{"name":"@jennifer/forensicgenetics","description":"Forensic and statistical genetics: STR match probabilities, kinship and paternity likelihood ratios, general-pedigree peeling, and mtDNA / Y-STR lineage markers.","versions":{"0.1.0":{"version":"0.1.0","kind":"git","url":"https://github.com/deckyard/deck-forensicgenetics.git","ref":"0.1.0","commit":"b673451817674d2c17ed9594a340bab64a53fb84","checksum":"","yanked":true,"license":"LGPL-3.0-only","requires":{},"engines":{"jennifer":"\u003e=0.25.0","jennifer-tiny":"\u003e=0.25.0"},"capabilities":[],"keywords":["forensics","genetics","str","kinship","paternity"],"description":"Forensic and statistical genetics: STR match probabilities, kinship and paternity likelihood ratios, general-pedigree peeling, and mtDNA / Y-STR lineage markers.","publishedAt":"1793622057","repoId":1350405155,"repoOwnerId":346943577,"repoOwner":"deckyard"}},"readme":"# @jennifer/forensicgenetics\n\n[![test](https://github.com/jennifer-language/deck-forensicgenetics/actions/workflows/test.yml/badge.svg)](https://github.com/jennifer-language/deck-forensicgenetics/actions/workflows/test.yml)\n[![Documentation](https://img.shields.io/badge/docs-github%20pages-blue)](https://jennifer-language.github.io/deck-forensicgenetics/)\n[![release](https://img.shields.io/github/v/release/jennifer-language/deck-forensicgenetics)](https://github.com/jennifer-language/deck-forensicgenetics/releases/latest)\n\nForensic and statistical genetics for [Jennifer](https://jennifer-lang.dev/) -\nthe statistical-genetics sibling of the sequence deck. It works on **profiles**\n(an unordered allele pair per autosomal STR locus, plus uniparental haplotypes\nfor mtDNA and Y-STR) and on reference **frequency / count** data, not on\nsequences.\n\nRequires Jennifer 0.25.0 or newer. Pure Jennifer over the system libraries: no\ndeck dependencies, and nothing that stops it running on `jennifer-tiny`.\n\n## Documentation\n\n**\u003chttps://jennifer-language.github.io/deck-forensicgenetics/\u003e**\n\nThe manual is the whole story - installing, the statistical model behind each\nestimator, worked examples, the complete API reference, and the limitations\nthat matter before you quote a number.\n\n| | |\n| --- | --- |\n| Start here | [Quick start](https://jennifer-language.github.io/deck-forensicgenetics/getting-started/quick-start.html), [Installing the deck](https://jennifer-language.github.io/deck-forensicgenetics/getting-started/installation.html) |\n| Casework | [match probability](https://jennifer-language.github.io/deck-forensicgenetics/casework/match-probability.html), [mixtures](https://jennifer-language.github.io/deck-forensicgenetics/casework/mixtures.html), [kinship](https://jennifer-language.github.io/deck-forensicgenetics/casework/kinship.html), [paternity](https://jennifer-language.github.io/deck-forensicgenetics/casework/paternity.html), [pedigrees](https://jennifer-language.github.io/deck-forensicgenetics/casework/pedigrees.html), [lineage markers](https://jennifer-language.github.io/deck-forensicgenetics/casework/lineage.html) |\n| API reference | [forensicgenetics](https://jennifer-language.github.io/deck-forensicgenetics/reference/forensicgenetics.html), [kinship](https://jennifer-language.github.io/deck-forensicgenetics/reference/kinship.html), [pedigree](https://jennifer-language.github.io/deck-forensicgenetics/reference/pedigree.html), [lineage](https://jennifer-language.github.io/deck-forensicgenetics/reference/lineage.html) |\n| The project | [Limitations](https://jennifer-language.github.io/deck-forensicgenetics/project/limitations.html), [Formulae and sources](https://jennifer-language.github.io/deck-forensicgenetics/project/formulae.html), [Testing and contributing](https://jennifer-language.github.io/deck-forensicgenetics/project/testing.html) |\n\n## At a glance\n\n```jennifer\nimport \"@jennifer/forensicgenetics/\" as forensics;\n\ndef db as forensics.FrequencyDb init forensics.withLocus(\n    forensics.db(\"example\"), \"D3S1358\", 1034,\n    {\"15\": 0.2456, \"16\": 0.2314, \"17\": 0.2007, \"18\": 0.3223});\ndef suspect as forensics.Profile init forensics.profile(\"S1\", [\n    forensics.genotype(\"D3S1358\", \"15\", \"16\"),\n    forensics.genotype(\"TH01\", \"6\", \"9.3\")\n]);\n\ndef rmp as float init forensics.randomMatchProbability($db, $suspect,\n    forensics.THETA_GENERAL);\ndef lr as float init forensics.matchLikelihoodRatio($db, $suspect,\n    forensics.THETA_GENERAL);\n```\n\n| Module | Import | What it does |\n| --- | --- | --- |\n| `forensicgenetics.j` | `@jennifer/forensicgenetics/` | Vendor-independent core types, Hardy-Weinberg with the NRC II theta correction, RMP, single-source LR, mixture CPI / CPE |\n| `kinship.j` | `@jennifer/forensicgenetics/kinship.j` | IBD coefficients, relationship likelihood ratios, trio paternity with a stepwise mutation model |\n| `pedigree.j` | `@jennifer/forensicgenetics/pedigree.j` | General-pedigree likelihoods by Elston-Stewart peeling |\n| `lineage.j` | `@jennifer/forensicgenetics/lineage.j` | mtDNA and Y-STR haplotypes, Clopper-Pearson counting estimates, rCRS difference nomenclature |\n\nThe core reads no published format at all - it defines the generic\n`FrequencyDb`, and a reader deck such as\n[`@mplx/strider`](https://github.com/mplx/deck-strider-frequency-converter)\nconverts a published table into it. See\n[Reference frequency data](https://jennifer-language.github.io/deck-forensicgenetics/concepts/frequency-data.html).\n\n## Not a validated forensic tool\n\nThis deck implements published estimators and is tested against them, but it\nhas not been through the validation any jurisdiction requires of software used\nin casework. Treat it as a library for research, teaching and cross-checking,\nand validate independently before it informs a real conclusion.\n\nThe bundled frequency table is synthetic - made-up numbers that exist only to\nexercise the examples. The full list of caveats is in\n[Limitations](https://jennifer-language.github.io/deck-forensicgenetics/project/limitations.html);\nit is short, and some of it will change what you do.\n\n**Do not use this deck for a legal proceeding** - a prosecution, a defence, a\npaternity ruling, an immigration decision, or any other legal determination.\nThose require validated, accredited software operated under an accredited\nprocess, and this is not that.\n\n**No warranty, no liability.** This software is provided as is, without\nwarranty of any kind, express or implied. You use it entirely at your own risk.\nThe author accepts no responsibility and no liability for any claim, damage,\nloss, or other consequence arising from this software or from any number it\nproduces. Checking that a result is correct, appropriate and lawful for your\npurpose is yours alone. This restates, and does not narrow or replace, the\ndisclaimers in the [licence](LICENSE); where they differ, the licence governs.\n\nFull text: [Not a validated forensic tool](https://jennifer-language.github.io/deck-forensicgenetics/#not-a-validated-forensic-tool).\n\n## Licence\n\nLGPL-3.0-only - see [LICENSE](LICENSE).\n"}