#@jennifer/forensicgenetics

Forensic and statistical genetics for Jennifer.

This deck works on profiles - an unordered allele pair per autosomal STR locus, plus uniparental haplotypes for mtDNA and Y-STR - and on reference frequency or count data. It does not work on sequences; that is the sequence deck's job, and the two share no code.

#What it answers

Four questions, each with its own module:

Could this stain have come from someone else? A random match probability from Hardy-Weinberg genotype frequencies with the NRC II theta correction, multiplied across a panel - and its reciprocal, the single-source likelihood ratio. For a mixed stain, the combined probability of inclusion and exclusion instead. See Match probability and Mixtures.

Are these two people related, and how? A likelihood ratio built from the pair's IBD coefficients, testing one relationship against another. See Kinship.

Is this man the child's father? A trio calculation over mother, child and alleged father, with a stepwise mutation model so that one inconsistent locus is not a false exclusion. See Paternity.

What about everyone else in the family? The likelihood of a whole pedigree by Elston-Stewart peeling, which sums out every untyped member - the question that arises the moment the person you actually want to test is unavailable. See General pedigrees.

Plus lineage markers: mtDNA and Y-STR haplotypes, where the estimate is a database count rather than a product over loci.

#The shape of it

import "@jennifer/forensicgenetics/" as forensics;

def db as forensics.FrequencyDb init forensics.withLocus(
    forensics.db("example"), "D3S1358", 1034,
    {"15": 0.2456, "16": 0.2314, "17": 0.2007, "18": 0.3223});

def suspect as forensics.Profile init forensics.profile("S1", [
    forensics.genotype("D3S1358", "15", "16"),
    forensics.genotype("TH01", "6", "9.3")
]);

def lr as float init forensics.matchLikelihoodRatio($db, $suspect,
    forensics.THETA_GENERAL);

Five modules, three of which you can ignore until you need them:

kinship and pedigree build on the core; lineage is independent and can be used on its own. The core imports nothing - it defines the generic FrequencyDb and reads no published format, so a reader deck for any source converts into the same type. @mplx/strider does that for STRidER-style XML.

Every module raises Error with its own kind - "forensicgenetics", "kinship", "pedigree", "lineage" - so a catch can tell an unusable frequency table from an impossible pedigree.

#Where to go next

New here: Installing the deck, then the Quick start.

Looking for a formula: Formulae and sources collects every estimator in one place with its citation.

About to rely on a number: read Limitations first. It is short, and some of it will change what you do.

#Not a validated forensic tool

This deck implements published estimators and is tested against them, but it has not been through the validation any jurisdiction requires of software used in casework. Treat it as a library for research, teaching and cross-checking, and validate independently before it informs a real conclusion.

The bundled frequency table is synthetic - made-up numbers that exist only to exercise the reader and the examples. Real reference data comes from STRidER and elsewhere; see Reference frequency data.

#Not for legal or court use

Do not use this deck for a legal proceeding. It is not intended for, and is not recommended for, any calculation that informs a prosecution, a defence, a paternity ruling, an immigration decision, a disaster-victim identification, or any other legal or official determination. Jurisdictions require validated, accredited software for that purpose, operated under an accredited process; this deck is neither. If a number from here would ever reach a court, reproduce it with validated software and let that result be the one you rely on.

#No warranty, no liability

This software is provided as is, without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose, and non-infringement. You use it entirely at your own risk.

The author accepts no responsibility and no liability for any claim, damage, loss, or other consequence arising from this software or from any number it produces, however that number was reached and whoever relied on it. Verifying that a result is correct, appropriate, and lawful for your purpose is your responsibility alone.

This restates - and does not narrow, extend, or replace - the warranty and liability disclaimers of the LGPL-3.0-only licence this deck is released under. Where the two differ, the licence governs.