Defines a (semi-continuous) drop model
drop_model.RdDefines a (semi-continuous) drop model
Arguments
- dropout_probabilities
Numeric vector with values between 0 and 1. Dropout probabilities for each contributor.
- drop_in_rate
Numeric vector of length one. Expected number of drop-ins per locus. Default is 0.
- freqs
Optionally a list with allele frequencies (needed when drop_in_rate > 0). See read_allele_freqs.
- model_settings
List. Possible parameters:
locus_names. Character vector.
size_regression. Function, see read_size_regression.
Details
Define the classes semi-continuous drop-model. The model may then be used to sample DNA profiles using the sample_mixture_from_genotypes function. Alternatively, to sample many models and profiles in one go with parameters according to a specified distribution, the sample_mixtures function can be used.
References
Slooten, K. (2017). Accurate assessment of the weight of evidence for DNA mixtures by integrating the likelihood ratio. Forensic Science International: Genetics, 27, 1-16. doi:10.1016/j.fsigen.2016.11.001
Examples
gf <- gf_configuration()
freqs <- read_allele_freqs(system.file("extdata","FBI_extended_Cauc_022024.csv",
package = "simDNAmixtures"))
settings <- list(locus_names = gf$autosomal_markers, size_regression = gf$size_regression)
model <- drop_model(dropout_probabilities = c(0.1),
drop_in_rate = 1e-3,
freqs = freqs, model_settings = settings)
g <- sample_contributor_genotypes(contributors = "U1", freqs = freqs,
loci = settings$locus_names)
# genotype
g
#> $U1
#> Sample Name Locus Allele1 Allele2
#> 1 U1 D3S1358 17 18
#> 2 U1 vWA 16 18
#> 3 U1 D16S539 9 11
#> 4 U1 CSF1PO 11 12
#> 5 U1 TPOX 11 12
#> 6 U1 D8S1179 10 14
#> 7 U1 D21S11 28 29
#> 8 U1 D18S51 12 14
#> 9 U1 D2S441 11 14
#> 10 U1 D19S433 13 14
#> 11 U1 TH01 9 9.3
#> 12 U1 FGA 23 26
#> 13 U1 D22S1045 15 16
#> 14 U1 D5S818 12 12
#> 15 U1 D13S317 10 13
#> 16 U1 D7S820 8 11
#> 17 U1 SE33 15 20.2
#> 18 U1 D10S1248 14 14
#> 19 U1 D1S1656 14 17
#> 20 U1 D12S391 21 23
#> 21 U1 D2S1338 17 17
#>
# sample with dropout
sample_mixture_from_genotypes(g, model)
#> SampleName Marker Allele Size Height n1 x1 n x
#> 1 mixture D3S1358 17 129.56 1000 1 1 1 1
#> 2 mixture D3S1358 18 133.64 1000 1 1 1 1
#> 3 mixture vWA 16 176.91 1000 1 1 1 1
#> 4 mixture vWA 18 184.99 1000 1 1 1 1
#> 5 mixture D16S539 9 243.61 1000 1 1 1 1
#> 6 mixture D16S539 11 251.67 1000 1 1 1 1
#> 7 mixture CSF1PO 11 302.30 1000 1 1 1 1
#> 8 mixture CSF1PO 12 306.26 1000 1 1 1 1
#> 9 mixture TPOX 11 361.78 1000 1 1 1 1
#> 10 mixture TPOX 12 365.81 1000 1 1 1 1
#> 11 mixture D8S1179 10 134.96 1000 1 1 1 1
#> 12 mixture D8S1179 14 151.36 1000 1 1 1 1
#> 13 mixture D21S11 28 199.61 1000 1 1 1 1
#> 14 mixture D21S11 29 203.65 1000 1 1 1 1
#> 15 mixture D18S51 12 281.63 1000 1 1 1 1
#> 16 mixture D18S51 14 289.71 1000 1 1 1 1
#> 17 mixture D2S441 11 89.42 1000 1 1 1 1
#> 18 mixture D2S441 14 101.60 1000 1 1 1 1
#> 19 mixture D19S433 13 145.75 1000 1 1 1 1
#> 20 mixture D19S433 14 149.74 1000 1 1 1 1
#> 21 mixture TH01 9 199.38 1000 1 1 1 1
#> 22 mixture TH01 9.3 200.62 1000 1 1 1 1
#> 23 mixture FGA 23 264.08 1000 1 1 1 1
#> 24 mixture FGA 26 276.29 1000 1 1 1 1
#> 25 mixture D22S1045 15 109.46 1000 1 1 1 1
#> 26 mixture D22S1045 16 112.44 1000 1 1 1 1
#> 27 mixture D5S818 12 158.92 1000 2 1 2 1
#> 28 mixture D13S317 10 218.93 1000 1 1 1 1
#> 29 mixture D13S317 13 231.06 1000 1 1 1 1
#> 30 mixture D7S820 8 270.42 1000 1 1 1 1
#> 31 mixture D7S820 11 282.34 1000 1 1 1 1
#> 32 mixture SE33 15 350.57 1000 1 1 1 1
#> 33 mixture SE33 20.2 371.72 1000 1 1 1 1
#> 34 mixture D10S1248 14 109.53 1000 2 2 2 2
#> 35 mixture D1S1656 14 180.67 1000 1 1 1 1
#> 36 mixture D1S1656 17 193.32 1000 1 1 1 1
#> 37 mixture D12S391 21 243.99 1000 1 1 1 1
#> 38 mixture D12S391 23 251.93 1000 1 1 1 1
#> 39 mixture D2S1338 17 304.78 1000 2 1 2 1
#> HeightAtOrAboveDetectionThreshold
#> 1 TRUE
#> 2 TRUE
#> 3 TRUE
#> 4 TRUE
#> 5 TRUE
#> 6 TRUE
#> 7 TRUE
#> 8 TRUE
#> 9 TRUE
#> 10 TRUE
#> 11 TRUE
#> 12 TRUE
#> 13 TRUE
#> 14 TRUE
#> 15 TRUE
#> 16 TRUE
#> 17 TRUE
#> 18 TRUE
#> 19 TRUE
#> 20 TRUE
#> 21 TRUE
#> 22 TRUE
#> 23 TRUE
#> 24 TRUE
#> 25 TRUE
#> 26 TRUE
#> 27 TRUE
#> 28 TRUE
#> 29 TRUE
#> 30 TRUE
#> 31 TRUE
#> 32 TRUE
#> 33 TRUE
#> 34 TRUE
#> 35 TRUE
#> 36 TRUE
#> 37 TRUE
#> 38 TRUE
#> 39 TRUE