Package: dvir 3.3.0

Magnus Dehli Vigeland

dvir: Disaster Victim Identification

Joint DNA-based disaster victim identification (DVI), as described in Vigeland and Egeland (2021) <doi:10.21203/rs.3.rs-296414/v1>. Identification is performed by optimising the joint likelihood of all victim samples and reference individuals. Individual identification probabilities, conditional on all available information, are derived from the joint solution in the form of posterior pairing probabilities. 'dvir' is part of the 'pedsuite' collection of packages for pedigree analysis.

Authors:Magnus Dehli Vigeland [aut, cre], Thore Egeland [aut]

dvir_3.3.0.tar.gz
dvir_3.3.0.tar.gz(r-4.5-noble)dvir_3.3.0.tar.gz(r-4.4-noble)
dvir_3.3.0.tgz(r-4.4-emscripten)dvir_3.3.0.tgz(r-4.3-emscripten)
dvir.pdf |dvir.html✨
dvir/json (API)
NEWS

# Install 'dvir' in R:
install.packages('dvir', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/magnusdv/dvir/issues

Datasets:
  • KETPch4 - Data used in the book Kling et al.
  • KETPex481 - Data used in the book Kling et al.
  • KETPex497 - Data used in the book Kling et al.
  • KETPex498 - Data used in the book Kling et al.
  • example1 - DVI dataset: Generational trio
  • example2 - DVI dataset: Two reference families
  • exclusionExample - Dataset: Exclusion example
  • fire - DVI dataset: Family of fire victims
  • grave - DVI dataset: Family grave
  • icmp - DVI dataset: A large reference pedigree
  • planecrash - DVI dataset: Simulated plane crash
  • symmetricSibs - Dataset: Symmetry examples

2.50 score 1 packages 21 scripts 283 downloads 1 mentions 33 exports 19 dependencies

Last updated 4 months agofrom:a45408a90d. Checks:2 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKJan 08 2025
R-4.5-linuxOKJan 08 2025

Exports:amDrivenDVIBmarginalcheckDVIcompactJointResdirectMatchdviComparedviDatadviJointdviSimdviSolveexcludePairingexclusionMatrixexpand.grid.nodupfamilias2dvirfindExcludedfindNonidentifiablefindUndisputedformatSummarygeneratePairingsgetFamilygetSimpleFamsjointDVImergePMncombpairwiseLRplotDVIplotSolutionplotUndisputedrelabelDVIsequentialDVIsetPairingsubsetDVIswapOrientation

Dependencies:evaluateforrelgluehighrkinship2knitrlatticeMatrixpbapplypedFamiliaspedmutpedprobrpedtoolsquadprogribdslamverbalisrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
AM driven DVIamDrivenDVI
Posterior pairing probabilitiesBmarginal
Direct match LRdirectMatch
Compare DVI approachesdviCompare
DVI datacheckDVI dviData
Finds Generalised Likelihood Ratios (GLRs)dviGLR
Joint DVI searchdviJoint
Simulate genotypes in a DVI datasetdviSim
A complete pipeline for solving a DVI casedviSolve
DVI dataset: Generational trioexample1
DVI dataset: Two reference familiesexample2
Exclude pairingsexcludePairing
Dataset: Exclusion exampleexclusionExample
Combinations without duplicationsexpand.grid.nodup
Convert a Familias file to DVI datafamilias2dvir
Excluded individuals and pairings in a DVI datasetexclusionMatrix findExcluded
Nonidentifiable missing personsfindNonidentifiable
Undisputed identifications in a DVI problemfindUndisputed
DVI dataset: Family of fire victimsfire
Format final summary tableformatSummary
Sex-consistent pairingsgeneratePairings
Get AM component of selected individualsgetFamily
Find the simple families of a DVI datasetgetSimpleFams
DVI dataset: Family gravegrave
DVI dataset: A large reference pedigreeicmp
Joint DVI searchcompactJointRes jointDVI
Data used in the book Kling et al. (2021)KETPch4
Data used in the book Kling et al. (2021)KETPex481
Data used in the book Kling et al. (2021)KETPex497
Data used in the book Kling et al. (2021)KETPex498
Identity and merge matching PM samplesmergePM
The number of assignments for DVI problemncomb
Pairwise LR matrixpairwiseLR
DVI dataset: Simulated plane crashplanecrash
Plot a DVI problemplotDVI
Plot DVI solutionplotSolution
Plot undisputed identificationsplotUndisputed
Automatic labelling of a DVI datasetrelabelDVI
Sequential DVI searchsequentialDVI
Set identifications manuallysetPairing
Extract a subset of a DVI datasetsubsetDVI
Swap orientation of an assignment tableswapOrientation
Dataset: Symmetry examplessymmetricSibs