Likelihood ratio for DNA evidence interpretation (2): a sophistacted version of function LR()

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Description

LR Allows the calculation of likelihood ratios for a piece of DNA evidence, for any number of replicates, any number of contributors, and when drop-in and drop-out are possible.

Usage

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LR(Repliste, Tp, Td, Vp, Vd, xp, xd, theta, prDHet, prDHom, prC, freq)

Arguments

Repliste

vector of alleles present at a given locus for any number of replicates. If there are two replicates, showing alleles 12,13, and 14 respectively, then Repliste should be given as c(12,13,0,14), where the 0 is used as a separator. An empty replicate is simply 0. For example, replicates (12,13) and and one empty replicate must be given as: c(12,14,0,0).

Tp

vector of genotypes for the known contributors under Hp. Genotype 12/17 should be given as a vector c(12,17) and genotypes 12/17,14/16, should be given as a unique vector: c(12,17,14,16).

Td

vector of genotypes for the known contributors under Hd. Should be in the same format as Tp. If there are no known contributors under Hd, then set Td to 0.

Vp

vector of genotypes for the known non-contributors (see References section) under Hp. See Tp for format.

Vd

vector of genotypes for the known non-contributors (see References section) under Hd. Should be in the same format than Vp, if empty, set to 0.

xp

Number of unknown individuals under Hd. Set to 0 if there are no unknown contributors.

xd

Number of unknown individuals under Hd. Set to 0 if there are no unknown contributors.

theta

thete correction, value must be taken in [0,1)

prDHet

probability of dropout for heterozygotes. It is possible to assign different values per contributor. In this case, prDHet must be a vector, of length the number of contributors in T + x, and the probabilities must be given in this order. if the probability of dropout for T is d1, and for the unknown is d2, then prDHet=(d1,d2). In case T is not a heterozygote, the given vector must still be of length length(T) +x, but the given value for T does not matter, because it won't be used, the value in prDHom is used instead. This is a bit ad hoc and an improvement is currently under development.

prDHom

probability of dropout for homozygotes. See description ofr argument PrDHom.

prC

probability of drop-in applied per locus

freq

vector of the corresponding allele frequencies of the analysed locus in the target population

Author(s)

Hinda Haned contact@hindahaned.info

References

Gill, P.; Kirkham, A. & Curran, J. LoComatioN: A software tool for the analysis of low copy number DNA profiles Forensic Science International, 2007, 166(2-3), 128-138

Curran, J. M.; Gill, P. & Bill, M. R. Interpretation of repeat measurement DNA evidence allowing for multiple contributors and population substructure Forensic Science International, 2005, 148, 47-53

See Also

LRmixTK

Examples

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#load allele frequencies
library(forensim)
data(ngm)
#create vector of allele frequencies
d10<-ngm$tab$D10
# heterozygote dropout probability (resp. homozygote) is set to 0.2 for all
# contributors (0.04 for homozygotes) 
LR(Repliste=c(12,13,14),Tp=c(12,13),Td=0,Vp=0,Vd=0,xd=2,xp=1,theta=0,prDHet=c(0.2,0.2),
prDHom=c(0.04,0.04),prC=0,freq=d10)

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