jointDVI {dvir}

Joint DVI search

Description

Victims are given as a list of singletons, and references as a list of pedigrees. All possible assignments are evaluated and solutions ranked according to the likelihood.

Usage

jointDVI(
  dvi,
  pairings = NULL,
  ignoreSex = FALSE,
  assignments = NULL,
  limit = 0,
  nkeep = NULL,
  undisputed = TRUE,
  markers = NULL,
  threshold = 10000,
  strict = FALSE,
  relax = !strict,
  disableMutations = NA,
  maxAssign = 1e+05,
  numCores = 1,
  check = TRUE,
  verbose = TRUE
)

compactJointRes(jointRes, LRthresh = NULL)

Arguments

dvi

A dviData object, typically created with dviData().

pairings

A list of possible pairings for each victim. If NULL, all sex-consistent pairings are used.

ignoreSex

A logical.

assignments

A data frame containing the assignments to be considered in the joint analysis. By default, this is automatically generated by taking all combinations from pairings.

limit

A positive number, by default 0. Only pairwise LR values above this are considered.

nkeep

An integer, or NULL. If given, only the nkeep most likely pairings are considered for each victim.

undisputed

A logical, by default TRUE.

markers

A vector indicating which markers should be included in the analysis. By default all markers are included.

threshold

A positive number, passed onto findUndisputed(). Default: 1e4.

strict

A logical, passed onto findUndisputed(). Default: FALSE.

relax

Deprecated.

disableMutations

A logical, or NA (default). The default action is to disable mutations in all reference families without Mendelian errors.

maxAssign

A positive integer. If the number of assignments going into the joint calculation exceeds this, the function will abort with an informative error message. Default: 1e5.

numCores

An integer; the number of cores used in parallelisation. Default: 1.

check

A logical, indicating if the input data should be checked for consistency.

verbose

A logical.

jointRes

A data frame produced by jointDVI().

LRthresh

A positive number, used as upper limit for the LR comparing the top result with all others.

Value

A data frame. Each row describes an assignment of victims to missing persons, accompanied with its log likelihood, the LR compared to the null (i.e., no identifications), and the posterior corresponding to a flat prior.

The function compactJointRes() removes columns without assignments, and solutions whose LR compared with the top result is below 1/LRthresh.

See Also

pairwiseLR(), findUndisputed()

Examples

jointDVI(example2)