- package/skills/database-lookup/references/emdb.md +0 -37
- package/skills/database-lookup/references/ena.md +0 -372
- package/skills/database-lookup/references/encode.md +0 -47
- package/skills/database-lookup/references/ensembl.md +0 -539
- package/skills/database-lookup/references/epa.md +0 -232
- package/skills/database-lookup/references/eurostat.md +0 -237
- package/skills/database-lookup/references/fda.md +0 -64
- package/skills/database-lookup/references/federal-reserve.md +0 -216
- package/skills/database-lookup/references/fred.md +0 -297
- package/skills/database-lookup/references/gene-ontology.md +0 -147
- package/skills/database-lookup/references/geo.md +0 -130
- package/skills/database-lookup/references/gnomad.md +0 -93
- package/skills/database-lookup/references/gtex.md +0 -136
- package/skills/database-lookup/references/gwas-catalog.md +0 -46
- package/skills/database-lookup/references/hca.md +0 -35
- package/skills/database-lookup/references/hpo.md +0 -48
- package/skills/database-lookup/references/human-protein-atlas.md +0 -57
- package/skills/database-lookup/references/interpro.md +0 -120
- package/skills/database-lookup/references/jaspar.md +0 -50
- package/skills/database-lookup/references/kegg.md +0 -78
- package/skills/database-lookup/references/lincs-l1000.md +0 -68
- package/skills/database-lookup/references/materials-project.md +0 -123
- package/skills/database-lookup/references/metabolomics-workbench.md +0 -98
- package/skills/database-lookup/references/monarch.md +0 -46
- package/skills/database-lookup/references/mousemine.md +0 -40
- package/skills/database-lookup/references/nasa-exoplanet-archive.md +0 -112
- package/skills/database-lookup/references/nasa.md +0 -121
- package/skills/database-lookup/references/ncbi-gene.md +0 -64
- package/skills/database-lookup/references/ncbi-protein.md +0 -104
- package/skills/database-lookup/references/ncbi-taxonomy.md +0 -121
- package/skills/database-lookup/references/nist.md +0 -105
- package/skills/database-lookup/references/noaa.md +0 -199
- package/skills/database-lookup/references/omim.md +0 -114
- package/skills/database-lookup/references/opentargets.md +0 -459
- package/skills/database-lookup/references/openweathermap.md +0 -255
- package/skills/database-lookup/references/pdb.md +0 -121
- package/skills/database-lookup/references/pride.md +0 -74
- package/skills/database-lookup/references/pubchem.md +0 -145
- package/skills/database-lookup/references/quickgo.md +0 -45
- package/skills/database-lookup/references/reactome.md +0 -140
- package/skills/database-lookup/references/retrieval-contract.md +0 -123
- package/skills/database-lookup/references/rummageo.md +0 -32
- package/skills/database-lookup/references/sdss.md +0 -130
- package/skills/database-lookup/references/sec-edgar.md +0 -315
- package/skills/database-lookup/references/simbad.md +0 -405
- package/skills/database-lookup/references/sra.md +0 -149
- package/skills/database-lookup/references/string.md +0 -283
- package/skills/database-lookup/references/tcga-gdc.md +0 -58
- package/skills/database-lookup/references/treasury.md +0 -215
- package/skills/database-lookup/references/ucsc-genome.md +0 -135
- package/skills/database-lookup/references/uniprot.md +0 -283
- package/skills/database-lookup/references/usgs.md +0 -260
- package/skills/database-lookup/references/uspto.md +0 -130
- package/skills/database-lookup/references/who.md +0 -283
- package/skills/database-lookup/references/worldbank.md +0 -239
- package/skills/database-lookup/references/zinc.md +0 -202
- package/skills/datamol/references/conformers_module.md +0 -131
- package/skills/datamol/references/core_api.md +0 -136
- package/skills/datamol/references/core_workflows.md +0 -451
- package/skills/datamol/references/descriptors_viz.md +0 -195
- package/skills/datamol/references/fragments_scaffolds.md +0 -174
- package/skills/datamol/references/io_module.md +0 -112
- package/skills/datamol/references/reactions_data.md +0 -218
- package/skills/datamol/references/workflow_patterns.md +0 -104
- package/skills/deepchem/references/api_reference.md +0 -305
- package/skills/deepchem/references/core_capabilities.md +0 -276
- package/skills/deepchem/references/typical_workflows.md +0 -109
- package/skills/deepchem/references/workflows.md +0 -491
- package/skills/deepchem/scripts/graph_neural_network.py +0 -350
- package/skills/deepchem/scripts/predict_solubility.py +0 -223
- package/skills/deepchem/scripts/transfer_learning.py +0 -443
- package/skills/deepspot-m/references/api.md +0 -186
- package/skills/deepspot-m/references/whole_slide.md +0 -174
- package/skills/deeptools/assets/quick_reference.md +0 -65
- package/skills/deeptools/references/core_workflows.md +0 -134
- package/skills/deeptools/references/effective_genome_sizes.md +0 -118
- package/skills/deeptools/references/normalization_methods.md +0 -424
- package/skills/deeptools/references/tools_reference.md +0 -569
- package/skills/deeptools/references/workflows.md +0 -476
- package/skills/deeptools/scripts/validate_files.py +0 -195
- package/skills/deeptools/scripts/workflow_generator.py +0 -520
- package/skills/depmap/references/dependency_analysis.md +0 -178
- package/skills/dhdna-profiler/references/advanced-profiling.md +0 -72
- package/skills/diffdock/assets/batch_template.csv +0 -4
- package/skills/diffdock/assets/custom_inference_config.yaml +0 -94
- package/skills/diffdock/references/confidence_and_limitations.md +0 -182
- package/skills/diffdock/references/parameters_reference.md +0 -173
- package/skills/diffdock/references/workflows_examples.md +0 -401
- package/skills/diffdock/scripts/analyze_results.py +0 -346
- package/skills/diffdock/scripts/prepare_batch_csv.py +0 -257
- package/skills/diffdock/scripts/setup_check.py +0 -283
- package/skills/dnanexus-integration/references/app-development.md +0 -371
- package/skills/dnanexus-integration/references/authentication.md +0 -226
- package/skills/dnanexus-integration/references/configuration.md +0 -444
- package/skills/dnanexus-integration/references/data-operations.md +0 -474
- package/skills/dnanexus-integration/references/job-execution.md +0 -482
- package/skills/dnanexus-integration/references/operations-and-troubleshooting.md +0 -506
- package/skills/dnanexus-integration/references/python-sdk.md +0 -548
- package/skills/dnanexus-integration/references/sources.md +0 -168
- package/skills/dnanexus-integration/references/workflow-languages.md +0 -292
- package/skills/dnanexus-integration/scripts/inspect_dxpy.py +0 -366
- package/skills/dnanexus-integration/scripts/validate_dxapp.py +0 -796
- package/skills/docx/LICENSE.txt +0 -30
- package/skills/docx/scripts/__init__.py +0 -1
- package/skills/docx/scripts/accept_changes.py +0 -135
- package/skills/docx/scripts/comment.py +0 -368
- package/skills/docx/scripts/merge_runs.py +0 -310
- package/skills/docx/scripts/office/helpers/__init__.py +0 -111
- package/skills/docx/scripts/office/helpers/pptx_chart.py +0 -170
- package/skills/docx/scripts/office/helpers/pptx_slide.py +0 -60
- package/skills/docx/scripts/office/helpers/pptx_theme.py +0 -114
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -1499
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -146
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -1085
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -11
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -3081
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -23
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -185
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -287
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -1676
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -28
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -144
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -174
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -25
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -18
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -59
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -56
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -195
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -582
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -25
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -4439
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -570
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -509
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -12
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -108
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -96
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -3646
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -116
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -42
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -50
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -49
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -33
- package/skills/docx/scripts/office/schemas/mce/mc.xsd +0 -75
- package/skills/docx/scripts/office/schemas/microsoft/wml-2010.xsd +0 -560
- package/skills/docx/scripts/office/schemas/microsoft/wml-2012.xsd +0 -67
- package/skills/docx/scripts/office/schemas/microsoft/wml-2018.xsd +0 -14
- package/skills/docx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +0 -20
- package/skills/docx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
- package/skills/docx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
- package/skills/docx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
- package/skills/docx/scripts/office/soffice.py +0 -232
- package/skills/docx/scripts/office/validate.py +0 -173
- package/skills/docx/scripts/office/validators/__init__.py +0 -15
- package/skills/docx/scripts/office/validators/base.py +0 -875
- package/skills/docx/scripts/office/validators/docx.py +0 -466
- package/skills/docx/scripts/office/validators/pptx.py +0 -441
- package/skills/docx/scripts/office/validators/redlining.py +0 -299
- package/skills/docx/scripts/templates/comments.xml +0 -3
- package/skills/docx/scripts/templates/commentsExtended.xml +0 -3
- package/skills/docx/scripts/templates/commentsExtensible.xml +0 -3
- package/skills/docx/scripts/templates/commentsIds.xml +0 -3
- package/skills/docx/scripts/templates/people.xml +0 -3
- package/skills/esm/references/biohub-platform.md +0 -111
- package/skills/esm/references/esm-c-api.md +0 -609
- package/skills/esm/references/esm3-api.md +0 -462
- package/skills/esm/references/forge-api.md +0 -675
- package/skills/esm/references/workflows.md +0 -685
- package/skills/etetoolkit/references/api_reference.md +0 -546
- package/skills/etetoolkit/references/migration-ete3-to-ete4.md +0 -579
- package/skills/etetoolkit/references/taxonomy.md +0 -362
- package/skills/etetoolkit/references/visualization.md +0 -516
- package/skills/etetoolkit/references/workflows.md +0 -537
- package/skills/etetoolkit/scripts/quick_visualize.py +0 -455
- package/skills/etetoolkit/scripts/tree_operations.py +0 -446
- package/skills/exa-search/references/web-extract.md +0 -53
- package/skills/exa-search/references/web-search.md +0 -119
- package/skills/exa-search/scripts/exa_extract.py +0 -117
- package/skills/exa-search/scripts/exa_search.py +0 -179
- package/skills/experimental-design/references/design_types.md +0 -129
- package/skills/experimental-design/references/factorial_and_doe.md +0 -130
- package/skills/experimental-design/references/randomization_and_blocking.md +0 -116
- package/skills/experimental-design/references/sequential_and_adaptive.md +0 -97
- package/skills/experimental-design/scripts/doe_designs.py +0 -183
- package/skills/experimental-design/scripts/randomization.py +0 -171
- package/skills/exploratory-data-analysis/assets/report_template.md +0 -202
- package/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +0 -192
- package/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +0 -183
- package/skills/exploratory-data-analysis/references/general_scientific_formats.md +0 -259
- package/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +0 -189
- package/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +0 -217
- package/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +0 -191
- package/skills/exploratory-data-analysis/scripts/__init__.py +0 -1
- package/skills/exploratory-data-analysis/scripts/_capabilities.py +0 -576
- package/skills/exploratory-data-analysis/scripts/_common.py +0 -460
- package/skills/exploratory-data-analysis/scripts/_structured.py +0 -391
- package/skills/exploratory-data-analysis/scripts/_tabular.py +0 -905
- package/skills/exploratory-data-analysis/scripts/capability_manifest.py +0 -184
- package/skills/exploratory-data-analysis/scripts/distribution_sensitivity.py +0 -117
- package/skills/exploratory-data-analysis/scripts/eda_analyzer.py +0 -345
- package/skills/exploratory-data-analysis/scripts/image_inspector.py +0 -214
- package/skills/exploratory-data-analysis/scripts/missingness_leakage_audit.py +0 -130
- package/skills/exploratory-data-analysis/scripts/report_scaffold.py +0 -143
- package/skills/exploratory-data-analysis/scripts/sequence_inspector.py +0 -255
- package/skills/exploratory-data-analysis/scripts/tabular_profile.py +0 -109
- package/skills/flowio/references/api_reference.md +0 -355
- package/skills/flowio/references/fcs_semantics.md +0 -315
- package/skills/flowio/references/sources.md +0 -89
- package/skills/flowio/references/troubleshooting.md +0 -399
- package/skills/flowio/references/workflows.md +0 -368
- package/skills/flowio/scripts/inspect_fcs.py +0 -439
- package/skills/fluidsim/references/advanced_features.md +0 -347
- package/skills/fluidsim/references/installation.md +0 -263
- package/skills/fluidsim/references/output_analysis.md +0 -314
- package/skills/fluidsim/references/parameters.md +0 -322
- package/skills/fluidsim/references/simulation_workflow.md +0 -329
- package/skills/fluidsim/references/solvers.md +0 -191
- package/skills/fluidsim/scripts/__init__.py +0 -1
- package/skills/fluidsim/scripts/_common.py +0 -491
- package/skills/fluidsim/scripts/_schema.py +0 -872
- package/skills/fluidsim/scripts/budget_summary.py +0 -396
- package/skills/fluidsim/scripts/grid_resource_estimator.py +0 -286
- package/skills/fluidsim/scripts/output_inventory.py +0 -353
- package/skills/fluidsim/scripts/restart_compatibility.py +0 -424
- package/skills/fluidsim/scripts/simulation_dry_run.py +0 -246
- package/skills/fluidsim/scripts/solver_config_validator.py +0 -70
- package/skills/generate-image/references/models.md +0 -173
- package/skills/generate-image/scripts/generate_image.py +0 -752
- package/skills/geniml/references/bedspace.md +0 -267
- package/skills/geniml/references/consensus_peaks.md +0 -334
- package/skills/geniml/references/region2vec.md +0 -289
- package/skills/geniml/references/scembed.md +0 -307
- package/skills/geniml/references/utilities.md +0 -385
- package/skills/geniml/scripts/__init__.py +0 -1
- package/skills/geniml/scripts/_common.py +0 -399
- package/skills/geniml/scripts/bed_validator.py +0 -363
- package/skills/geniml/scripts/consensus_plan.py +0 -416
- package/skills/geniml/scripts/corpus_auditor.py +0 -304
- package/skills/geniml/scripts/embedding_plan.py +0 -476
- package/skills/geniml/scripts/model_artifact_inspector.py +0 -358
- package/skills/geniml/scripts/tokenizer_compatibility.py +0 -321
- package/skills/genomic-coordinates/references/format-conventions.md +0 -205
- package/skills/genomic-coordinates/references/reference-builds.md +0 -154
- package/skills/genomic-coordinates/references/transcript-coordinates.md +0 -141
- package/skills/genomic-coordinates/references/variant-representation.md +0 -155
- package/skills/genomic-coordinates/scripts/_common.py +0 -335
- package/skills/genomic-coordinates/scripts/audit_intervals.py +0 -511
- package/skills/genomic-coordinates/scripts/check_contigs.py +0 -382
- package/skills/genomic-coordinates/scripts/convert_coords.py +0 -180
- package/skills/genomic-coordinates/scripts/normalize_variant.py +0 -290
- package/skills/genomic-intelligence/references/api-and-auth.md +0 -45
- package/skills/genomic-intelligence/references/mcp.md +0 -94
- package/skills/genomic-intelligence/references/sequence-acquisition.md +0 -52
- package/skills/genomic-intelligence/references/tasks.md +0 -75
- package/skills/geomaster/references/advanced-gis.md +0 -376
- package/skills/geomaster/references/big-data.md +0 -363
- package/skills/geomaster/references/code-examples.md +0 -531
- package/skills/geomaster/references/coordinate-systems.md +0 -364
- package/skills/geomaster/references/core-libraries.md +0 -273
- package/skills/geomaster/references/data-sources.md +0 -330
- package/skills/geomaster/references/gis-software.md +0 -369
- package/skills/geomaster/references/industry-applications.md +0 -420
- package/skills/geomaster/references/machine-learning.md +0 -462
- package/skills/geomaster/references/programming-languages.md +0 -456
- package/skills/geomaster/references/remote-sensing.md +0 -370
- package/skills/geomaster/references/scientific-domains.md +0 -416
- package/skills/geomaster/references/specialized-topics.md +0 -428
- package/skills/geomaster/references/troubleshooting.md +0 -439
- package/skills/geopandas/references/crs-management.md +0 -231
- package/skills/geopandas/references/data-io.md +0 -323
- package/skills/geopandas/references/data-structures.md +0 -207
- package/skills/geopandas/references/geometric-operations.md +0 -262
- package/skills/geopandas/references/spatial-analysis.md +0 -294
- package/skills/geopandas/references/visualization.md +0 -230
- package/skills/geopandas/scripts/_common.py +0 -605
- package/skills/geopandas/scripts/crs_reprojection_plan.py +0 -210
- package/skills/geopandas/scripts/export_plan.py +0 -305
- package/skills/geopandas/scripts/geometry_validity_report.py +0 -227
- package/skills/geopandas/scripts/sensitive_coordinates_checklist.py +0 -230
- package/skills/geopandas/scripts/spatial_join_audit.py +0 -368
- package/skills/geopandas/scripts/vector_inventory.py +0 -140
- package/skills/get-available-resources/references/resource_semantics.md +0 -206
- package/skills/get-available-resources/references/snapshot_schema.md +0 -172
- package/skills/get-available-resources/references/sources.md +0 -124
- package/skills/get-available-resources/scripts/_common.py +0 -190
- package/skills/get-available-resources/scripts/accelerator_diagnostics.py +0 -151
- package/skills/get-available-resources/scripts/detect_resources.py +0 -1767
- package/skills/get-available-resources/scripts/plan_workload.py +0 -311
- package/skills/get-available-resources/scripts/snapshot_tools.py +0 -486
- package/skills/gget/references/common_workflows.md +0 -120
- package/skills/gget/references/database_info.md +0 -336
- package/skills/gget/references/module_catalog.md +0 -733
- package/skills/gget/references/module_reference.md +0 -526
- package/skills/gget/references/workflows.md +0 -815
- package/skills/gget/scripts/batch_sequence_analysis.py +0 -192
- package/skills/gget/scripts/enrichment_pipeline.py +0 -235
- package/skills/gget/scripts/gene_analysis.py +0 -175
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-hibit.md +0 -53
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md +0 -85
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md +0 -71
- package/skills/ginkgo-cloud-lab/references/cfps-expression-purification-quantification.md +0 -60
- package/skills/ginkgo-cloud-lab/references/cfps-strep-purification-thermal-shift.md +0 -63
- package/skills/ginkgo-cloud-lab/references/cfps-strep-tag-purification-a280.md +0 -55
- package/skills/ginkgo-cloud-lab/references/echo-ms-cfps-detection.md +0 -49
- package/skills/ginkgo-cloud-lab/references/echo-ms-method-onboarding.md +0 -56
- package/skills/ginkgo-cloud-lab/references/ecoli-expression-purification-quantification.md +0 -49
- package/skills/ginkgo-cloud-lab/references/ecoli-minibinder-expression-histag-a280.md +0 -62
- package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-hibit.md +0 -44
- package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-histag-a280.md +0 -47
- package/skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md +0 -73
- package/skills/ginkgo-cloud-lab/references/ivt-rna-synthesis-qpcr.md +0 -67
- package/skills/ginkgo-cloud-lab/references/minibinder-strep-tag-a280.md +0 -58
- package/skills/ginkgo-cloud-lab/references/pichia-protein-expression-labchip.md +0 -43
- package/skills/ginkgo-cloud-lab/references/spr-target-onboarding.md +0 -58
- package/skills/glycoengineering/references/glycan_databases.md +0 -165
- package/skills/gtars/references/cli.md +0 -334
- package/skills/gtars/references/coverage.md +0 -224
- package/skills/gtars/references/overlap.md +0 -220
- package/skills/gtars/references/python-api.md +0 -280
- package/skills/gtars/references/refget.md +0 -318
- package/skills/gtars/references/tokenizers.md +0 -256
- package/skills/gtars/scripts/__init__.py +0 -1
- package/skills/gtars/scripts/_common.py +0 -461
- package/skills/gtars/scripts/artifact_inspector.py +0 -328
- package/skills/gtars/scripts/bed_validator.py +0 -183
- package/skills/gtars/scripts/coverage_preflight.py +0 -256
- package/skills/gtars/scripts/execution_plan.py +0 -365
- package/skills/gtars/scripts/refget_digest_plan.py +0 -311
- package/skills/gtars/scripts/tokenizer_manifest.py +0 -238
- package/skills/histolab/references/core_capabilities.md +0 -305
- package/skills/histolab/references/filters_preprocessing.md +0 -537
- package/skills/histolab/references/slide_management.md +0 -184
- package/skills/histolab/references/tile_extraction.md +0 -421
- package/skills/histolab/references/tissue_masks.md +0 -251
- package/skills/histolab/references/typical_workflows.md +0 -196
- package/skills/histolab/references/visualization.md +0 -548
- package/skills/hugging-science/references/flagship-resources.md +0 -81
- package/skills/hugging-science/references/topics-and-slugs.md +0 -82
- package/skills/hugging-science/references/using-datasets.md +0 -107
- package/skills/hugging-science/references/using-models.md +0 -122
- package/skills/hugging-science/references/using-spaces.md +0 -119
- package/skills/hugging-science/scripts/fetch_catalog.py +0 -358
- package/skills/hypogenic/assets/dataset_manifest.example.json +0 -30
- package/skills/hypogenic/assets/result.example.json +0 -18
- package/skills/hypogenic/assets/run_config.example.json +0 -46
- package/skills/hypogenic/assets/task_config.example.yaml +0 -38
- package/skills/hypogenic/references/configuration.md +0 -136
- package/skills/hypogenic/references/datasets.md +0 -146
- package/skills/hypogenic/references/evaluation.md +0 -155
- package/skills/hypogenic/references/security.md +0 -167
- package/skills/hypogenic/references/sources.md +0 -113
- package/skills/hypogenic/references/upstream.md +0 -188
- package/skills/hypogenic/scripts/__init__.py +0 -1
- package/skills/hypogenic/scripts/_common.py +0 -1312
- package/skills/hypogenic/scripts/audit_dataset.py +0 -410
- package/skills/hypogenic/scripts/evaluate_local.py +0 -250
- package/skills/hypogenic/scripts/inspect_outputs.py +0 -166
- package/skills/hypogenic/scripts/plan_run.py +0 -247
- package/skills/hypogenic/scripts/validate_config.py +0 -192
- package/skills/hypothesis-generation/assets/evidence_ledger_template.csv +0 -2
- package/skills/hypothesis-generation/assets/falsification_controls_template.json +0 -116
- package/skills/hypothesis-generation/assets/hypothesis_record_template.json +0 -331
- package/skills/hypothesis-generation/assets/operationalization_template.json +0 -56
- package/skills/hypothesis-generation/assets/prediction_rival_matrix_template.csv +0 -3
- package/skills/hypothesis-generation/assets/preregistration_scaffold_template.md +0 -137
- package/skills/hypothesis-generation/assets/search_boundary_template.json +0 -23
- package/skills/hypothesis-generation/assets/source_ledger.csv +0 -37
- package/skills/hypothesis-generation/references/causal_inference_and_claims.md +0 -190
- package/skills/hypothesis-generation/references/concepts_and_workflow.md +0 -173
- package/skills/hypothesis-generation/references/ethics_safety_and_ai.md +0 -216
- package/skills/hypothesis-generation/references/experimental_design_patterns.md +0 -301
- package/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +0 -203
- package/skills/hypothesis-generation/references/literature_search_strategies.md +0 -208
- package/skills/hypothesis-generation/references/preregistration_and_open_science.md +0 -205
- package/skills/hypothesis-generation/references/security_validation.md +0 -74
- package/skills/hypothesis-generation/references/source_ledger.md +0 -116
- package/skills/hypothesis-generation/references/tool_reference.md +0 -246
- package/skills/hypothesis-generation/scripts/_common.py +0 -412
- package/skills/hypothesis-generation/scripts/audit_evidence_ledger.py +0 -337
- package/skills/hypothesis-generation/scripts/check_falsification_controls.py +0 -455
- package/skills/hypothesis-generation/scripts/check_operationalization.py +0 -237
- package/skills/hypothesis-generation/scripts/generate_preregistration_scaffold.py +0 -384
- package/skills/hypothesis-generation/scripts/lint_causal_claims.py +0 -189
- package/skills/hypothesis-generation/scripts/validate_hypothesis_schema.py +0 -1078
- package/skills/hypothesis-generation/scripts/validate_prediction_matrix.py +0 -286
- package/skills/imaging-data-commons/references/bigquery_guide.md +0 -858
- package/skills/imaging-data-commons/references/cli_guide.md +0 -287
- package/skills/imaging-data-commons/references/clinical_data_guide.md +0 -328
- package/skills/imaging-data-commons/references/cloud_storage_guide.md +0 -333
- package/skills/imaging-data-commons/references/dicomweb_guide.md +0 -399
- package/skills/imaging-data-commons/references/digital_pathology_guide.md +0 -403
- package/skills/imaging-data-commons/references/index_tables_guide.md +0 -203
- package/skills/imaging-data-commons/references/licensing_and_citation.md +0 -230
- package/skills/imaging-data-commons/references/mcp_guide.md +0 -181
- package/skills/imaging-data-commons/references/parquet_access_guide.md +0 -200
- package/skills/imaging-data-commons/references/rest_api_guide.md +0 -612
- package/skills/imaging-data-commons/references/sql_patterns.md +0 -462
- package/skills/imaging-data-commons/references/use_cases.md +0 -277
- package/skills/imaging-data-commons/scripts/check_version.py +0 -132
- package/skills/infographics/references/color_palettes.md +0 -496
- package/skills/infographics/references/design_principles.md +0 -636
- package/skills/infographics/references/infographic_type_catalog.md +0 -158
- package/skills/infographics/references/infographic_types.md +0 -907
- package/skills/infographics/references/iterative_refinement.md +0 -119
- package/skills/infographics/scripts/generate_infographic.py +0 -291
- package/skills/infographics/scripts/generate_infographic_ai.py +0 -1446
- package/skills/iso-standards-readiness/assets/templates/capa-record-template.json +0 -99
- package/skills/iso-standards-readiness/assets/templates/document-register-template.json +0 -75
- package/skills/iso-standards-readiness/assets/templates/evidence-manifest-template.json +0 -65
- package/skills/iso-standards-readiness/assets/templates/laboratory-scope-intake-template.json +0 -111
- package/skills/iso-standards-readiness/assets/templates/medical-laboratory-scope-intake-template.json +0 -111
- package/skills/iso-standards-readiness/assets/templates/procedures/CAPA-procedure-template.md +0 -148
- package/skills/iso-standards-readiness/assets/templates/procedures/document-control-procedure-template.md +0 -132
- package/skills/iso-standards-readiness/assets/templates/qmsr-transition-template.json +0 -181
- package/skills/iso-standards-readiness/assets/templates/quality-manual-template.md +0 -182
- package/skills/iso-standards-readiness/assets/templates/scope-intake-template.json +0 -109
- package/skills/iso-standards-readiness/assets/templates/supplier-controls-template.json +0 -119
- package/skills/iso-standards-readiness/assets/templates/traceability-matrix-template.json +0 -154
- package/skills/iso-standards-readiness/references/assurance-lanes.md +0 -116
- package/skills/iso-standards-readiness/references/evidence-architecture.md +0 -282
- package/skills/iso-standards-readiness/references/gap-analysis-checklist.md +0 -346
- package/skills/iso-standards-readiness/references/iso-13485.md +0 -236
- package/skills/iso-standards-readiness/references/iso-14971.md +0 -172
- package/skills/iso-standards-readiness/references/iso-15189.md +0 -219
- package/skills/iso-standards-readiness/references/iso-17025.md +0 -208
- package/skills/iso-standards-readiness/references/quality-manual-guide.md +0 -282
- package/skills/iso-standards-readiness/references/source-ledger.md +0 -357
- package/skills/iso-standards-readiness/scripts/_catalog.py +0 -248
- package/skills/iso-standards-readiness/scripts/_common.py +0 -558
- package/skills/iso-standards-readiness/scripts/audit_document_records.py +0 -148
- package/skills/iso-standards-readiness/scripts/check_capa.py +0 -240
- package/skills/iso-standards-readiness/scripts/check_qmsr_transition.py +0 -164
- package/skills/iso-standards-readiness/scripts/check_supplier_controls.py +0 -166
- package/skills/iso-standards-readiness/scripts/check_traceability.py +0 -171
- package/skills/iso-standards-readiness/scripts/gap_analyzer.py +0 -167
- package/skills/iso-standards-readiness/scripts/validate_evidence_manifest.py +0 -246
- package/skills/iso-standards-readiness/scripts/validate_scope_intake.py +0 -209
- package/skills/lab-hardware-cad/assets/standards.json +0 -198
- package/skills/lab-hardware-cad/references/behavior-rigs.md +0 -136
- package/skills/lab-hardware-cad/references/build123d-patterns.md +0 -363
- package/skills/lab-hardware-cad/references/fabrication-limits.md +0 -156
- package/skills/lab-hardware-cad/references/labware-adapters.md +0 -190
- package/skills/lab-hardware-cad/references/microfluidics.md +0 -157
- package/skills/lab-hardware-cad/references/optomechanics.md +0 -148
- package/skills/lab-hardware-cad/references/validation.md +0 -132
- package/skills/lab-hardware-cad/scripts/_common.py +0 -650
- package/skills/lab-hardware-cad/scripts/check.py +0 -645
- package/skills/lab-hardware-cad/scripts/gen.py +0 -264
- package/skills/lab-hardware-cad/scripts/snapshot.py +0 -278
- package/skills/labarchive-integration/references/api_reference.md +0 -250
- package/skills/labarchive-integration/references/authentication_guide.md +0 -191
- package/skills/labarchive-integration/references/integrations.md +0 -162
- package/skills/labarchive-integration/references/sources.md +0 -213
- package/skills/labarchive-integration/scripts/entry_operations.py +0 -381
- package/skills/labarchive-integration/scripts/notebook_operations.py +0 -451
- package/skills/labarchive-integration/scripts/setup_config.py +0 -258
- package/skills/lamindb/references/annotation-validation.md +0 -510
- package/skills/lamindb/references/core-concepts.md +0 -383
- package/skills/lamindb/references/data-management.md +0 -432
- package/skills/lamindb/references/integrations.md +0 -663
- package/skills/lamindb/references/ontologies.md +0 -498
- package/skills/lamindb/references/setup-deployment.md +0 -755
- package/skills/latchbio-integration/references/data-management.md +0 -257
- package/skills/latchbio-integration/references/latch-mcp.md +0 -158
- package/skills/latchbio-integration/references/nextflow-snakemake.md +0 -258
- package/skills/latchbio-integration/references/operations-and-debugging.md +0 -320
- package/skills/latchbio-integration/references/registry.md +0 -275
- package/skills/latchbio-integration/references/resource-configuration.md +0 -274
- package/skills/latchbio-integration/references/ui-and-automation.md +0 -355
- package/skills/latchbio-integration/references/verified-workflows.md +0 -226
- package/skills/latchbio-integration/references/workflow-creation.md +0 -275
- package/skills/latchbio-integration/scripts/inspect_latch_sdk.py +0 -290
- package/skills/latex-posters/assets/baposter_template.tex +0 -257
- package/skills/latex-posters/assets/beamerposter_template.tex +0 -244
- package/skills/latex-posters/assets/poster_quality_checklist.md +0 -358
- package/skills/latex-posters/assets/tikzposter_template.tex +0 -251
- package/skills/latex-posters/references/ai_graphics_for_posters.md +0 -524
- package/skills/latex-posters/references/compilation_and_quality_control.md +0 -467
- package/skills/latex-posters/references/latex_poster_packages.md +0 -745
- package/skills/latex-posters/references/latex_poster_reference.md +0 -241
- package/skills/latex-posters/references/poster_content_guide.md +0 -748
- package/skills/latex-posters/references/poster_design_principles.md +0 -806
- package/skills/latex-posters/references/poster_layout_design.md +0 -900
- package/skills/latex-posters/references/poster_patterns_and_presentation.md +0 -81
- package/skills/latex-posters/scripts/generate_schematic.py +0 -198
- package/skills/latex-posters/scripts/generate_schematic_ai.py +0 -950
- package/skills/latex-posters/scripts/review_poster.sh +0 -214
- package/skills/liteparse/references/api_reference.md +0 -169
- package/skills/liteparse/references/choosing_a_parser.md +0 -70
- package/skills/liteparse/references/cli_reference.md +0 -118
- package/skills/liteparse/references/ocr_and_formats.md +0 -143
- package/skills/liteparse/references/output_formats.md +0 -146
- package/skills/liteparse/scripts/batch_parse_dir.py +0 -163
- package/skills/literature-review/assets/review_template.md +0 -412
- package/skills/literature-review/references/citation_styles.md +0 -166
- package/skills/literature-review/references/core_workflow.md +0 -260
- package/skills/literature-review/references/database_strategies.md +0 -455
- package/skills/literature-review/references/example_workflow.md +0 -68
- package/skills/literature-review/references/search_and_citation.md +0 -157
- package/skills/literature-review/scripts/generate_pdf.py +0 -176
- package/skills/literature-review/scripts/generate_schematic.py +0 -198
- package/skills/literature-review/scripts/generate_schematic_ai.py +0 -950
- package/skills/literature-review/scripts/search_databases.py +0 -303
- package/skills/literature-review/scripts/verify_citations.py +0 -222
- package/skills/markdown-mermaid-writing/assets/examples/example-research-report.md +0 -221
- package/skills/markdown-mermaid-writing/references/diagrams/architecture.md +0 -108
- package/skills/markdown-mermaid-writing/references/diagrams/block.md +0 -177
- package/skills/markdown-mermaid-writing/references/diagrams/c4.md +0 -136
- package/skills/markdown-mermaid-writing/references/diagrams/class.md +0 -246
- package/skills/markdown-mermaid-writing/references/diagrams/complex_examples.md +0 -384
- package/skills/markdown-mermaid-writing/references/diagrams/er.md +0 -222
- package/skills/markdown-mermaid-writing/references/diagrams/flowchart.md +0 -177
- package/skills/markdown-mermaid-writing/references/diagrams/gantt.md +0 -138
- package/skills/markdown-mermaid-writing/references/diagrams/git_graph.md +0 -74
- package/skills/markdown-mermaid-writing/references/diagrams/kanban.md +0 -107
- package/skills/markdown-mermaid-writing/references/diagrams/mindmap.md +0 -74
- package/skills/markdown-mermaid-writing/references/diagrams/packet.md +0 -55
- package/skills/markdown-mermaid-writing/references/diagrams/pie.md +0 -52
- package/skills/markdown-mermaid-writing/references/diagrams/quadrant.md +0 -66
- package/skills/markdown-mermaid-writing/references/diagrams/radar.md +0 -59
- package/skills/markdown-mermaid-writing/references/diagrams/requirement.md +0 -88
- package/skills/markdown-mermaid-writing/references/diagrams/sankey.md +0 -71
- package/skills/markdown-mermaid-writing/references/diagrams/sequence.md +0 -174
- package/skills/markdown-mermaid-writing/references/diagrams/state.md +0 -150
- package/skills/markdown-mermaid-writing/references/diagrams/timeline.md +0 -96
- package/skills/markdown-mermaid-writing/references/diagrams/treemap.md +0 -66
- package/skills/markdown-mermaid-writing/references/diagrams/user_journey.md +0 -108
- package/skills/markdown-mermaid-writing/references/diagrams/xy_chart.md +0 -53
- package/skills/markdown-mermaid-writing/references/diagrams/zenuml.md +0 -71
- package/skills/markdown-mermaid-writing/references/markdown_style_guide.md +0 -733
- package/skills/markdown-mermaid-writing/references/mermaid_style_guide.md +0 -458
- package/skills/markdown-mermaid-writing/templates/decision_record.md +0 -211
- package/skills/markdown-mermaid-writing/templates/how_to_guide.md +0 -275
- package/skills/markdown-mermaid-writing/templates/issue.md +0 -303
- package/skills/markdown-mermaid-writing/templates/kanban.md +0 -223
- package/skills/markdown-mermaid-writing/templates/presentation.md +0 -312
- package/skills/markdown-mermaid-writing/templates/project_documentation.md +0 -412
- package/skills/markdown-mermaid-writing/templates/pull_request.md +0 -319
- package/skills/markdown-mermaid-writing/templates/research_paper.md +0 -304
- package/skills/markdown-mermaid-writing/templates/status_report.md +0 -185
- package/skills/market-research-reports/assets/FORMATTING_GUIDE.md +0 -149
- package/skills/market-research-reports/assets/claims_ledger_template.csv +0 -4
- package/skills/market-research-reports/assets/competitor_feature_matrix_template.csv +0 -5
- package/skills/market-research-reports/assets/consistency_check_template.csv +0 -3
- package/skills/market-research-reports/assets/forecast_sensitivity_template.json +0 -90
- package/skills/market-research-reports/assets/market_report_template.tex +0 -279
- package/skills/market-research-reports/assets/market_research.sty +0 -241
- package/skills/market-research-reports/assets/market_sizing_scenarios_template.json +0 -129
- package/skills/market-research-reports/assets/report_manifest_template.json +0 -27
- package/skills/market-research-reports/assets/source_ledger_template.csv +0 -4
- package/skills/market-research-reports/references/data_analysis_patterns.md +0 -290
- package/skills/market-research-reports/references/evidence_model.md +0 -148
- package/skills/market-research-reports/references/methods_and_ethics.md +0 -162
- package/skills/market-research-reports/references/official_data_sources.md +0 -196
- package/skills/market-research-reports/references/report_structure_guide.md +0 -283
- package/skills/market-research-reports/references/sources.md +0 -73
- package/skills/market-research-reports/references/visual_generation_guide.md +0 -158
- package/skills/market-research-reports/scripts/_common.py +0 -312
- package/skills/market-research-reports/scripts/audit_claim_citations.py +0 -326
- package/skills/market-research-reports/scripts/calculate_market_sizing.py +0 -389
- package/skills/market-research-reports/scripts/check_unit_consistency.py +0 -217
- package/skills/market-research-reports/scripts/forecast_sensitivity.py +0 -326
- package/skills/market-research-reports/scripts/generate_report_scaffold.py +0 -444
- package/skills/market-research-reports/scripts/validate_competitor_matrix.py +0 -223
- package/skills/market-research-reports/scripts/validate_evidence_ledger.py +0 -291
- package/skills/markitdown/references/api_reference.md +0 -418
- package/skills/markitdown/references/cloud_and_ocr.md +0 -320
- package/skills/markitdown/references/file_formats.md +0 -281
- package/skills/markitdown/references/mcp_and_plugins.md +0 -243
- package/skills/markitdown/references/migration.md +0 -356
- package/skills/markitdown/references/security.md +0 -246
- package/skills/markitdown/references/workflows.md +0 -309
- package/skills/markitdown/scripts/batch_convert.py +0 -354
- package/skills/markitdown/scripts/convert_literature.py +0 -405
- package/skills/markitdown/scripts/inspect_installation.py +0 -162
- package/skills/matchms/references/filtering.md +0 -299
- package/skills/matchms/references/importing_exporting.md +0 -323
- package/skills/matchms/references/migration.md +0 -387
- package/skills/matchms/references/similarity.md +0 -413
- package/skills/matchms/references/sources.md +0 -113
- package/skills/matchms/references/workflows.md +0 -451
- package/skills/matchms/scripts/library_search.py +0 -593
- package/skills/matlab/assets/project_manifest_template.json +0 -33
- package/skills/matlab/assets/python_compatibility_r2026a.json +0 -27
- package/skills/matlab/assets/reproducibility_manifest_template.json +0 -32
- package/skills/matlab/references/data-import-export.md +0 -221
- package/skills/matlab/references/executing-scripts.md +0 -213
- package/skills/matlab/references/graphics-visualization.md +0 -181
- package/skills/matlab/references/mathematics.md +0 -208
- package/skills/matlab/references/matrices-arrays.md +0 -228
- package/skills/matlab/references/octave-compatibility.md +0 -212
- package/skills/matlab/references/programming.md +0 -225
- package/skills/matlab/references/python-integration.md +0 -248
- package/skills/matlab/scripts/_common.py +0 -263
- package/skills/matlab/scripts/generate_function_scaffold.py +0 -165
- package/skills/matlab/scripts/inventory_mat_file.py +0 -351
- package/skills/matlab/scripts/plan_batch_command.py +0 -257
- package/skills/matlab/scripts/plan_python_compatibility.py +0 -176
- package/skills/matlab/scripts/reproducibility_report.py +0 -233
- package/skills/matlab/scripts/scan_m_code.py +0 -433
- package/skills/matlab/scripts/validate_project_manifest.py +0 -348
- package/skills/matplotlib/references/api_reference.md +0 -409
- package/skills/matplotlib/references/common_issues.md +0 -562
- package/skills/matplotlib/references/plot_types.md +0 -469
- package/skills/matplotlib/references/styling_guide.md +0 -600
- package/skills/matplotlib/scripts/plot_template.py +0 -406
- package/skills/matplotlib/scripts/style_configurator.py +0 -412
- package/skills/medchem/references/api_guide.md +0 -331
- package/skills/medchem/references/rules_catalog.md +0 -328
- package/skills/medchem/scripts/filter_molecules.py +0 -302
- package/skills/modal/references/api_reference.md +0 -225
- package/skills/modal/references/examples.md +0 -276
- package/skills/modal/references/functions.md +0 -260
- package/skills/modal/references/getting-started.md +0 -171
- package/skills/modal/references/gpu.md +0 -177
- package/skills/modal/references/images.md +0 -266
- package/skills/modal/references/resources.md +0 -117
- package/skills/modal/references/scaling.md +0 -173
- package/skills/modal/references/scheduled-jobs.md +0 -147
- package/skills/modal/references/secrets.md +0 -119
- package/skills/modal/references/volumes.md +0 -247
- package/skills/modal/references/web-endpoints.md +0 -259
- package/skills/molecular-dynamics/references/mdanalysis_analysis.md +0 -208
- package/skills/molfeat/references/api_reference.md +0 -429
- package/skills/molfeat/references/available_featurizers.md +0 -335
- package/skills/molfeat/references/choosing_a_featurizer.md +0 -192
- package/skills/molfeat/references/examples.md +0 -720
- package/skills/ncats-arax/references/output-schema.md +0 -186
- package/skills/ncats-arax/references/query-contract.md +0 -140
- package/skills/ncats-arax/scripts/arax_client.py +0 -2087
- package/skills/networkx/references/algorithms.md +0 -384
- package/skills/networkx/references/generators.md +0 -385
- package/skills/networkx/references/graph-basics.md +0 -284
- package/skills/networkx/references/io.md +0 -457
- package/skills/networkx/references/visualization.md +0 -531
- package/skills/neurokit2/references/bio_module.md +0 -244
- package/skills/neurokit2/references/complexity.md +0 -212
- package/skills/neurokit2/references/ecg_cardiac.md +0 -193
- package/skills/neurokit2/references/eda.md +0 -185
- package/skills/neurokit2/references/eeg.md +0 -204
- package/skills/neurokit2/references/emg.md +0 -157
- package/skills/neurokit2/references/eog.md +0 -154
- package/skills/neurokit2/references/epochs_events.md +0 -199
- package/skills/neurokit2/references/hrv.md +0 -205
- package/skills/neurokit2/references/ppg.md +0 -191
- package/skills/neurokit2/references/rsp.md +0 -212
- package/skills/neurokit2/references/signal_processing.md +0 -160
- package/skills/neurokit2/scripts/_common.py +0 -567
- package/skills/neurokit2/scripts/ecg_hrv_pipeline.py +0 -303
- package/skills/neurokit2/scripts/eda_pipeline.py +0 -288
- package/skills/neurokit2/scripts/generate_synthetic.py +0 -221
- package/skills/neurokit2/scripts/inspect_signal.py +0 -362
- package/skills/neurokit2/scripts/plan_epochs.py +0 -281
- package/skills/neurokit2/scripts/validate_multimodal.py +0 -350
- package/skills/neuropixels-analysis/assets/analysis_template.py +0 -271
- package/skills/neuropixels-analysis/references/AI_CURATION.md +0 -164
- package/skills/neuropixels-analysis/references/ANALYSIS.md +0 -392
- package/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md +0 -435
- package/skills/neuropixels-analysis/references/MOTION_CORRECTION.md +0 -323
- package/skills/neuropixels-analysis/references/PREPROCESSING.md +0 -273
- package/skills/neuropixels-analysis/references/QUALITY_METRICS.md +0 -359
- package/skills/neuropixels-analysis/references/SPIKE_SORTING.md +0 -339
- package/skills/neuropixels-analysis/references/api_reference.md +0 -229
- package/skills/neuropixels-analysis/references/plotting_guide.md +0 -454
- package/skills/neuropixels-analysis/references/standard_workflow.md +0 -305
- package/skills/neuropixels-analysis/scripts/compute_metrics.py +0 -182
- package/skills/neuropixels-analysis/scripts/explore_recording.py +0 -168
- package/skills/neuropixels-analysis/scripts/export_to_phy.py +0 -79
- package/skills/neuropixels-analysis/scripts/neuropixels_pipeline.py +0 -442
- package/skills/neuropixels-analysis/scripts/preprocess_recording.py +0 -122
- package/skills/neuropixels-analysis/scripts/run_sorting.py +0 -98
- package/skills/nextflow/references/configuration.md +0 -276
- package/skills/nextflow/references/containers.md +0 -92
- package/skills/nextflow/references/developing.md +0 -301
- package/skills/nextflow/references/language.md +0 -327
- package/skills/nextflow/references/nf-core-tools.md +0 -130
- package/skills/nextflow/references/running-pipelines.md +0 -131
- package/skills/nextflow/references/testing.md +0 -189
- package/skills/omero-integration/references/advanced.md +0 -273
- package/skills/omero-integration/references/connection.md +0 -293
- package/skills/omero-integration/references/data_access.md +0 -359
- package/skills/omero-integration/references/image_processing.md +0 -286
- package/skills/omero-integration/references/metadata.md +0 -313
- package/skills/omero-integration/references/rois.md +0 -291
- package/skills/omero-integration/references/scripts.md +0 -304
- package/skills/omero-integration/references/sources.md +0 -194
- package/skills/omero-integration/references/tables.md +0 -269
- package/skills/omero-integration/scripts/export_image_metadata.py +0 -560
- package/skills/omero-integration/scripts/inventory.py +0 -302
- package/skills/omero-integration/scripts/omero_common.py +0 -490
- package/skills/omero-integration/scripts/plan_transfer.py +0 -393
- package/skills/omero-integration/scripts/validate_config.py +0 -140
- package/skills/onekgpd/assets/kgpe.json +0 -48032
- package/skills/onekgpd/references/annotation_vocabularies.md +0 -187
- package/skills/onekgpd/references/onekgpd_commands.md +0 -296
- package/skills/onekgpd/scripts/onekgpd_api.py +0 -794
- package/skills/onekgpd/scripts/onekgpd_meta.py +0 -485
- package/skills/ontology-term-resolution/references/curation-rules.md +0 -110
- package/skills/ontology-term-resolution/references/ols4-api.md +0 -135
- package/skills/ontology-term-resolution/references/ontology-registry.md +0 -110
- package/skills/ontology-term-resolution/scripts/ols_client.py +0 -341
- package/skills/ontology-term-resolution/scripts/resolve_terms.py +0 -255
- package/skills/ontology-term-resolution/scripts/validate_terms.py +0 -297
- package/skills/open-notebook/references/api_reference.md +0 -715
- package/skills/open-notebook/references/architecture.md +0 -163
- package/skills/open-notebook/references/configuration.md +0 -226
- package/skills/open-notebook/references/examples.md +0 -290
- package/skills/open-notebook/scripts/chat_interaction.py +0 -190
- package/skills/open-notebook/scripts/notebook_management.py +0 -142
- package/skills/open-notebook/scripts/source_ingestion.py +0 -160
- package/skills/openpiv/references/advanced_algorithms.md +0 -233
- package/skills/openpiv/scripts/__init__.py +0 -1
- package/skills/openpiv/scripts/analyze.py +0 -143
- package/skills/openpiv/scripts/run_example.py +0 -78
- package/skills/openpiv/scripts/runner.py +0 -214
- package/skills/opentrons-integration/references/api_reference.md +0 -382
- package/skills/opentrons-integration/references/liquid_handling.md +0 -387
- package/skills/opentrons-integration/references/migration-api-2-19-to-2-29.md +0 -328
- package/skills/opentrons-integration/references/modules_and_deck.md +0 -409
- package/skills/opentrons-integration/references/protocol_authoring.md +0 -352
- package/skills/opentrons-integration/references/sources.md +0 -151
- package/skills/opentrons-integration/references/validation_and_operations.md +0 -314
- package/skills/opentrons-integration/requirements-flex.txt +0 -1
- package/skills/opentrons-integration/requirements-ot2.txt +0 -1
- package/skills/opentrons-integration/scripts/absorbance_reader_template.py +0 -82
- package/skills/opentrons-integration/scripts/basic_protocol_template.py +0 -68
- package/skills/opentrons-integration/scripts/ot2_basic_protocol_template.py +0 -63
- package/skills/opentrons-integration/scripts/pcr_setup_template.py +0 -146
- package/skills/opentrons-integration/scripts/runtime_parameters_template.py +0 -110
- package/skills/opentrons-integration/scripts/serial_dilution_template.py +0 -113
- package/skills/optimize-for-gpu/references/code_transformation_patterns.md +0 -301
- package/skills/optimize-for-gpu/references/cucim.md +0 -679
- package/skills/optimize-for-gpu/references/cudf.md +0 -762
- package/skills/optimize-for-gpu/references/cugraph.md +0 -733
- package/skills/optimize-for-gpu/references/cuml.md +0 -710
- package/skills/optimize-for-gpu/references/cupy.md +0 -668
- package/skills/optimize-for-gpu/references/cuspatial.md +0 -420
- package/skills/optimize-for-gpu/references/cuvs.md +0 -671
- package/skills/optimize-for-gpu/references/cuxfilter.md +0 -600
- package/skills/optimize-for-gpu/references/decision_framework.md +0 -234
- package/skills/optimize-for-gpu/references/installation.md +0 -121
- package/skills/optimize-for-gpu/references/kvikio.md +0 -612
- package/skills/optimize-for-gpu/references/numba.md +0 -808
- package/skills/optimize-for-gpu/references/raft.md +0 -312
- package/skills/optimize-for-gpu/references/warp.md +0 -623
- package/skills/pacsomatic/config.yaml +0 -42
- package/skills/pacsomatic/references/agent-playbook.md +0 -73
- package/skills/pacsomatic/references/config-and-output.md +0 -100
- package/skills/pacsomatic/references/pacsomatic_guide.md +0 -254
- package/skills/pacsomatic/scripts/run_pacsomatic.py +0 -794
- package/skills/paper-lookup/references/arxiv.md +0 -275
- package/skills/paper-lookup/references/biorxiv.md +0 -163
- package/skills/paper-lookup/references/core.md +0 -150
- package/skills/paper-lookup/references/crossref.md +0 -181
- package/skills/paper-lookup/references/europepmc.md +0 -226
- package/skills/paper-lookup/references/medrxiv.md +0 -126
- package/skills/paper-lookup/references/openalex.md +0 -174
- package/skills/paper-lookup/references/pmc.md +0 -228
- package/skills/paper-lookup/references/pubmed.md +0 -124
- package/skills/paper-lookup/references/semantic-scholar.md +0 -203
- package/skills/paper-lookup/references/unpaywall.md +0 -127
- package/skills/paper-lookup/scripts/_common.py +0 -227
- package/skills/paper-lookup/scripts/arxiv_atom.py +0 -200
- package/skills/paper-lookup/scripts/jats_to_text.py +0 -324
- package/skills/paper-lookup/scripts/openalex_abstract.py +0 -163
- package/skills/paper-lookup/scripts/paginate.py +0 -490
- package/skills/paperclip/references/cli-reference.md +0 -389
- package/skills/paperclip/references/installation.md +0 -341
- package/skills/paperclip/references/map-reduce.md +0 -252
- package/skills/paperclip/references/python-sdk.md +0 -323
- package/skills/paperclip/references/repos-and-workspace.md +0 -271
- package/skills/paperclip/references/search-and-retrieval.md +0 -281
- package/skills/parallel-web/references/data-enrichment.md +0 -104
- package/skills/parallel-web/references/deep-research.md +0 -91
- package/skills/parallel-web/references/findall.md +0 -81
- package/skills/parallel-web/references/monitor.md +0 -83
- package/skills/parallel-web/references/web-extract.md +0 -59
- package/skills/parallel-web/references/web-search.md +0 -100
- package/skills/pathml/references/data_management.md +0 -357
- package/skills/pathml/references/graphs.md +0 -335
- package/skills/pathml/references/image_loading.md +0 -301
- package/skills/pathml/references/machine_learning.md +0 -408
- package/skills/pathml/references/multiparametric.md +0 -352
- package/skills/pathml/references/preprocessing.md +0 -371
- package/skills/pathml/scripts/_common.py +0 -385
- package/skills/pathml/scripts/image_qc.py +0 -325
- package/skills/pathml/scripts/plan_inference.py +0 -282
- package/skills/pathml/scripts/plan_pipeline.py +0 -239
- package/skills/pathml/scripts/slide_manifest.py +0 -405
- package/skills/pathml/scripts/validate_spatial_schema.py +0 -420
- package/skills/pathogen-variant-surveillance/references/lapis-api.md +0 -209
- package/skills/pathogen-variant-surveillance/references/lineage-nomenclature.md +0 -126
- package/skills/pathogen-variant-surveillance/references/surveillance-caveats.md +0 -149
- package/skills/pathogen-variant-surveillance/scripts/lapis_client.py +0 -776
- package/skills/pathogen-variant-surveillance/scripts/lineage_prevalence.py +0 -310
- package/skills/pathogen-variant-surveillance/scripts/mutation_profile.py +0 -215
- package/skills/pathogen-variant-surveillance/scripts/reporting_lag.py +0 -217
- package/skills/pathogen-variant-surveillance/scripts/resolve_lineage.py +0 -198
- package/skills/pathway-enrichment/references/databases-and-gene-sets.md +0 -140
- package/skills/pathway-enrichment/references/gseapy.md +0 -189
- package/skills/pathway-enrichment/references/interpretation.md +0 -118
- package/skills/pathway-enrichment/scripts/run_enrichment.py +0 -231
- package/skills/pdf/LICENSE.txt +0 -30
- package/skills/pdf/forms.md +0 -294
- package/skills/pdf/reference.md +0 -612
- package/skills/pdf/scripts/check_bounding_boxes.py +0 -65
- package/skills/pdf/scripts/check_fillable_fields.py +0 -11
- package/skills/pdf/scripts/convert_pdf_to_images.py +0 -33
- package/skills/pdf/scripts/create_validation_image.py +0 -37
- package/skills/pdf/scripts/extract_form_field_info.py +0 -122
- package/skills/pdf/scripts/extract_form_structure.py +0 -115
- package/skills/pdf/scripts/fill_fillable_fields.py +0 -98
- package/skills/pdf/scripts/fill_pdf_form_with_annotations.py +0 -107
- package/skills/peer-review/assets/citation_references_template.csv +0 -2
- package/skills/peer-review/assets/claim_evidence_matrix_template.csv +0 -4
- package/skills/peer-review/assets/reporting_checklist_template.csv +0 -31
- package/skills/peer-review/assets/reporting_guidelines.json +0 -466
- package/skills/peer-review/assets/review_intake_template.json +0 -52
- package/skills/peer-review/assets/review_scaffold_template.md +0 -68
- package/skills/peer-review/assets/source_ledger.csv +0 -32
- package/skills/peer-review/assets/statistical_reproducibility_template.json +0 -210
- package/skills/peer-review/assets/study_profile_template.json +0 -12
- package/skills/peer-review/references/common_issues.md +0 -257
- package/skills/peer-review/references/ethical_review_practice.md +0 -233
- package/skills/peer-review/references/reporting_standards.md +0 -249
- package/skills/peer-review/references/security_validation.md +0 -75
- package/skills/peer-review/references/statistical_reproducibility.md +0 -329
- package/skills/peer-review/references/tool_reference.md +0 -253
- package/skills/peer-review/scripts/_common.py +0 -398
- package/skills/peer-review/scripts/audit_citations.py +0 -207
- package/skills/peer-review/scripts/audit_statistics_reproducibility.py +0 -305
- package/skills/peer-review/scripts/generate_review_scaffold.py +0 -81
- package/skills/peer-review/scripts/lint_review.py +0 -254
- package/skills/peer-review/scripts/select_reporting_guidelines.py +0 -383
- package/skills/peer-review/scripts/validate_claim_evidence.py +0 -221
- package/skills/peer-review/scripts/validate_review_intake.py +0 -452
- package/skills/pennylane/references/advanced_features.md +0 -667
- package/skills/pennylane/references/devices_backends.md +0 -562
- package/skills/pennylane/references/getting_started.md +0 -232
- package/skills/pennylane/references/optimization.md +0 -670
- package/skills/pennylane/references/quantum_chemistry.md +0 -576
- package/skills/pennylane/references/quantum_circuits.md +0 -443
- package/skills/pennylane/references/quantum_ml.md +0 -555
- package/skills/phylogenetics/references/iqtree_inference.md +0 -181
- package/skills/phylogenetics/scripts/phylogenetic_analysis.py +0 -272
- package/skills/pi-agent/references/compaction.md +0 -76
- package/skills/pi-agent/references/containerization.md +0 -80
- package/skills/pi-agent/references/custom-provider.md +0 -131
- package/skills/pi-agent/references/development.md +0 -61
- package/skills/pi-agent/references/environment-variables.md +0 -57
- package/skills/pi-agent/references/extensions.md +0 -185
- package/skills/pi-agent/references/json.md +0 -69
- package/skills/pi-agent/references/keybindings.md +0 -58
- package/skills/pi-agent/references/llama-cpp.md +0 -69
- package/skills/pi-agent/references/models.md +0 -114
- package/skills/pi-agent/references/overview.md +0 -37
- package/skills/pi-agent/references/packages.md +0 -103
- package/skills/pi-agent/references/pi-interview.md +0 -123
- package/skills/pi-agent/references/pi-mcp-adapter.md +0 -191
- package/skills/pi-agent/references/pi-subagents.md +0 -371
- package/skills/pi-agent/references/pi-web-access.md +0 -243
- package/skills/pi-agent/references/prompt-templates.md +0 -48
- package/skills/pi-agent/references/providers.md +0 -122
- package/skills/pi-agent/references/quickstart.md +0 -73
- package/skills/pi-agent/references/rpc.md +0 -95
- package/skills/pi-agent/references/sdk.md +0 -151
- package/skills/pi-agent/references/security.md +0 -52
- package/skills/pi-agent/references/session-format.md +0 -90
- package/skills/pi-agent/references/sessions.md +0 -56
- package/skills/pi-agent/references/settings.md +0 -102
- package/skills/pi-agent/references/shell-aliases.md +0 -15
- package/skills/pi-agent/references/skills.md +0 -83
- package/skills/pi-agent/references/terminal-setup.md +0 -87
- package/skills/pi-agent/references/termux.md +0 -31
- package/skills/pi-agent/references/themes.md +0 -69
- package/skills/pi-agent/references/tmux.md +0 -44
- package/skills/pi-agent/references/tui.md +0 -97
- package/skills/pi-agent/references/usage.md +0 -129
- package/skills/pi-agent/references/windows.md +0 -23
- package/skills/pkpd-modeling/assets/nca-reporting-checklist.md +0 -72
- package/skills/pkpd-modeling/assets/popk-analysis-plan.md +0 -136
- package/skills/pkpd-modeling/references/antimicrobial-and-tdm.md +0 -110
- package/skills/pkpd-modeling/references/bioequivalence.md +0 -132
- package/skills/pkpd-modeling/references/dataset-standards.md +0 -103
- package/skills/pkpd-modeling/references/ddi-and-qt.md +0 -132
- package/skills/pkpd-modeling/references/nca-conventions.md +0 -128
- package/skills/pkpd-modeling/references/pbpk.md +0 -103
- package/skills/pkpd-modeling/references/pd-and-exposure-response.md +0 -149
- package/skills/pkpd-modeling/references/population-pk.md +0 -133
- package/skills/pkpd-modeling/references/regulatory-guidance.md +0 -82
- package/skills/pkpd-modeling/references/software-ecosystem.md +0 -123
- package/skills/pkpd-modeling/references/source-ledger.md +0 -89
- package/skills/pkpd-modeling/references/special-populations.md +0 -126
- package/skills/pkpd-modeling/references/structural-models.md +0 -140
- package/skills/pkpd-modeling/references/tmdd-and-biologics.md +0 -115
- package/skills/pkpd-modeling/scripts/_common.py +0 -327
- package/skills/pkpd-modeling/scripts/_models.py +0 -673
- package/skills/pkpd-modeling/scripts/allometry_and_fih.py +0 -346
- package/skills/pkpd-modeling/scripts/bioequivalence.py +0 -480
- package/skills/pkpd-modeling/scripts/check_popk_dataset.py +0 -400
- package/skills/pkpd-modeling/scripts/ddi_static.py +0 -346
- package/skills/pkpd-modeling/scripts/exposure_response.py +0 -328
- package/skills/pkpd-modeling/scripts/fit_compartmental.py +0 -558
- package/skills/pkpd-modeling/scripts/nca.py +0 -587
- package/skills/pkpd-modeling/scripts/simulate_regimen.py +0 -323
- package/skills/pkpd-modeling/scripts/tdm_bayes.py +0 -312
- package/skills/polars/references/best_practices.md +0 -651
- package/skills/polars/references/core_concepts.md +0 -380
- package/skills/polars/references/io_guide.md +0 -564
- package/skills/polars/references/operations.md +0 -602
- package/skills/polars/references/pandas_migration.md +0 -417
- package/skills/polars/references/transformations.md +0 -549
- package/skills/polars-bio/references/bioframe_migration.md +0 -250
- package/skills/polars-bio/references/configuration.md +0 -187
- package/skills/polars-bio/references/file_io.md +0 -469
- package/skills/polars-bio/references/interval_operations.md +0 -370
- package/skills/polars-bio/references/pileup_operations.md +0 -176
- package/skills/polars-bio/references/sql_processing.md +0 -224
- package/skills/pptx/LICENSE.txt +0 -30
- package/skills/pptx/scripts/__init__.py +0 -0
- package/skills/pptx/scripts/add_slide.py +0 -367
- package/skills/pptx/scripts/clean.py +0 -309
- package/skills/pptx/scripts/office/helpers/__init__.py +0 -111
- package/skills/pptx/scripts/office/helpers/pptx_chart.py +0 -170
- package/skills/pptx/scripts/office/helpers/pptx_slide.py +0 -60
- package/skills/pptx/scripts/office/helpers/pptx_theme.py +0 -114
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -1499
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -146
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -1085
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -11
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -3081
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -23
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -185
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -287
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -1676
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -28
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -144
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -174
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -25
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -18
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -59
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -56
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -195
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -582
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -25
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -4439
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -570
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -509
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -12
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -108
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -96
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -3646
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -116
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -42
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -50
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -49
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -33
- package/skills/pptx/scripts/office/schemas/mce/mc.xsd +0 -75
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2010.xsd +0 -560
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2012.xsd +0 -67
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2018.xsd +0 -14
- package/skills/pptx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +0 -20
- package/skills/pptx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
- package/skills/pptx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
- package/skills/pptx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
- package/skills/pptx/scripts/office/soffice.py +0 -232
- package/skills/pptx/scripts/office/validate.py +0 -173
- package/skills/pptx/scripts/office/validators/__init__.py +0 -15
- package/skills/pptx/scripts/office/validators/base.py +0 -875
- package/skills/pptx/scripts/office/validators/docx.py +0 -466
- package/skills/pptx/scripts/office/validators/pptx.py +0 -441
- package/skills/pptx/scripts/office/validators/redlining.py +0 -299
- package/skills/pptx/scripts/thumbnail.py +0 -311
- package/skills/pptx-posters/assets/generation_dependencies.json +0 -5
- package/skills/pptx-posters/assets/poster_manifest_template.json +0 -154
- package/skills/pptx-posters/assets/poster_quality_checklist.md +0 -192
- package/skills/pptx-posters/references/manifest_spec.md +0 -297
- package/skills/pptx-posters/references/poster_content_guide.md +0 -176
- package/skills/pptx-posters/references/poster_design_principles.md +0 -226
- package/skills/pptx-posters/references/poster_layout_design.md +0 -189
- package/skills/pptx-posters/references/pptx_security.md +0 -202
- package/skills/pptx-posters/references/security_validation.md +0 -90
- package/skills/pptx-posters/references/source_ledger.md +0 -256
- package/skills/pptx-posters/scripts/_common.py +0 -396
- package/skills/pptx-posters/scripts/_manifest.py +0 -1318
- package/skills/pptx-posters/scripts/_pptx.py +0 -1484
- package/skills/pptx-posters/scripts/check_layout.py +0 -179
- package/skills/pptx-posters/scripts/check_palette.py +0 -142
- package/skills/pptx-posters/scripts/generate_poster.py +0 -427
- package/skills/pptx-posters/scripts/inspect_pptx.py +0 -40
- package/skills/pptx-posters/scripts/inventory_images.py +0 -252
- package/skills/pptx-posters/scripts/plan_export.py +0 -201
- package/skills/pptx-posters/scripts/validate_manifest.py +0 -55
- package/skills/primekg/scripts/query_primekg.py +0 -128
- package/skills/protocolsio-integration/assets/protocol-snapshot.schema.json +0 -179
- package/skills/protocolsio-integration/references/additional_features.md +0 -202
- package/skills/protocolsio-integration/references/authentication.md +0 -135
- package/skills/protocolsio-integration/references/discussions.md +0 -192
- package/skills/protocolsio-integration/references/file_manager.md +0 -256
- package/skills/protocolsio-integration/references/protocols_api.md +0 -256
- package/skills/protocolsio-integration/references/workspaces.md +0 -192
- package/skills/protocolsio-integration/scripts/__init__.py +0 -1
- package/skills/protocolsio-integration/scripts/_common.py +0 -613
- package/skills/protocolsio-integration/scripts/pagination_helper.py +0 -248
- package/skills/protocolsio-integration/scripts/plan_write_request.py +0 -657
- package/skills/protocolsio-integration/scripts/protocols_read.py +0 -493
- package/skills/protocolsio-integration/scripts/validate_auth_config.py +0 -128
- package/skills/protocolsio-integration/scripts/validate_protocol_json.py +0 -358
- package/skills/pufferlib/references/environments.md +0 -260
- package/skills/pufferlib/references/integration.md +0 -192
- package/skills/pufferlib/references/policies.md +0 -181
- package/skills/pufferlib/references/training.md +0 -287
- package/skills/pufferlib/references/vectorization.md +0 -210
- package/skills/pufferlib/scripts/__init__.py +0 -1
- package/skills/pufferlib/scripts/_common.py +0 -199
- package/skills/pufferlib/scripts/benchmark_vectorization.py +0 -244
- package/skills/pufferlib/scripts/env_contract_validator.py +0 -198
- package/skills/pufferlib/scripts/env_template.py +0 -210
- package/skills/pufferlib/scripts/inspect_checkpoint.py +0 -225
- package/skills/pufferlib/scripts/repro_plan.py +0 -177
- package/skills/pufferlib/scripts/train_template.py +0 -282
- package/skills/pufferlib/scripts/validate_plan.py +0 -570
- package/skills/pydeseq2/references/analysis_patterns.md +0 -70
- package/skills/pydeseq2/references/api_reference.md +0 -256
- package/skills/pydeseq2/references/core_workflow_steps.md +0 -162
- package/skills/pydeseq2/references/workflow_guide.md +0 -603
- package/skills/pydeseq2/scripts/run_deseq2_analysis.py +0 -388
- package/skills/pydicom/references/common_tags.md +0 -277
- package/skills/pydicom/references/transfer_syntaxes.md +0 -348
- package/skills/pydicom/scripts/__init__.py +0 -1
- package/skills/pydicom/scripts/_common.py +0 -916
- package/skills/pydicom/scripts/anonymize_dicom.py +0 -713
- package/skills/pydicom/scripts/deidentification_audit.py +0 -380
- package/skills/pydicom/scripts/dicom_inventory.py +0 -402
- package/skills/pydicom/scripts/dicom_to_image.py +0 -459
- package/skills/pydicom/scripts/extract_metadata.py +0 -330
- package/skills/pydicom/scripts/pixel_frame_planner.py +0 -303
- package/skills/pydicom/scripts/transfer_syntax_inspector.py +0 -245
- package/skills/pydicom/scripts/uid_mapping_validator.py +0 -240
- package/skills/pyhealth/assets/starter_pipeline.py +0 -58
- package/skills/pyhealth/references/datasets.md +0 -126
- package/skills/pyhealth/references/examples.md +0 -237
- package/skills/pyhealth/references/installation.md +0 -112
- package/skills/pyhealth/references/medcode.md +0 -94
- package/skills/pyhealth/references/models.md +0 -114
- package/skills/pyhealth/references/tasks.md +0 -143
- package/skills/pylabrobot/assets/protocol-manifest.schema.json +0 -367
- package/skills/pylabrobot/references/analytical-equipment.md +0 -200
- package/skills/pylabrobot/references/hardware-backends.md +0 -215
- package/skills/pylabrobot/references/liquid-handling.md +0 -223
- package/skills/pylabrobot/references/material-handling.md +0 -229
- package/skills/pylabrobot/references/resources.md +0 -238
- package/skills/pylabrobot/references/visualization.md +0 -187
- package/skills/pylabrobot/scripts/__init__.py +0 -1
- package/skills/pylabrobot/scripts/_common.py +0 -718
- package/skills/pylabrobot/scripts/check_deck_geometry.py +0 -52
- package/skills/pylabrobot/scripts/generate_simulation_plan.py +0 -140
- package/skills/pylabrobot/scripts/inspect_backends.py +0 -216
- package/skills/pylabrobot/scripts/plan_transfers.py +0 -59
- package/skills/pylabrobot/scripts/validate_manifest.py +0 -47
- package/skills/pymatgen/references/analysis_modules.md +0 -352
- package/skills/pymatgen/references/core_classes.md +0 -290
- package/skills/pymatgen/references/io_formats.md +0 -323
- package/skills/pymatgen/references/materials_project_api.md +0 -406
- package/skills/pymatgen/references/transformations_workflows.md +0 -385
- package/skills/pymatgen/scripts/_common.py +0 -316
- package/skills/pymatgen/scripts/artifact_manifest.py +0 -172
- package/skills/pymatgen/scripts/composition_structure_validator.py +0 -300
- package/skills/pymatgen/scripts/io_conversion_plan.py +0 -204
- package/skills/pymatgen/scripts/mp_query.py +0 -416
- package/skills/pymatgen/scripts/phase_diagram_generator.py +0 -415
- package/skills/pymatgen/scripts/structure_analyzer.py +0 -293
- package/skills/pymatgen/scripts/structure_converter.py +0 -219
- package/skills/pymatgen/scripts/symmetry_sensitivity_report.py +0 -212
- package/skills/pymc/assets/hierarchical_model_template.py +0 -332
- package/skills/pymc/assets/linear_regression_template.py +0 -244
- package/skills/pymc/references/distributions.md +0 -345
- package/skills/pymc/references/model_patterns.md +0 -130
- package/skills/pymc/references/sampling_inference.md +0 -432
- package/skills/pymc/references/standard_workflow.md +0 -176
- package/skills/pymc/references/workflows.md +0 -530
- package/skills/pymc/scripts/model_comparison.py +0 -409
- package/skills/pymc/scripts/model_diagnostics.py +0 -328
- package/skills/pymoo/references/algorithms.md +0 -232
- package/skills/pymoo/references/constraints_mcdm.md +0 -417
- package/skills/pymoo/references/operators.md +0 -345
- package/skills/pymoo/references/parallelization.md +0 -80
- package/skills/pymoo/references/problems.md +0 -265
- package/skills/pymoo/references/quick_start_workflows.md +0 -404
- package/skills/pymoo/references/visualization.md +0 -353
- package/skills/pymoo/scripts/custom_problem_example.py +0 -181
- package/skills/pymoo/scripts/decision_making_example.py +0 -161
- package/skills/pymoo/scripts/many_objective_example.py +0 -74
- package/skills/pymoo/scripts/multi_objective_example.py +0 -63
- package/skills/pymoo/scripts/single_objective_example.py +0 -59
- package/skills/pyopenms/references/data_structures.md +0 -498
- package/skills/pyopenms/references/feature_detection.md +0 -495
- package/skills/pyopenms/references/file_io.md +0 -359
- package/skills/pyopenms/references/identification.md +0 -431
- package/skills/pyopenms/references/metabolomics.md +0 -548
- package/skills/pyopenms/references/signal_processing.md +0 -444
- package/skills/pyopenms/scripts/accurate_mass_search.py +0 -111
- package/skills/pyopenms/scripts/align_link_quantify.py +0 -140
- package/skills/pyopenms/scripts/consensus_to_matrix.py +0 -70
- package/skills/pyopenms/scripts/convert_format.py +0 -95
- package/skills/pyopenms/scripts/detect_adducts.py +0 -90
- package/skills/pyopenms/scripts/detect_features_centroided.py +0 -80
- package/skills/pyopenms/scripts/detect_features_metabo.py +0 -110
- package/skills/pyopenms/scripts/digest_protein.py +0 -102
- package/skills/pyopenms/scripts/export_gnps_sirius.py +0 -90
- package/skills/pyopenms/scripts/extract_chromatograms.py +0 -105
- package/skills/pyopenms/scripts/inspect_ms_data.py +0 -167
- package/skills/pyopenms/scripts/mass_calculator.py +0 -92
- package/skills/pyopenms/scripts/plot_ms_data.py +0 -129
- package/skills/pyopenms/scripts/process_identifications.py +0 -111
- package/skills/pyopenms/scripts/process_spectra.py +0 -124
- package/skills/pyopenms/scripts/theoretical_spectrum.py +0 -75
- package/skills/pysam/references/alignment_files.md +0 -374
- package/skills/pysam/references/api_reference.md +0 -421
- package/skills/pysam/references/common_workflows.md +0 -442
- package/skills/pysam/references/coordinates_and_indexing.md +0 -318
- package/skills/pysam/references/cram_and_performance.md +0 -314
- package/skills/pysam/references/migration_to_0_24.md +0 -177
- package/skills/pysam/references/sequence_files.md +0 -316
- package/skills/pysam/references/sources.md +0 -132
- package/skills/pysam/references/variant_files.md +0 -396
- package/skills/pysam/scripts/alignment_qc.py +0 -326
- package/skills/pysam/scripts/filter_alignments.py +0 -359
- package/skills/pysam/scripts/inspect_hts.py +0 -485
- package/skills/pysam/scripts/variant_summary.py +0 -362
- package/skills/pytdc/references/datasets.md +0 -242
- package/skills/pytdc/references/oracles.md +0 -273
- package/skills/pytdc/references/sources.md +0 -165
- package/skills/pytdc/references/utilities.md +0 -364
- package/skills/pytdc/scripts/_common.py +0 -205
- package/skills/pytdc/scripts/benchmark_evaluation.py +0 -367
- package/skills/pytdc/scripts/cache_audit.py +0 -146
- package/skills/pytdc/scripts/discover_metadata.py +0 -174
- package/skills/pytdc/scripts/load_and_split_data.py +0 -374
- package/skills/pytdc/scripts/molecular_generation.py +0 -417
- package/skills/pytorch-lightning/references/best_practices.md +0 -724
- package/skills/pytorch-lightning/references/callbacks.md +0 -564
- package/skills/pytorch-lightning/references/data_module.md +0 -565
- package/skills/pytorch-lightning/references/distributed_training.md +0 -644
- package/skills/pytorch-lightning/references/lightning_module.md +0 -487
- package/skills/pytorch-lightning/references/logging.md +0 -636
- package/skills/pytorch-lightning/references/trainer.md +0 -641
- package/skills/pytorch-lightning/scripts/quick_trainer_setup.py +0 -473
- package/skills/pytorch-lightning/scripts/template_datamodule.py +0 -328
- package/skills/pytorch-lightning/scripts/template_lightning_module.py +0 -220
- package/skills/pyzotero/references/authentication.md +0 -105
- package/skills/pyzotero/references/cli.md +0 -102
- package/skills/pyzotero/references/collections.md +0 -113
- package/skills/pyzotero/references/error-handling.md +0 -108
- package/skills/pyzotero/references/exports.md +0 -102
- package/skills/pyzotero/references/files-attachments.md +0 -97
- package/skills/pyzotero/references/full-text.md +0 -68
- package/skills/pyzotero/references/mcp.md +0 -90
- package/skills/pyzotero/references/pagination.md +0 -79
- package/skills/pyzotero/references/read-api.md +0 -137
- package/skills/pyzotero/references/saved-searches.md +0 -77
- package/skills/pyzotero/references/search-params.md +0 -90
- package/skills/pyzotero/references/tags.md +0 -87
- package/skills/pyzotero/references/write-api.md +0 -123
- package/skills/qiskit/references/algorithms.md +0 -311
- package/skills/qiskit/references/backends.md +0 -382
- package/skills/qiskit/references/circuits.md +0 -319
- package/skills/qiskit/references/migration.md +0 -338
- package/skills/qiskit/references/patterns.md +0 -386
- package/skills/qiskit/references/primitives.md +0 -400
- package/skills/qiskit/references/setup.md +0 -253
- package/skills/qiskit/references/sources.md +0 -156
- package/skills/qiskit/references/testing.md +0 -428
- package/skills/qiskit/references/transpilation.md +0 -333
- package/skills/qiskit/references/visualization.md +0 -361
- package/skills/qiskit/scripts/check_environment.py +0 -260
- package/skills/qiskit/scripts/inspect_runtime.py +0 -224
- package/skills/qiskit/scripts/run_local_primitives.py +0 -200
- package/skills/qutip/references/advanced.md +0 -413
- package/skills/qutip/references/analysis.md +0 -319
- package/skills/qutip/references/core_concepts.md +0 -300
- package/skills/qutip/references/time_evolution.md +0 -373
- package/skills/qutip/references/visualization.md +0 -334
- package/skills/qutip/scripts/_common.py +0 -370
- package/skills/qutip/scripts/convergence_sweep.py +0 -358
- package/skills/qutip/scripts/qobj_model_validator.py +0 -327
- package/skills/qutip/scripts/result_audit.py +0 -395
- package/skills/qutip/scripts/solver_config_planner.py +0 -297
- package/skills/qutip/scripts/steady_state_spectrum_planner.py +0 -245
- package/skills/qutip/scripts/two_level_simulation.py +0 -394
- package/skills/rdkit/references/api_reference.md +0 -443
- package/skills/rdkit/references/core_capabilities.md +0 -604
- package/skills/rdkit/references/descriptors_reference.md +0 -595
- package/skills/rdkit/references/smarts_patterns.md +0 -668
- package/skills/rdkit/references/workflows_and_best_practices.md +0 -169
- package/skills/rdkit/scripts/molecular_properties.py +0 -243
- package/skills/rdkit/scripts/similarity_search.py +0 -297
- package/skills/rdkit/scripts/substructure_filter.py +0 -386
- package/skills/relsa-severity-assessment/assets/example_cohort.csv +0 -55
- package/skills/relsa-severity-assessment/references/forecasting.md +0 -155
- package/skills/relsa-severity-assessment/references/relsa-method.md +0 -175
- package/skills/relsa-severity-assessment/references/thresholds-and-zones.md +0 -154
- package/skills/relsa-severity-assessment/scripts/_common.py +0 -287
- package/skills/relsa-severity-assessment/scripts/forecast_relsa.py +0 -757
- package/skills/relsa-severity-assessment/scripts/kde_thresholds.py +0 -369
- package/skills/relsa-severity-assessment/scripts/relsa_score.py +0 -488
- package/skills/research-grants/assets/budget_justification_template.md +0 -453
- package/skills/research-grants/assets/nih_specific_aims_template.md +0 -166
- package/skills/research-grants/assets/nsf_project_summary_template.md +0 -92
- package/skills/research-grants/references/broader_impacts.md +0 -392
- package/skills/research-grants/references/core_components.md +0 -397
- package/skills/research-grants/references/darpa_guidelines.md +0 -636
- package/skills/research-grants/references/doe_guidelines.md +0 -586
- package/skills/research-grants/references/nih_guidelines.md +0 -853
- package/skills/research-grants/references/nsf_guidelines.md +0 -570
- package/skills/research-grants/references/nstc_guidelines.md +0 -733
- package/skills/research-grants/references/proposal_types_and_resubmission.md +0 -81
- package/skills/research-grants/references/review_criteria.md +0 -93
- package/skills/research-grants/references/specific_aims_guide.md +0 -458
- package/skills/research-grants/references/writing_principles.md +0 -94
- package/skills/research-lookup/scripts/manuscript_packet.py +0 -754
- package/skills/research-lookup/scripts/research_lookup.py +0 -1204
- package/skills/rowan/references/access_and_pricing.md +0 -37
- package/skills/rowan/references/batch_and_webhooks.md +0 -255
- package/skills/rowan/references/end_to_end_example.md +0 -119
- package/skills/rowan/references/troubleshooting.md +0 -106
- package/skills/rowan/references/workflow_catalog.md +0 -308
- package/skills/scanpy/assets/analysis_template.py +0 -301
- package/skills/scanpy/assets/celltype_mapping.json +0 -10
- package/skills/scanpy/assets/gene_signatures.json +0 -9
- package/skills/scanpy/assets/pipeline_config.json +0 -19
- package/skills/scanpy/references/analysis_workflow.md +0 -236
- package/skills/scanpy/references/api_reference.md +0 -267
- package/skills/scanpy/references/plotting_guide.md +0 -365
- package/skills/scanpy/references/r_interop.md +0 -292
- package/skills/scanpy/references/standard_workflow.md +0 -223
- package/skills/scanpy/scripts/_common.py +0 -127
- package/skills/scanpy/scripts/annotate.py +0 -84
- package/skills/scanpy/scripts/batch_correct.py +0 -65
- package/skills/scanpy/scripts/cluster.py +0 -63
- package/skills/scanpy/scripts/convert.py +0 -43
- package/skills/scanpy/scripts/find_markers.py +0 -75
- package/skills/scanpy/scripts/inspect_data.py +0 -81
- package/skills/scanpy/scripts/plot.py +0 -78
- package/skills/scanpy/scripts/preprocess.py +0 -88
- package/skills/scanpy/scripts/pseudobulk.py +0 -74
- package/skills/scanpy/scripts/qc_analysis.py +0 -104
- package/skills/scanpy/scripts/reduce_dimensions.py +0 -64
- package/skills/scanpy/scripts/run_pipeline.py +0 -182
- package/skills/scanpy/scripts/score_genes.py +0 -82
- package/skills/scanpy/scripts/subset.py +0 -64
- package/skills/scholar-evaluation/assets/evaluation_template.json +0 -50
- package/skills/scholar-evaluation/assets/evidence_manifest_template.json +0 -63
- package/skills/scholar-evaluation/assets/process_checklist_template.json +0 -70
- package/skills/scholar-evaluation/assets/ratings_template.csv +0 -21
- package/skills/scholar-evaluation/assets/rubric_template.json +0 -301
- package/skills/scholar-evaluation/references/evaluation_framework.md +0 -264
- package/skills/scholar-evaluation/references/local_tooling.md +0 -232
- package/skills/scholar-evaluation/references/responsible_assessment.md +0 -196
- package/skills/scholar-evaluation/references/security_validation.md +0 -95
- package/skills/scholar-evaluation/references/source_ledger.md +0 -222
- package/skills/scholar-evaluation/scripts/_common.py +0 -986
- package/skills/scholar-evaluation/scripts/calculate_scores.py +0 -57
- package/skills/scholar-evaluation/scripts/check_process.py +0 -231
- package/skills/scholar-evaluation/scripts/check_traceability.py +0 -233
- package/skills/scholar-evaluation/scripts/generate_report_scaffold.py +0 -231
- package/skills/scholar-evaluation/scripts/summarize_agreement.py +0 -235
- package/skills/scholar-evaluation/scripts/validate_rubric.py +0 -54
- package/skills/scholar-evaluation/scripts/weight_sensitivity.py +0 -251
- package/skills/scientific-brainstorming/references/brainstorming_methods.md +0 -292
- package/skills/scientific-brainstorming/references/facilitation_workflows.md +0 -284
- package/skills/scientific-brainstorming/references/idea_evaluation.md +0 -268
- package/skills/scientific-brainstorming/references/responsible_ai.md +0 -220
- package/skills/scientific-brainstorming/references/sources.md +0 -364
- package/skills/scientific-brainstorming/scripts/_common.py +0 -307
- package/skills/scientific-brainstorming/scripts/evaluate_matrix.py +0 -518
- package/skills/scientific-brainstorming/scripts/session_scaffold.py +0 -248
- package/skills/scientific-brainstorming/scripts/validate_register.py +0 -654
- package/skills/scientific-critical-thinking/references/common_biases.md +0 -364
- package/skills/scientific-critical-thinking/references/core_capabilities.md +0 -407
- package/skills/scientific-critical-thinking/references/evidence_hierarchy.md +0 -485
- package/skills/scientific-critical-thinking/references/experimental_design.md +0 -496
- package/skills/scientific-critical-thinking/references/logical_fallacies.md +0 -478
- package/skills/scientific-critical-thinking/references/scientific_method.md +0 -169
- package/skills/scientific-critical-thinking/references/statistical_pitfalls.md +0 -506
- package/skills/scientific-schematics/references/best_practices.md +0 -574
- package/skills/scientific-schematics/references/iterative_refinement.md +0 -315
- package/skills/scientific-schematics/scripts/example_usage.sh +0 -92
- package/skills/scientific-schematics/scripts/generate_schematic.py +0 -198
- package/skills/scientific-schematics/scripts/generate_schematic_ai.py +0 -950
- package/skills/scientific-slides/assets/beamer_template_conference.tex +0 -407
- package/skills/scientific-slides/assets/beamer_template_defense.tex +0 -906
- package/skills/scientific-slides/assets/beamer_template_seminar.tex +0 -870
- package/skills/scientific-slides/assets/powerpoint_design_guide.md +0 -662
- package/skills/scientific-slides/assets/timing_guidelines.md +0 -597
- package/skills/scientific-slides/references/beamer_guide.md +0 -1019
- package/skills/scientific-slides/references/common_pitfalls.md +0 -85
- package/skills/scientific-slides/references/data_visualization_slides.md +0 -708
- package/skills/scientific-slides/references/presentation_structure.md +0 -642
- package/skills/scientific-slides/references/presentation_workflow.md +0 -196
- package/skills/scientific-slides/references/prompt_writing.md +0 -42
- package/skills/scientific-slides/references/script_reference.md +0 -143
- package/skills/scientific-slides/references/slide_capabilities.md +0 -360
- package/skills/scientific-slides/references/slide_design_principles.md +0 -849
- package/skills/scientific-slides/references/talk_types_guide.md +0 -687
- package/skills/scientific-slides/references/visual_review_workflow.md +0 -775
- package/skills/scientific-slides/scripts/generate_schematic.py +0 -198
- package/skills/scientific-slides/scripts/generate_schematic_ai.py +0 -950
- package/skills/scientific-slides/scripts/generate_slide_image.py +0 -197
- package/skills/scientific-slides/scripts/generate_slide_image_ai.py +0 -877
- package/skills/scientific-slides/scripts/pdf_to_images.py +0 -221
- package/skills/scientific-slides/scripts/slides_to_pdf.py +0 -235
- package/skills/scientific-slides/scripts/validate_presentation.py +0 -408
- package/skills/scientific-visualization/assets/color_palettes.py +0 -263
- package/skills/scientific-visualization/assets/nature.mplstyle +0 -68
- package/skills/scientific-visualization/assets/presentation.mplstyle +0 -68
- package/skills/scientific-visualization/assets/publication.mplstyle +0 -77
- package/skills/scientific-visualization/assets/publisher_profiles.json +0 -269
- package/skills/scientific-visualization/references/color_palettes.md +0 -227
- package/skills/scientific-visualization/references/journal_requirements.md +0 -169
- package/skills/scientific-visualization/references/matplotlib_examples.md +0 -336
- package/skills/scientific-visualization/references/publication_guidelines.md +0 -196
- package/skills/scientific-visualization/references/sources.md +0 -76
- package/skills/scientific-visualization/scripts/_common.py +0 -136
- package/skills/scientific-visualization/scripts/export_plan.py +0 -493
- package/skills/scientific-visualization/scripts/figure_export.py +0 -642
- package/skills/scientific-visualization/scripts/image_metadata.py +0 -731
- package/skills/scientific-visualization/scripts/palette_audit.py +0 -327
- package/skills/scientific-visualization/scripts/style_presets.py +0 -501
- package/skills/scientific-visualization/scripts/style_preview.py +0 -232
- package/skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md +0 -60
- package/skills/scientific-writing/assets/authorship_template.json +0 -56
- package/skills/scientific-writing/assets/claim_evidence_template.csv +0 -2
- package/skills/scientific-writing/assets/consistency_manifest_template.json +0 -43
- package/skills/scientific-writing/assets/manuscript_manifest_template.json +0 -37
- package/skills/scientific-writing/assets/manuscript_scaffold.md +0 -65
- package/skills/scientific-writing/assets/reporting_coverage_template.json +0 -6
- package/skills/scientific-writing/assets/reporting_guidelines.json +0 -529
- package/skills/scientific-writing/assets/source_manifest_template.json +0 -27
- package/skills/scientific-writing/references/authorship_ai_confidentiality.md +0 -111
- package/skills/scientific-writing/references/citation_styles.md +0 -92
- package/skills/scientific-writing/references/cli_reference.md +0 -113
- package/skills/scientific-writing/references/evidence_workflow.md +0 -94
- package/skills/scientific-writing/references/figures_tables.md +0 -94
- package/skills/scientific-writing/references/imrad_structure.md +0 -114
- package/skills/scientific-writing/references/journal_policies.md +0 -56
- package/skills/scientific-writing/references/professional_report_formatting.md +0 -82
- package/skills/scientific-writing/references/reporting_guidelines.md +0 -107
- package/skills/scientific-writing/references/research_integrity_open_science.md +0 -97
- package/skills/scientific-writing/references/source_ledger.md +0 -268
- package/skills/scientific-writing/references/writing_principles.md +0 -97
- package/skills/scientific-writing/scripts/_common.py +0 -240
- package/skills/scientific-writing/scripts/audit_claims.py +0 -241
- package/skills/scientific-writing/scripts/check_consistency.py +0 -408
- package/skills/scientific-writing/scripts/check_references.py +0 -219
- package/skills/scientific-writing/scripts/lint_manuscript.py +0 -171
- package/skills/scientific-writing/scripts/scaffold_manuscript.py +0 -143
- package/skills/scientific-writing/scripts/select_reporting_guidelines.py +0 -214
- package/skills/scientific-writing/scripts/validate_authorship.py +0 -322
- package/skills/scientific-writing/scripts/validate_manifest.py +0 -460
- package/skills/scikit-bio/references/api_reference.md +0 -766
- package/skills/scikit-learn/references/common_workflows.md +0 -107
- package/skills/scikit-learn/references/core_capabilities.md +0 -133
- package/skills/scikit-learn/references/model_evaluation.md +0 -592
- package/skills/scikit-learn/references/pipelines_and_composition.md +0 -612
- package/skills/scikit-learn/references/preprocessing.md +0 -606
- package/skills/scikit-learn/references/quick_reference.md +0 -436
- package/skills/scikit-learn/references/supervised_learning.md +0 -379
- package/skills/scikit-learn/references/unsupervised_learning.md +0 -517
- package/skills/scikit-learn/scripts/classification_pipeline.py +0 -257
- package/skills/scikit-learn/scripts/clustering_analysis.py +0 -386
- package/skills/scikit-survival/references/competing-risks.md +0 -302
- package/skills/scikit-survival/references/cox-models.md +0 -252
- package/skills/scikit-survival/references/data-handling.md +0 -278
- package/skills/scikit-survival/references/ensemble-models.md +0 -287
- package/skills/scikit-survival/references/evaluation-metrics.md +0 -391
- package/skills/scikit-survival/references/svm-models.md +0 -277
- package/skills/scikit-survival/scripts/_common.py +0 -456
- package/skills/scikit-survival/scripts/competing_risk_cif.py +0 -286
- package/skills/scikit-survival/scripts/evaluate_survival_metrics.py +0 -296
- package/skills/scikit-survival/scripts/model_report.py +0 -297
- package/skills/scikit-survival/scripts/train_survival_model.py +0 -583
- package/skills/scikit-survival/scripts/validate_survival_csv.py +0 -172
- package/skills/scvelo/references/velocity_models.md +0 -168
- package/skills/scvelo/scripts/rna_velocity_workflow.py +0 -240
- package/skills/scvi-tools/references/differential-expression.md +0 -597
- package/skills/scvi-tools/references/models-atac-seq.md +0 -329
- package/skills/scvi-tools/references/models-multimodal.md +0 -400
- package/skills/scvi-tools/references/models-scrna-seq.md +0 -333
- package/skills/scvi-tools/references/models-spatial.md +0 -432
- package/skills/scvi-tools/references/models-specialized.md +0 -376
- package/skills/scvi-tools/references/theoretical-foundations.md +0 -438
- package/skills/scvi-tools/references/workflows.md +0 -559
- package/skills/seaborn/references/examples.md +0 -824
- package/skills/seaborn/references/function_reference.md +0 -772
- package/skills/seaborn/references/grids_and_levels.md +0 -85
- package/skills/seaborn/references/objects_interface.md +0 -963
- package/skills/seaborn/references/palettes_and_theming.md +0 -110
- package/skills/seaborn/references/patterns_and_troubleshooting.md +0 -114
- package/skills/seaborn/references/plotting_functions.md +0 -178
- package/skills/shap/references/data-maskers.md +0 -287
- package/skills/shap/references/explainers.md +0 -376
- package/skills/shap/references/migration.md +0 -415
- package/skills/shap/references/modalities.md +0 -353
- package/skills/shap/references/plots.md +0 -406
- package/skills/shap/references/theory.md +0 -352
- package/skills/shap/references/troubleshooting.md +0 -442
- package/skills/shap/references/workflows.md +0 -565
- package/skills/shap/scripts/tabular_report.py +0 -326
- package/skills/simpy/references/cli-guide.md +0 -266
- package/skills/simpy/references/events.md +0 -225
- package/skills/simpy/references/monitoring.md +0 -260
- package/skills/simpy/references/process-interaction.md +0 -269
- package/skills/simpy/references/real-time.md +0 -174
- package/skills/simpy/references/resources.md +0 -274
- package/skills/simpy/references/simulation-methodology.md +0 -293
- package/skills/simpy/references/sources.md +0 -167
- package/skills/simpy/scripts/_common.py +0 -473
- package/skills/simpy/scripts/basic_simulation_template.py +0 -415
- package/skills/simpy/scripts/bounded_queue_scenario.py +0 -126
- package/skills/simpy/scripts/event_trace_summary.py +0 -296
- package/skills/simpy/scripts/replication_runner.py +0 -194
- package/skills/simpy/scripts/resource_monitor.py +0 -474
- package/skills/simpy/scripts/validate_simulation_config.py +0 -111
- package/skills/stable-baselines3/references/algorithms.md +0 -348
- package/skills/stable-baselines3/references/callbacks.md +0 -571
- package/skills/stable-baselines3/references/custom_environments.md +0 -528
- package/skills/stable-baselines3/references/vectorized_envs.md +0 -580
- package/skills/stable-baselines3/scripts/custom_env_template.py +0 -314
- package/skills/stable-baselines3/scripts/evaluate_agent.py +0 -245
- package/skills/stable-baselines3/scripts/train_rl_agent.py +0 -165
- package/skills/statistical-analysis/references/assumptions_and_diagnostics.md +0 -379
- package/skills/statistical-analysis/references/bayesian_statistics.md +0 -686
- package/skills/statistical-analysis/references/effect_sizes_and_power.md +0 -649
- package/skills/statistical-analysis/references/reporting_standards.md +0 -482
- package/skills/statistical-analysis/references/test_selection_guide.md +0 -129
- package/skills/statistical-analysis/scripts/assumption_checks.py +0 -652
- package/skills/statistical-power/references/closed_form_recipes.md +0 -174
- package/skills/statistical-power/references/effect_sizes.md +0 -121
- package/skills/statistical-power/references/simulation_based_power.md +0 -101
- package/skills/statistical-power/scripts/power.py +0 -320
- package/skills/statistical-power/scripts/simulate_power.py +0 -217
- package/skills/statsmodels/references/discrete_choice.md +0 -669
- package/skills/statsmodels/references/glm.md +0 -619
- package/skills/statsmodels/references/linear_models.md +0 -447
- package/skills/statsmodels/references/model_selection.md +0 -99
- package/skills/statsmodels/references/modeling_capabilities.md +0 -168
- package/skills/statsmodels/references/quick_start_guide.md +0 -154
- package/skills/statsmodels/references/stats_diagnostics.md +0 -859
- package/skills/statsmodels/references/time_series.md +0 -723
- package/skills/sympy/references/advanced-topics.md +0 -635
- package/skills/sympy/references/code-generation-printing.md +0 -628
- package/skills/sympy/references/core-capabilities.md +0 -348
- package/skills/sympy/references/core_capabilities.md +0 -190
- package/skills/sympy/references/matrices-linear-algebra.md +0 -526
- package/skills/sympy/references/physics-mechanics.md +0 -592
- package/skills/tamarind/references/api_reference.md +0 -165
- package/skills/tamarind/references/examples.md +0 -132
- package/skills/tamarind/references/tool_catalog.md +0 -66
- package/skills/tamarind/references/workflows.md +0 -263
- package/skills/timesfm-forecasting/examples/anomaly-detection/detect_anomalies.py +0 -524
- package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.json +0 -448
- package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.png +0 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py +0 -568
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_data.png +0 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_metadata.json +0 -59
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/sales_with_covariates.csv +0 -109
- package/skills/timesfm-forecasting/examples/global-temperature/generate_animation_data.py +0 -147
- package/skills/timesfm-forecasting/examples/global-temperature/generate_gif.py +0 -248
- package/skills/timesfm-forecasting/examples/global-temperature/generate_html.py +0 -544
- package/skills/timesfm-forecasting/examples/global-temperature/output/animation_data.json +0 -5441
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_animation.gif +0 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.csv +0 -13
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.json +0 -188
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_visualization.png +0 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/interactive_forecast.html +0 -5939
- package/skills/timesfm-forecasting/examples/global-temperature/run_example.sh +0 -53
- package/skills/timesfm-forecasting/examples/global-temperature/run_forecast.py +0 -167
- package/skills/timesfm-forecasting/examples/global-temperature/temperature_anomaly.csv +0 -37
- package/skills/timesfm-forecasting/examples/global-temperature/visualize_forecast.py +0 -123
- package/skills/timesfm-forecasting/references/api_reference.md +0 -231
- package/skills/timesfm-forecasting/references/data_preparation.md +0 -272
- package/skills/timesfm-forecasting/references/examples_and_validation.md +0 -103
- package/skills/timesfm-forecasting/references/output_and_config.md +0 -93
- package/skills/timesfm-forecasting/references/performance_tuning.md +0 -80
- package/skills/timesfm-forecasting/references/system_requirements.md +0 -201
- package/skills/timesfm-forecasting/references/workflows.md +0 -126
- package/skills/timesfm-forecasting/scripts/check_system.py +0 -521
- package/skills/timesfm-forecasting/scripts/forecast_csv.py +0 -269
- package/skills/torch-geometric/references/custom_datasets.md +0 -239
- package/skills/torch-geometric/references/explainability.md +0 -208
- package/skills/torch-geometric/references/heterogeneous.md +0 -241
- package/skills/torch-geometric/references/link_prediction.md +0 -226
- package/skills/torch-geometric/references/message_passing.md +0 -121
- package/skills/torch-geometric/references/scaling.md +0 -269
- package/skills/torchdrug/references/core_concepts.md +0 -241
- package/skills/torchdrug/references/datasets.md +0 -179
- package/skills/torchdrug/references/knowledge_graphs.md +0 -226
- package/skills/torchdrug/references/models_architectures.md +0 -223
- package/skills/torchdrug/references/molecular_generation.md +0 -246
- package/skills/torchdrug/references/molecular_property_prediction.md +0 -239
- package/skills/torchdrug/references/protein_modeling.md +0 -221
- package/skills/torchdrug/references/retrosynthesis.md +0 -247
- package/skills/transformers/references/generation.md +0 -473
- package/skills/transformers/references/models.md +0 -371
- package/skills/transformers/references/pipelines.md +0 -334
- package/skills/transformers/references/tokenizers.md +0 -449
- package/skills/transformers/references/training.md +0 -504
- package/skills/treatment-plans/assets/clinician_authored_intervention_template.json +0 -11
- package/skills/treatment-plans/assets/goals_monitoring_checkpoint_template.json +0 -13
- package/skills/treatment-plans/assets/informed_preference_shared_decision_template.json +0 -11
- package/skills/treatment-plans/assets/intended_use_handoff_template.json +0 -83
- package/skills/treatment-plans/assets/source_fact_manifest_template.json +0 -11
- package/skills/treatment-plans/assets/transition_reconciliation_template.json +0 -27
- package/skills/treatment-plans/references/documentation_workflow.md +0 -165
- package/skills/treatment-plans/references/privacy_governance.md +0 -119
- package/skills/treatment-plans/references/safety_scope.md +0 -101
- package/skills/treatment-plans/references/security_validation.md +0 -68
- package/skills/treatment-plans/references/shared_decision_handoff.md +0 -138
- package/skills/treatment-plans/references/source_boundaries.md +0 -127
- package/skills/treatment-plans/references/source_ledger.md +0 -131
- package/skills/treatment-plans/scripts/_common.py +0 -1160
- package/skills/treatment-plans/scripts/check_completeness.py +0 -572
- package/skills/treatment-plans/scripts/check_consistency.py +0 -386
- package/skills/treatment-plans/scripts/generate_template.py +0 -133
- package/skills/treatment-plans/scripts/privacy_process_check.py +0 -213
- package/skills/treatment-plans/scripts/timeline_generator.py +0 -260
- package/skills/treatment-plans/scripts/validate_traceability.py +0 -147
- package/skills/treatment-plans/scripts/validate_treatment_plan.py +0 -95
- package/skills/umap-learn/references/api_reference.md +0 -574
- package/skills/uncertainty-and-units/references/domain-conversions.md +0 -188
- package/skills/uncertainty-and-units/references/gum-methodology.md +0 -219
- package/skills/uncertainty-and-units/references/pint-recipes.md +0 -228
- package/skills/uncertainty-and-units/references/plausibility-scales.md +0 -168
- package/skills/uncertainty-and-units/references/reporting-rules.md +0 -133
- package/skills/uncertainty-and-units/references/uncertainties-recipes.md +0 -167
- package/skills/uncertainty-and-units/scripts/_common.py +0 -666
- package/skills/uncertainty-and-units/scripts/audit_units.py +0 -575
- package/skills/uncertainty-and-units/scripts/check_plausibility.py +0 -894
- package/skills/uncertainty-and-units/scripts/convert_units.py +0 -280
- package/skills/uncertainty-and-units/scripts/format_result.py +0 -326
- package/skills/uncertainty-and-units/scripts/propagate_uncertainty.py +0 -662
- package/skills/uncertainty-and-units/scripts/uncertainty_budget.py +0 -363
- package/skills/usfiscaldata/references/api-basics.md +0 -105
- package/skills/usfiscaldata/references/datasets-debt.md +0 -166
- package/skills/usfiscaldata/references/datasets-fiscal.md +0 -212
- package/skills/usfiscaldata/references/datasets-interest-rates.md +0 -188
- package/skills/usfiscaldata/references/datasets-securities.md +0 -238
- package/skills/usfiscaldata/references/examples.md +0 -258
- package/skills/usfiscaldata/references/parameters.md +0 -182
- package/skills/usfiscaldata/references/response-format.md +0 -178
- package/skills/vaex/references/core_dataframes.md +0 -373
- package/skills/vaex/references/data_processing.md +0 -555
- package/skills/vaex/references/io_operations.md +0 -718
- package/skills/vaex/references/machine_learning.md +0 -728
- package/skills/vaex/references/performance.md +0 -571
- package/skills/vaex/references/visualization.md +0 -644
- package/skills/venue-templates/assets/examples/cell_summary_example.md +0 -247
- package/skills/venue-templates/assets/examples/medical_structured_abstract.md +0 -313
- package/skills/venue-templates/assets/examples/nature_abstract_examples.md +0 -213
- package/skills/venue-templates/assets/examples/neurips_introduction_example.md +0 -245
- package/skills/venue-templates/assets/grants/nih_specific_aims.tex +0 -237
- package/skills/venue-templates/assets/grants/nsf_proposal_template.tex +0 -384
- package/skills/venue-templates/assets/journals/elsarticle-harv.bst +0 -1598
- package/skills/venue-templates/assets/journals/elsarticle-num-names.bst +0 -1535
- package/skills/venue-templates/assets/journals/elsarticle-num.bst +0 -1509
- package/skills/venue-templates/assets/journals/elsarticle-template-harv.tex +0 -286
- package/skills/venue-templates/assets/journals/elsarticle-template-num-names.tex +0 -284
- package/skills/venue-templates/assets/journals/elsarticle-template-num.tex +0 -286
- package/skills/venue-templates/assets/journals/nature_article.tex +0 -174
- package/skills/venue-templates/assets/journals/neurips_article.tex +0 -292
- package/skills/venue-templates/assets/journals/plos_one.tex +0 -320
- package/skills/venue-templates/assets/posters/beamerposter_academic.tex +0 -312
- package/skills/venue-templates/references/cell_press_style.md +0 -486
- package/skills/venue-templates/references/conferences_formatting.md +0 -175
- package/skills/venue-templates/references/cs_conference_style.md +0 -465
- package/skills/venue-templates/references/grants_requirements.md +0 -267
- package/skills/venue-templates/references/journals_formatting.md +0 -200
- package/skills/venue-templates/references/medical_journal_styles.md +0 -536
- package/skills/venue-templates/references/ml_conference_style.md +0 -562
- package/skills/venue-templates/references/nature_science_style.md +0 -407
- package/skills/venue-templates/references/posters_guidelines.md +0 -630
- package/skills/venue-templates/references/reviewer_expectations.md +0 -422
- package/skills/venue-templates/references/venue_writing_styles.md +0 -323
- package/skills/venue-templates/scripts/customize_template.py +0 -206
- package/skills/venue-templates/scripts/query_template.py +0 -202
- package/skills/venue-templates/scripts/validate_format.py +0 -321
- package/skills/waypoint-bio/references/cli-reference.md +0 -210
- package/skills/waypoint-bio/references/compass-benchmark.md +0 -124
- package/skills/waypoint-bio/references/data-preparation.md +0 -200
- package/skills/waypoint-bio/references/python-api.md +0 -219
- package/skills/waypoint-bio/scripts/profiler_to_waypoint.py +0 -481
- package/skills/waypoint-bio/scripts/vocab_coverage.py +0 -235
- package/skills/what-if-oracle/references/scenario-templates.md +0 -137
- package/skills/xlsx/LICENSE.txt +0 -30
- package/skills/xlsx/scripts/office/helpers/__init__.py +0 -111
- package/skills/xlsx/scripts/office/helpers/pptx_chart.py +0 -170
- package/skills/xlsx/scripts/office/helpers/pptx_slide.py +0 -60
- package/skills/xlsx/scripts/office/helpers/pptx_theme.py +0 -114
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -1499
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -146
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -1085
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -11
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -3081
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -23
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -185
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -287
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -1676
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -28
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -144
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -174
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -25
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -18
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -59
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -56
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -195
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -582
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -25
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -4439
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -570
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -509
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -12
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -108
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -96
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -3646
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -116
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -42
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -50
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -49
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -33
- package/skills/xlsx/scripts/office/schemas/mce/mc.xsd +0 -75
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +0 -560
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +0 -67
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +0 -14
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +0 -20
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
- package/skills/xlsx/scripts/office/soffice.py +0 -232
- package/skills/xlsx/scripts/office/validate.py +0 -173
- package/skills/xlsx/scripts/office/validators/__init__.py +0 -15
- package/skills/xlsx/scripts/office/validators/base.py +0 -875
- package/skills/xlsx/scripts/office/validators/docx.py +0 -466
- package/skills/xlsx/scripts/office/validators/pptx.py +0 -441
- package/skills/xlsx/scripts/office/validators/redlining.py +0 -299
- package/skills/xlsx/scripts/recalc.py +0 -308
- package/skills/zarr-python/references/api_reference.md +0 -162
- package/skills/zarr-python/references/chunking_and_compression.md +0 -138
- package/skills/zarr-python/references/integration.md +0 -147
- package/skills/zarr-python/references/performance_and_patterns.md +0 -198
- package/skills/zarr-python/references/storage_backends.md +0 -91
- package/skills/zarr-python/references/v3_migration.md +0 -127
|
@@ -1,859 +0,0 @@
|
|
|
1
|
-
# Statistical Tests and Diagnostics Reference
|
|
2
|
-
|
|
3
|
-
This document provides comprehensive guidance on statistical tests, diagnostics, and tools available in statsmodels.
|
|
4
|
-
|
|
5
|
-
## Overview
|
|
6
|
-
|
|
7
|
-
Statsmodels provides extensive statistical testing capabilities:
|
|
8
|
-
- Residual diagnostics and specification tests
|
|
9
|
-
- Hypothesis testing (parametric and non-parametric)
|
|
10
|
-
- Goodness-of-fit tests
|
|
11
|
-
- Multiple comparisons and post-hoc tests
|
|
12
|
-
- Power and sample size calculations
|
|
13
|
-
- Robust covariance matrices
|
|
14
|
-
- Influence and outlier detection
|
|
15
|
-
|
|
16
|
-
## Residual Diagnostics
|
|
17
|
-
|
|
18
|
-
### Autocorrelation Tests
|
|
19
|
-
|
|
20
|
-
**Ljung-Box Test**: Tests for autocorrelation in residuals
|
|
21
|
-
|
|
22
|
-
```python
|
|
23
|
-
from statsmodels.stats.diagnostic import acorr_ljungbox
|
|
24
|
-
|
|
25
|
-
# Test residuals for autocorrelation
|
|
26
|
-
lb_test = acorr_ljungbox(residuals, lags=10, return_df=True)
|
|
27
|
-
print(lb_test)
|
|
28
|
-
|
|
29
|
-
# H0: No autocorrelation up to lag k
|
|
30
|
-
# If p-value < 0.05, reject H0 (autocorrelation present)
|
|
31
|
-
```
|
|
32
|
-
|
|
33
|
-
**Durbin-Watson Test**: Tests for first-order autocorrelation
|
|
34
|
-
|
|
35
|
-
```python
|
|
36
|
-
from statsmodels.stats.stattools import durbin_watson
|
|
37
|
-
|
|
38
|
-
dw_stat = durbin_watson(residuals)
|
|
39
|
-
print(f"Durbin-Watson: {dw_stat:.4f}")
|
|
40
|
-
|
|
41
|
-
# DW ≈ 2: no autocorrelation
|
|
42
|
-
# DW < 2: positive autocorrelation
|
|
43
|
-
# DW > 2: negative autocorrelation
|
|
44
|
-
# Exact critical values depend on n and k
|
|
45
|
-
```
|
|
46
|
-
|
|
47
|
-
**Breusch-Godfrey Test**: More general test for autocorrelation
|
|
48
|
-
|
|
49
|
-
```python
|
|
50
|
-
from statsmodels.stats.diagnostic import acorr_breusch_godfrey
|
|
51
|
-
|
|
52
|
-
bg_test = acorr_breusch_godfrey(results, nlags=5)
|
|
53
|
-
lm_stat, lm_pval, f_stat, f_pval = bg_test
|
|
54
|
-
|
|
55
|
-
print(f"LM statistic: {lm_stat:.4f}, p-value: {lm_pval:.4f}")
|
|
56
|
-
# H0: No autocorrelation up to lag k
|
|
57
|
-
```
|
|
58
|
-
|
|
59
|
-
### Heteroskedasticity Tests
|
|
60
|
-
|
|
61
|
-
**Breusch-Pagan Test**: Tests for heteroskedasticity
|
|
62
|
-
|
|
63
|
-
```python
|
|
64
|
-
from statsmodels.stats.diagnostic import het_breuschpagan
|
|
65
|
-
|
|
66
|
-
bp_test = het_breuschpagan(residuals, exog)
|
|
67
|
-
lm_stat, lm_pval, f_stat, f_pval = bp_test
|
|
68
|
-
|
|
69
|
-
print(f"Breusch-Pagan test p-value: {lm_pval:.4f}")
|
|
70
|
-
# H0: Homoskedasticity (constant variance)
|
|
71
|
-
# If p-value < 0.05, reject H0 (heteroskedasticity present)
|
|
72
|
-
```
|
|
73
|
-
|
|
74
|
-
**White Test**: More general test for heteroskedasticity
|
|
75
|
-
|
|
76
|
-
```python
|
|
77
|
-
from statsmodels.stats.diagnostic import het_white
|
|
78
|
-
|
|
79
|
-
white_test = het_white(residuals, exog)
|
|
80
|
-
lm_stat, lm_pval, f_stat, f_pval = white_test
|
|
81
|
-
|
|
82
|
-
print(f"White test p-value: {lm_pval:.4f}")
|
|
83
|
-
# H0: Homoskedasticity
|
|
84
|
-
```
|
|
85
|
-
|
|
86
|
-
**ARCH Test**: Tests for autoregressive conditional heteroskedasticity
|
|
87
|
-
|
|
88
|
-
```python
|
|
89
|
-
from statsmodels.stats.diagnostic import het_arch
|
|
90
|
-
|
|
91
|
-
arch_test = het_arch(residuals, nlags=5)
|
|
92
|
-
lm_stat, lm_pval, f_stat, f_pval = arch_test
|
|
93
|
-
|
|
94
|
-
print(f"ARCH test p-value: {lm_pval:.4f}")
|
|
95
|
-
# H0: No ARCH effects
|
|
96
|
-
# If significant, consider GARCH model
|
|
97
|
-
```
|
|
98
|
-
|
|
99
|
-
### Normality Tests
|
|
100
|
-
|
|
101
|
-
**Jarque-Bera Test**: Tests for normality using skewness and kurtosis
|
|
102
|
-
|
|
103
|
-
```python
|
|
104
|
-
from statsmodels.stats.stattools import jarque_bera
|
|
105
|
-
|
|
106
|
-
jb_stat, jb_pval, skew, kurtosis = jarque_bera(residuals)
|
|
107
|
-
|
|
108
|
-
print(f"Jarque-Bera statistic: {jb_stat:.4f}")
|
|
109
|
-
print(f"p-value: {jb_pval:.4f}")
|
|
110
|
-
print(f"Skewness: {skew:.4f}")
|
|
111
|
-
print(f"Kurtosis: {kurtosis:.4f}")
|
|
112
|
-
|
|
113
|
-
# H0: Residuals are normally distributed
|
|
114
|
-
# Normal: skewness ≈ 0, kurtosis ≈ 3
|
|
115
|
-
```
|
|
116
|
-
|
|
117
|
-
**Omnibus Test**: Another normality test (also based on skewness/kurtosis)
|
|
118
|
-
|
|
119
|
-
```python
|
|
120
|
-
from statsmodels.stats.stattools import omni_normtest
|
|
121
|
-
|
|
122
|
-
omni_stat, omni_pval = omni_normtest(residuals)
|
|
123
|
-
print(f"Omnibus test p-value: {omni_pval:.4f}")
|
|
124
|
-
# H0: Normality
|
|
125
|
-
```
|
|
126
|
-
|
|
127
|
-
**Anderson-Darling Test**: Distribution fit test
|
|
128
|
-
|
|
129
|
-
```python
|
|
130
|
-
from statsmodels.stats.diagnostic import normal_ad
|
|
131
|
-
|
|
132
|
-
ad_stat, ad_pval = normal_ad(residuals)
|
|
133
|
-
print(f"Anderson-Darling test p-value: {ad_pval:.4f}")
|
|
134
|
-
```
|
|
135
|
-
|
|
136
|
-
**Lilliefors Test**: Modified Kolmogorov-Smirnov test
|
|
137
|
-
|
|
138
|
-
```python
|
|
139
|
-
from statsmodels.stats.diagnostic import lilliefors
|
|
140
|
-
|
|
141
|
-
lf_stat, lf_pval = lilliefors(residuals, dist='norm')
|
|
142
|
-
print(f"Lilliefors test p-value: {lf_pval:.4f}")
|
|
143
|
-
```
|
|
144
|
-
|
|
145
|
-
### Linearity and Specification Tests
|
|
146
|
-
|
|
147
|
-
**Ramsey RESET Test**: Tests for functional form misspecification
|
|
148
|
-
|
|
149
|
-
```python
|
|
150
|
-
from statsmodels.stats.diagnostic import linear_reset
|
|
151
|
-
|
|
152
|
-
reset_test = linear_reset(results, power=2)
|
|
153
|
-
f_stat, f_pval = reset_test
|
|
154
|
-
|
|
155
|
-
print(f"RESET test p-value: {f_pval:.4f}")
|
|
156
|
-
# H0: Model is correctly specified (linear)
|
|
157
|
-
# If rejected, may need polynomial terms or transformations
|
|
158
|
-
```
|
|
159
|
-
|
|
160
|
-
**Harvey-Collier Test**: Tests for linearity
|
|
161
|
-
|
|
162
|
-
```python
|
|
163
|
-
from statsmodels.stats.diagnostic import linear_harvey_collier
|
|
164
|
-
|
|
165
|
-
hc_stat, hc_pval = linear_harvey_collier(results)
|
|
166
|
-
print(f"Harvey-Collier test p-value: {hc_pval:.4f}")
|
|
167
|
-
# H0: Linear specification is correct
|
|
168
|
-
```
|
|
169
|
-
|
|
170
|
-
## Multicollinearity Detection
|
|
171
|
-
|
|
172
|
-
**Variance Inflation Factor (VIF)**:
|
|
173
|
-
|
|
174
|
-
```python
|
|
175
|
-
from statsmodels.stats.outliers_influence import variance_inflation_factor
|
|
176
|
-
import pandas as pd
|
|
177
|
-
|
|
178
|
-
# Calculate VIF for each variable
|
|
179
|
-
vif_data = pd.DataFrame()
|
|
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
|