Package: dvir 3.4.2

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_3.4.2.tar.gz
dvir_3.4.2.zip(r-4.7)dvir_3.4.2.zip(r-4.6)dvir_3.4.2.zip(r-4.5)
dvir_3.4.2.tgz(r-4.6-any)dvir_3.4.2.tgz(r-4.5-any)
dvir_3.4.2.tar.gz(r-4.7-any)dvir_3.4.2.tar.gz(r-4.6-any)
dvir_3.4.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dvir/json (API)

# Install 'dvir' in R:

install.packages('dvir', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org'))

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

Datasets:

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
KETPchap481 - Data used in the book Kling et al.
KETPchap484 - Data used in the book Kling et al.
KETPexer497 - Data used in the book Kling et al.
KETPexer498 - Data used in the book Kling et al.
planecrash - DVI dataset: Simulated plane crash
symmetricSibs - Dataset: Symmetry examples

On CRAN:

dvi forensic-genetics kinship-testing pedsuite

4.91 score 3 stars 1 packages 18 scripts 588 downloads 1 mentions 36 exports 21 dependencies

Last updated from:bedfb4adaa. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	159
source / vignettes	OK	171
linux-release-x86_64	OK	156
macos-release-arm64	OK	129
macos-oldrel-arm64	OK	134
windows-devel	OK	127
windows-release	OK	144
windows-oldrel	OK	114
wasm-release	OK	114

Exports:addVictims amDrivenDVI Bmarginal checkDVI compactJointRes directMatch dviCompare dviData dviGridSize dviJoint dviSim dviSolve excludePairing exclusionMatrix expand.grid.nodup familias2dvir findExcluded findNonidentifiable findUndisputed formatSummary generatePairings getDatabase getFamily getSimpleFams jointDVI mergePM ncomb pairwiseLR plotDVI plotSolution plotUndisputed relabelDVI sequentialDVI setPairing subsetDVI swapOrientation

Dependencies:evaluate forrel glue highr kinship2 knitr lattice lpSolve Matrix mirai nanonext pedFamilias pedmut pedprobr pedtools quadprog ribd slam verbalisr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add victim samples to a DVI dataset	addVictims
AM-driven DVI	amDrivenDVI
Posterior pairing probabilities	Bmarginal
Direct match LR	directMatch
Compare DVI approaches	dviCompare
DVI data	checkDVI dviData
Finds Generalised Likelihood Ratios (GLRs)	dviGLR
Size of joint assignment grid	dviGridSize
Joint DVI search	dviJoint
Simulate genotypes in a DVI dataset	dviSim
A complete workflow for solving a DVI case	dviSolve
DVI dataset: Generational trio	example1
DVI dataset: Two reference families	example2
Exclude pairings	excludePairing
Dataset: Exclusion example	exclusionExample
Assignment grid for joint analysis	expand.grid.nodup
Convert a Familias file to DVI data	familias2dvir
Excluded individuals and pairings in a DVI dataset	exclusionMatrix findExcluded
Nonidentifiable missing persons	findNonidentifiable
Undisputed identifications in a DVI problem	findUndisputed
DVI dataset: Family of fire victims	fire
Format final summary table	formatSummary
Sex-consistent pairings	generatePairings
Extract the marker database from a DVI dataset	getDatabase
Get AM component of selected individuals	getFamily
Find the simple families of a DVI dataset	getSimpleFams
DVI dataset: Family grave	grave
DVI dataset: A large reference pedigree	icmp
Legacy DVI workflow with joint analysis	compactJointRes jointDVI
Data used in the book Kling et al. (2021)	KETPchap481
Data used in the book Kling et al. (2021)	KETPchap484
Data used in the book Kling et al. (2021)	KETPexer497
Data used in the book Kling et al. (2021)	KETPexer498
Identify and merge matching PM samples	mergePM
The total a priori number of assignments in a DVI problem	ncomb
Pairwise LR matrix	pairwiseLR
DVI dataset: Simulated plane crash	planecrash
Plot a DVI problem	plotDVI
Plot DVI solution	plotSolution
Plot undisputed identifications	plotUndisputed
Automatic labelling of a DVI dataset	relabelDVI
Sequential DVI search	sequentialDVI
Set identifications manually	setPairing
Extract a subset of a DVI dataset	subsetDVI
Swap orientation of an assignment table	swapOrientation
Dataset: Symmetry examples	symmetricSibs