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 15 15
#> 2 U1 vWA 15 16
#> 3 U1 D16S539 9 9
#> 4 U1 CSF1PO 10 12
#> 5 U1 TPOX 8 9
#> 6 U1 D8S1179 11 14
#> 7 U1 D21S11 29 31.2
#> 8 U1 D18S51 13 15
#> 9 U1 D2S441 11 14
#> 10 U1 D19S433 12 15.2
#> 11 U1 TH01 6 9.3
#> 12 U1 FGA 23 24
#> 13 U1 D22S1045 11 15
#> 14 U1 D5S818 11 11
#> 15 U1 D13S317 8 12
#> 16 U1 D7S820 8 8
#> 17 U1 SE33 23.2 30.2
#> 18 U1 D10S1248 12 14
#> 19 U1 D1S1656 15 15.3
#> 20 U1 D12S391 19 22
#> 21 U1 D2S1338 20 23
#>
# sample with dropout
sample_mixture_from_genotypes(g, model)
#> SampleName Marker Allele Size Height n1 x1 n x
#> 1 mixture D3S1358 15 121.40 1000 2 2 2 2
#> 2 mixture vWA 15 172.87 1000 1 1 1 1
#> 3 mixture vWA 16 176.91 1000 1 1 1 1
#> 4 mixture D16S539 9 243.61 1000 2 2 2 2
#> 5 mixture CSF1PO 10 298.34 1000 1 1 1 1
#> 6 mixture CSF1PO 12 306.26 1000 1 1 1 1
#> 7 mixture TPOX 8 349.70 1000 1 1 1 1
#> 8 mixture TPOX 9 353.72 1000 1 1 1 1
#> 9 mixture D8S1179 11 139.06 1000 1 1 1 1
#> 10 mixture D8S1179 14 151.36 1000 1 1 1 1
#> 11 mixture D21S11 29 203.65 1000 1 1 1 1
#> 12 mixture D21S11 31.2 212.54 1000 1 1 1 1
#> 13 mixture D18S51 13 285.67 1000 1 1 1 1
#> 14 mixture D18S51 15 293.75 1000 1 1 1 1
#> 15 mixture D2S441 11 89.42 0 1 0 1 0
#> 16 mixture D2S441 14 101.60 1000 1 1 1 1
#> 17 mixture D19S433 12 141.77 1000 1 1 1 1
#> 18 mixture D19S433 15.2 154.52 1000 1 1 1 1
#> 19 mixture TH01 6 186.89 1000 1 1 1 1
#> 20 mixture TH01 9.3 200.62 1000 1 1 1 1
#> 21 mixture FGA 23 264.08 0 1 0 1 0
#> 22 mixture FGA 24 268.15 1000 1 1 1 1
#> 23 mixture D22S1045 11 97.51 1000 1 1 1 1
#> 24 mixture D22S1045 15 109.46 1000 1 1 1 1
#> 25 mixture D5S818 11 154.87 1000 2 2 2 2
#> 26 mixture D13S317 8 210.84 0 1 0 1 0
#> 27 mixture D13S317 12 227.02 1000 1 1 1 1
#> 28 mixture D7S820 8 270.42 1000 2 1 2 1
#> 29 mixture SE33 23.2 383.92 1000 1 1 1 1
#> 30 mixture SE33 30.2 412.39 1000 1 1 1 1
#> 31 mixture D10S1248 12 101.53 1000 1 1 1 1
#> 32 mixture D10S1248 14 109.53 1000 1 1 1 1
#> 33 mixture D1S1656 15 184.88 1000 1 1 1 1
#> 34 mixture D1S1656 15.3 186.15 1000 1 1 1 1
#> 35 mixture D12S391 19 236.04 1000 1 1 1 1
#> 36 mixture D12S391 22 247.96 1000 1 1 1 1
#> 37 mixture D2S1338 20 316.84 1000 1 1 1 1
#> 38 mixture D2S1338 23 328.89 0 1 0 1 0
#> 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 FALSE
#> 16 TRUE
#> 17 TRUE
#> 18 TRUE
#> 19 TRUE
#> 20 TRUE
#> 21 FALSE
#> 22 TRUE
#> 23 TRUE
#> 24 TRUE
#> 25 TRUE
#> 26 FALSE
#> 27 TRUE
#> 28 TRUE
#> 29 TRUE
#> 30 TRUE
#> 31 TRUE
#> 32 TRUE
#> 33 TRUE
#> 34 TRUE
#> 35 TRUE
#> 36 TRUE
#> 37 TRUE
#> 38 FALSE