@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
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- 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
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# Numerical Methods, Tolerances, and Reproducibility
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This reference targets MATLAB R2026a. Confirm every non-base product before
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using toolbox-specific functions.
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## Linear systems and decompositions
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Solve systems; do not form an inverse as an intermediate:
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```matlab
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x = A \ b;
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residual = A*x - b;
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relativeResidual = norm(residual) / ...
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max(norm(A)*norm(x) + norm(b), realmin(class(A)));
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```
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Check dimensions, rank/conditioning, scaling, symmetry, definiteness, and
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sparsity. A small residual does not guarantee a small forward error for an
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ill-conditioned problem.
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Common base MATLAB operations include:
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- `lu`, `qr`, `chol`, `ldl`, `schur`;
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- `eig`, `svd`, `eigs`, `svds`;
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- `rank`, `cond`, `rcond`, `norm`, `pinv`;
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- `lsqminnorm`, `lsqnonneg`, and backslash least squares.
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Use an economy decomposition where appropriate and request only the spectrum
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needed for large/sparse problems. Eigenvector signs/phases and bases in
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degenerate subspaces are not unique; compare invariant quantities rather than
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raw vectors.
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## Floating-point comparison
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Binary floating point does not represent most decimal fractions exactly.
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Choose tolerances from the model, scale, conditioning, discretization,
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measurement uncertainty, and algorithm—not from a universal constant.
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A robust scalar/elementwise policy often has the form:
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```matlab
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errorMagnitude = abs(actual - expected);
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limit = absoluteTolerance + relativeTolerance .* abs(expected);
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isAcceptable = errorMagnitude <= limit;
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```
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Handle these explicitly:
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- expected values near zero need an absolute tolerance;
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- large expected values often need a relative tolerance;
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- `NaN` equality is a semantic decision (`isequaln` differs from `==`);
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- `Inf` signs should match when infinity is expected;
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- class, size, sparsity, and complex values are part of the contract.
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R2026a documents `isapprox` alongside equality operations. In
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`matlab.unittest`, use `AbsTol`/`RelTol` or
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`AbsoluteTolerance`/`RelativeTolerance`. Record why values are scientifically
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acceptable.
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Do not widen tolerances automatically after an upgrade. First investigate RNG,
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ordering, reduction order, solver defaults/options, data type, threading,
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compiler, library, and release-note changes.
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## Random streams
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Record algorithm and seed, not only a seed:
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```matlab
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rng(1729, "twister");
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stateAtStart = rng;
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samples = randn(1000, 1);
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```
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For local independent streams:
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```matlab
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stream = RandStream("Threefry", Seed=1729);
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stream.Substream = 4;
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samples = randn(stream, 1000, 1);
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```
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Generator availability and bitwise sequences can vary by algorithm/release.
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Avoid `rng("shuffle")` for reproducible work. On parallel workers, time-based
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seeding can collide; use supported independent streams/substreams and record
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worker mapping. Parallel computing requires Parallel Computing Toolbox.
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## Integration, roots, and differential equations
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Base MATLAB provides general numerical methods including:
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- `integral`, `integral2`, `integral3`, `trapz`, `cumtrapz`;
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- `gradient`, `diff`;
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- `fzero`;
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- ODE solvers such as `ode45`, `ode23`, `ode113`, `ode15s`, `ode23s`,
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`ode23t`, and `ode23tb`;
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- boundary-value solvers such as `bvp4c` and `bvp5c`.
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Define tolerances and failure criteria:
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```matlab
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options = odeset( ...
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RelTol=1e-7, ...
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AbsTol=1e-10, ...
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MaxStep=0.05);
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[t, y] = ode45(@rhs, [0 5], 1, options);
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```
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Solver tolerances control local error estimates, not proof of a globally
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correct model. Check conservation laws, event localization, stiffness,
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step-size convergence, and an independent formulation. R2026a adds an
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automatic-differentiation Jacobian option for the `ode` object; verify the
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specific solver/problem and release notes before using it.
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## Optimization and fitting boundaries
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Base MATLAB includes `fminsearch` and `fminbnd`. These do not replace
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constrained or specialized solvers.
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Examples of separately licensed boundaries:
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| Capability | Representative API | Product to confirm |
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|---|---|---|
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| constrained/nonlinear optimization | `fmincon`, `fminunc`, `lsqnonlin`, `lsqcurvefit` | Optimization Toolbox |
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| global/metaheuristic optimization | `ga`, `particleswarm`, `surrogateopt` | Global Optimization Toolbox |
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| curve fitting objects/apps | `fit`, Curve Fitter | Curve Fitting Toolbox |
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| statistical modeling/distributions | `fitlm`, `fitdist`, `anova`, many tests | Statistics and Machine Learning Toolbox |
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| symbolic algebra | `syms`, `solve`, symbolic differentiation | Symbolic Math Toolbox |
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| signal design/analysis | `fir1`, `filtfilt`, `designfilt`, `spectrogram` | Signal Processing Toolbox |
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| parallel loops/GPU | `parfor`, `parpool`, `gpuArray` | Parallel Computing Toolbox |
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Some base functions have similarly named toolbox alternatives. Check the
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function's current product page and the project dependency report; never infer
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ownership from a code example.
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Optimization reproducibility requires objective/constraint definitions,
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starting points, bounds, solver/options, stopping tolerances, gradients,
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scaling, RNG state for stochastic methods, and exit diagnostics. Compare
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feasibility and optimality measures, not only the objective value.
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## Statistics and signal processing
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Base array summaries include `mean`, `median`, `std`, `var`, `min`, `max`,
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`movmean`, `movmedian`, `cov`, `corrcoef`, `histcounts`, and polynomial
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`polyfit`/`polyval`. Some distribution, model, hypothesis-test, robust,
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classification, and specialized plotting APIs require Statistics and Machine
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Learning Toolbox.
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For FFT work:
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```matlab
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n = numel(x);
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Y = fft(x);
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frequency = (0:n-1).' * (sampleRate/n);
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```
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Document sample rate, units, window, detrending, normalization, one- versus
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two-sided spectrum, zero padding, and endpoint convention. `fft` and `conv` are
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base MATLAB; many filter-design and spectral-estimation functions are Signal
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Processing Toolbox.
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## Verification patterns
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Use several layers:
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1. **Dimensional/invariant checks**: sizes, units, conservation, monotonicity,
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positivity, symmetry.
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2. **Analytic cases**: small problems with known solutions.
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3. **Refinement studies**: mesh, step, quadrature, or tolerance convergence.
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4. **Independent implementation**: alternative solver or formulation.
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5. **Condition/sensitivity analysis**: perturb inputs and options.
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6. **Release comparison**: compare scientifically meaningful observables with
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a documented tolerance.
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7. **Performance measurement**: after correctness, measure representative
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workloads with `timeit`.
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Do not claim bitwise reproducibility across releases, hardware, thread counts,
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GPU/CPU, or external libraries unless it was actually tested and documented.
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## Reproducibility record
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At minimum capture:
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- MATLAB release/update or Octave version;
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- OS and architecture, only as named fields;
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- required products and license status separately;
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- source/input hashes and schema versions;
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- numeric classes and shapes;
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- RNG algorithm, seed, substream, and parallel mapping;
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- solver names/options/tolerances and stopping diagnostics;
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- expected invariants and acceptance tolerances;
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- output format/version and graphics export settings.
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Use `scripts/reproducibility_report.py` to hash only named local artifacts. It
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does not inspect the broad environment.
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## Sources (verified 2026-07-23)
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- [Linear Algebra](https://www.mathworks.com/help/matlab/linear-algebra.html)
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- [`mldivide`](https://www.mathworks.com/help/matlab/ref/double.mldivide.html)
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- [`eq` floating-point guidance and `isapprox`](https://www.mathworks.com/help/matlab/ref/double.eq.html)
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- [`AbsoluteTolerance`](https://www.mathworks.com/help/matlab/ref/matlab.unittest.constraints.absolutetolerance-class.html)
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- [`RelativeTolerance`](https://www.mathworks.com/help/matlab/ref/matlab.unittest.constraints.relativetolerance-class.html)
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- [`rng`](https://www.mathworks.com/help/matlab/ref/rng.html)
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- [`RandStream`](https://www.mathworks.com/help/matlab/ref/randstream.html)
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- [ODE Solvers](https://www.mathworks.com/help/matlab/ordinary-differential-equations.html)
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- [Optimization](https://www.mathworks.com/help/matlab/optimization.html)
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- [MATLAB product list and pricing/licensing](https://www.mathworks.com/pricing-licensing.html)
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- [MATLAB R2026a release notes](https://www.mathworks.com/help/matlab/release-notes.html)
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@@ -1,228 +0,0 @@
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# Arrays, Indexing, Data Types, and Performance
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This reference targets MATLAB R2026a. Verify GNU Octave behavior separately.
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## Array model
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MATLAB is 1-based and column-major. Most numeric literals are `double`.
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Orientation and trailing singleton dimensions matter.
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```matlab
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row = 1:5; % 1-by-5
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column = (1:5).'; % 5-by-1, nonconjugate transpose
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A = reshape(1:12, 3, 4); % values fill down columns
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sameShape = zeros(size(A), "like", A);
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singleData = zeros(100, 1, "single");
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logicalMask = false(size(A));
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```
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Use `.'` for a plain transpose and `'` for a conjugate transpose. Use
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`size(A,dim)`, `numel`, and `ndims`; avoid `length` when a specific dimension
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is intended.
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### Core storage choices
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| Type | Use | Caution |
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|---|---|---|
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| dense numeric/logical array | homogeneous computation | implicit conversion and memory |
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| sparse numeric/logical array | low-density 2-D matrices | not every operation preserves sparsity |
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| string array | text with missing values | differs from character arrays |
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| categorical | finite labels and ordering | undefined category is missing |
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| cell array | heterogeneous containers | `{}` versus `()` semantics |
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| structure | named heterogeneous fields | structure arrays complicate shape |
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| table | named, equal-height variables | `()` versus `{}` versus dot indexing |
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| timetable | table with row times | time zone, sorting, duplicates, alignment |
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| datetime/duration | time points/elapsed time | time zones and calendar duration differ |
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Choose integer classes for storage or exact integer semantics, not as a drop-in
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for floating computation. Integer overflow and mixed-class operations need
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explicit tests. Preserve units in names or metadata.
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## Indexing
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```matlab
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value = A(2, 3); % row 2, column 3
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linear = A(5); % column-major linear index
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row = A(2, :);
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lastRows = A(max(1,end-2):end, :);
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positive = A(A > 0);
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A(A < 0) = 0;
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[r, c] = ind2sub(size(A), linearIndex);
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linearIndex = sub2ind(size(A), r, c);
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```
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Prefer logical indexing for selection and `find` only when numeric indices are
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needed. Verify mask shape. Deleting with `A(index)=[]` changes shape and can be
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ambiguous for multidimensional arrays.
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### Cell, structure, and table indexing
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```matlab
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C = {42, "sample"; [1 2], datetime("today")};
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cellContainer = C(1, :); % still a cell array
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cellContent = C{1, 1}; % contained value
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S.SampleID = "S01";
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name = S.("SampleID");
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tableSlice = T(1:10, ["Time" "Value"]); % table
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numericValues = T{:, "Value"}; % underlying content
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oneVariable = T.Value; % variable content
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```
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Curly extraction from a table succeeds only when selected variable contents
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can concatenate. Preserve table form when variable names and metadata matter.
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## Operators and implicit expansion
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| Operation | Matrix | Element-wise |
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|---|---|---|
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| multiply | `A*B` | `A.*B` |
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rank must be stable.
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diagnosis.
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speedups that can change old trade-offs.
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shape. `zeros(size(x),"like",x)` is usually safer than an unqualified `zeros`.
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## Numerical review checklist
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- [ ] Preallocation and vectorization are measured, not assumed.
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- [ ] Memory estimates include temporaries and expanded outputs.
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## Sources (verified 2026-07-23)
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- [Array Indexing](https://www.mathworks.com/help/matlab/math/array-indexing.html)
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- [Compatible Array Sizes for Basic Operations](https://www.mathworks.com/help/matlab/matlab_prog/compatible-array-sizes-for-basic-operations.html)
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- [MATLAB Data Types](https://www.mathworks.com/help/matlab/data-types.html)
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- [Tables](https://www.mathworks.com/help/matlab/tables.html)
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- [Missing Data in MATLAB](https://www.mathworks.com/help/matlab/data_analysis/missing-data-in-matlab.html)
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- [Vectorization](https://www.mathworks.com/help/matlab/matlab_prog/vectorization.html)
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- [Preallocation](https://www.mathworks.com/help/matlab/matlab_prog/preallocating-arrays.html)
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- [`timeit`](https://www.mathworks.com/help/matlab/ref/timeit.html)
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- [Profile MATLAB Code](https://www.mathworks.com/help/matlab/matlab_prog/profiling-for-improving-performance.html)
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# GNU Octave 11.3.0 Compatibility
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GNU Octave 11.3.0 is the current stable release as of 2026-07-23 (released
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## Command-line differences
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```
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The bundled planner returns argv but never executes it.
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validation, object models, and release schedules differ.
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Octave's built-in self-test system scans `%!` blocks and uses `test`. It is not
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`matlab.unittest`.
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separate when test syntax differs. The nonexecuting planner can prepare an
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Octave BIST argv, but an approved runtime is required to run it.
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## MAT and HDF5 compatibility
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Octave 11 supports writing MATLAB v4, v6, and v7 binary formats. It **does not
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Octave can save its own HDF5 representation when built with HDF5. Its `load
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-hdf5` has limited ability to read MATLAB v7.3, mainly for supported numeric
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content; many types are unsupported. An Octave HDF5 file is not automatically
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a MATLAB v7.3 file.
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Octave's current manual states that `classdef` objects are saved as structures
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in supporting formats and are not restored as `classdef` objects. This differs
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substantially from MATLAB object serialization.
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technical inventory first, then escalate object/opaque/function/external-link
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content.
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text, sparse/complex values, and metadata. Prefer schema-documented
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language-neutral formats where feasible.
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## Graphics
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similar, but renderers, fonts, properties, layout, transparency, callbacks,
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and export formats differ.
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`tiledlayout`, UI objects, or property behavior. Build a small compatibility
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test and compare exported dimensions, font embedding, vector/raster content,
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colors, and clipping.
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Octave 11 NEWS documents graphics compatibility changes such as colorbar and
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170
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event-field behavior. Review NEWS for each update.
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171
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172
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## Numerical differences
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173
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-
|
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174
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Even when both runtimes call similarly named LAPACK/BLAS-backed functions,
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175
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results can differ because of:
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176
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-
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177
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- linked libraries, versions, threads, and architecture;
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178
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- solver implementation/default/tolerance changes;
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179
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- sparse ordering and pivot choices;
|
|
180
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-
- random generator algorithms and streams;
|
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181
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- toolbox/package algorithms;
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182
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- floating reduction order;
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183
|
-
- unsupported or converted classes.
|
|
184
|
-
|
|
185
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-
Compare residuals, invariants, objective/feasibility, and domain observables.
|
|
186
|
-
Do not demand identical eigenvector signs, cluster bases, or bitwise
|
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187
|
-
floating-point output without a justified contract.
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|
188
|
-
|
|
189
|
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## Portability checklist
|
|
190
|
-
|
|
191
|
-
- [ ] Exact MATLAB and Octave versions recorded.
|
|
192
|
-
- [ ] Core versus toolbox/package requirements separated.
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|
193
|
-
- [ ] Only portable syntax used in shared source.
|
|
194
|
-
- [ ] Shapes, missing values, strings, and implicit expansion tested.
|
|
195
|
-
- [ ] RNG algorithm/seed behavior tested separately.
|
|
196
|
-
- [ ] Numerical tolerances justified.
|
|
197
|
-
- [ ] MAT/HDF5 round trips cover every used class.
|
|
198
|
-
- [ ] Graphics compared from exported files.
|
|
199
|
-
- [ ] Runtime-specific tests and deployment kept separate.
|
|
200
|
-
- [ ] No package installation or code execution occurred implicitly.
|
|
201
|
-
|
|
202
|
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## Sources (verified 2026-07-23)
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|
203
|
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|
|
204
|
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- [GNU Octave home/current release](https://octave.org/)
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|
205
|
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- [GNU Octave 11 release notes](https://octave.org/NEWS-11.html)
|
|
206
|
-
- [GNU Octave current manual](https://docs.octave.org/latest/)
|
|
207
|
-
- [Command-Line Options](https://docs.octave.org/latest/Command-Line-Options.html)
|
|
208
|
-
- [Startup Files](https://docs.octave.org/latest/Startup-Files.html)
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|
209
|
-
- [Simple File I/O and MAT v7.3 limitation](https://docs.octave.org/latest/Simple-File-I_002fO.html)
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|
210
|
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- [`classdef` compatibility status](https://docs.octave.org/latest/classdef-Classes.html)
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211
|
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- [Test Functions](https://docs.octave.org/latest/Test-Functions.html)
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212
|
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- [GNU GPL](https://octave.org/license.html)
|