Package: fbnet 1.0.3

fbnet: Forensic Bayesian Networks

Open-source package for computing likelihood ratios in kinship testing and human identification cases (Chernomoretz et al. (2021) <doi:10.1016/j.fsir.2020.100132>). It has the core function of the software GENis, developed by Fundación Sadosky. It relies on a Bayesian Networks framework and is particularly well suited to efficiently perform large-size queries against databases of missing individuals (Darwiche (2009) <doi:10.1017/CBO9780511811357>).

Authors:Franco Marsico [aut, cre], Ariel Chernomoretz [aut]

fbnet_1.0.3.tar.gz
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fbnet_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
fbnet/json (API)

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

Bug tracker:https://github.com/marsicofl/fbnet/issues

Pkgdown/docs site:https://marsicofl.github.io

Datasets:
  • Argentina_STRs - STRs allelic frequencies from Argentina.
  • bnet - Initialized bayesian network.
  • pbn - Prepared pedigree for bayesian network trimming.
  • toybase - Toy allele frequency database.
  • toyped - STRs allelic frequencies from specified country.

On CRAN:

Conda:

statistics

3.00 score 1 stars 6 scripts 317 downloads 32 exports 23 dependencies

Last updated from:12cfc8abe7. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK139
source / vignettesOK266
linux-releaseOK134
macos-releaseOK97
macos-oldrelOK101
windows-develOK84
windows-releaseOK73
windows-oldrelOK95
wasm-releaseOK108

Exports:buildBNbuildCPTsconvertPedformatevidencePrunningfactorHeteroFoundersFamiliasLocusFamiliasPedigreefrom_pedtoolsgetConditionalgetGenotypeTablesgetLocusCPTgetMAPgetQSetRMPgetValuesOutimposeEvidenceinitBNinitBN.fromPedinitBN.fromVarsminOrderingpreparePedprodFactorpruneNodesremoveEvidenceFromPedreportLRreportPQreverseSplitsetOrderingstateRemovalstateRemoval2stateRemovalSubnucssumFactorvelim.bn

Dependencies:clicodetoolscpp11digestfuturefuture.applyglobalsglueigraphlatticelifecyclelistenvmagrittrMatrixnumDerivparallellypkgconfigRcppRcppArmadillorlangRsolnptruncnormvctrs

Readme and manuals

Help Manual

Help pageTopics
STRs allelic frequencies from Argentina.Argentina_STRs
Initialized bayesian network.bnet
buildBN: a function for building the bayesian network.buildBN
buildCPTs: a function for building conditional probability tables based on pedigree bayesian network.buildCPTs
convertPedformat: a function for converting a pedtools ped onject to a famlink ped object.convertPedformat
evidencePrunning: a fuction for pruning instantiated variables.evidencePrunning
factorHeteroFounders: a function for multiplying probabilities in case of heterocigote founders.factorHeteroFounders
FamiliasLocus: a function for reading Familias locus data.FamiliasLocus
FamiliasPedigree: a function for constructing Familias pedigree format.FamiliasPedigree
fbnet: Forensic Bayesian Networksfbnet-package fbnet
Initialize a Bayesian network from a pedtools pedigreefrom_pedtools
getConditional: a function for obtaining the coditional probability tables based on a given evidence.getConditional
getGenotypeTables: a function for obtaining genotypetables after variable elimination and using available genetic evidence.getGenotypeTables
getLocusCPT: a function for obtaining the coditional probability table from a specific locus.getLocusCPT
factorHeteroFounders: a function for multiplying probabilities in case of heterocigote founders.getMAP
getGenotypeTables: a function for obtaining genotypetables after variable elimination and using available genetic evidence.getQSetRMP
getValuesOut: a function for getting out variables with zero probability in the bayesian networkgetValuesOut
imposeEvidence: a fuction for imposing evidence in the bayesian network.imposeEvidence
initBN: a function to initialize the bayesian network.initBN
initBN.fromPed: a function to initialize the bayesian network.initBN.fromPed
initBN.fromVars: a function to initialize the bayesian network.initBN.fromVars
minOrdering: a function for getting an ordering of bayesian network variables not in Q using min fill criteria on interaction graphs.minOrdering
Prepared pedigree for bayesian network trimming.pbn
preparePed: a function for simulating genetic data from untyped individuals conditioned on known genotypes.preparePed
prodFactor: a function for performing product between probability tables.prodFactor
pruneNodes: a fuction for clasical pruning in bayesian networks.pruneNodes
removeEvidenceFromPed: a function for removing evidence from specific individuals in a ped object.removeEvidenceFromPed
reportLR: a function for calculating the LRs of specified genotypes in a pedigree.reportLR
reportPQ: a function for calculating the probability of specified genotypes in a pedigree.reportPQ
reverseSpit: a function for formatting.reverseSplit
setOrdering: a function for selecting the ordering method in the elimination process.setOrdering
stateRemoval: a function for processing the bayesian network.stateRemoval
stateRemoval2: a function for processing the bayesian network. It implements another approach from the described in stateRemoval function.stateRemoval2
stateRemovalSubnucs: a fuctiong for variable state pruning.stateRemovalSubnucs
prodFactor: a function for performing sum between probability tables.sumFactor
Toy allele frequency database.toybase
STRs allelic frequencies from specified country.toyped
velim.bn: a function for variable elimination in a bayesian network.velim.bn