Package: simDNAmixtures 1.0.1

simDNAmixtures: Simulate Forensic DNA Mixtures

Mixed DNA profiles can be sampled according to models for probabilistic genotyping. Peak height variability is modelled using a log normal distribution or a gamma distribution. Sample contributors may be related according to a pedigree.

Authors:Maarten Kruijver [aut, cre]

simDNAmixtures_1.0.1.tar.gz
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simDNAmixtures_1.0.1.tgz(r-4.4-any)simDNAmixtures_1.0.1.tgz(r-4.3-any)
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simDNAmixtures.pdf |simDNAmixtures.html✨
simDNAmixtures/json (API)

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

Peer review:

Bug tracker:https://github.com/mkruijver/simdnamixtures/issues

Datasets:
  • kits - Properties such as loci, dye, sizes for most standard forensic kits

On CRAN:

29 exports 1.33 score 30 dependencies 9 scripts 172 downloads

Last updated 15 days agofrom:de297fec8b. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILSep 03 2024
R-4.5-winWARNINGSep 03 2024
R-4.5-linuxWARNINGSep 03 2024
R-4.4-winWARNINGSep 03 2024
R-4.4-macWARNINGSep 03 2024
R-4.3-winWARNINGSep 03 2024
R-4.3-macWARNINGSep 03 2024

Exports:allele_specific_stutter_modeldrop_modelgamma_modelgf_configurationglobal_stutter_modellog_normal_modelread_allele_freqsread_size_regressionread_STRmix_kit_settingsread_stutter_exceptionsread_stutter_regressionread_wide_tablesample_contributor_genotypessample_drop_modelsample_gamma_modelsample_genotypesample_log_normal_modelsample_log_normal_parameterssample_log_normal_stutter_variancesample_LSAEsample_many_pedigree_genotypessample_mixture_from_genotypessample_mixturessample_mixtures_fixed_parameterssample_mixtures_from_genotypessample_offspringsample_pedigree_genotypesSMASH_to_wide_tablestutter_type

Dependencies:clidplyrevaluatefansigenericsgluehighrkinship2knitrlatticelifecyclemagrittrMatrixnaturalsortpedmutpedprobrpedtoolspillarpkgconfigquadprogR6rlangtibbletidyselectutf8vctrswithrxfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Stutter model where the expected stutter rate depends on the allele and locusallele_specific_stutter_model
Defines a (semi-continuous) drop modeldrop_model
Defines a gamma model for peak height variabilitygamma_model
Stutters and size regressions for a GlobalFiler 3500 kitgf_configuration
Global stutter model where the expected stutter rate is constant across alleles and lociglobal_stutter_model
Properties such as loci, dye, sizes for most standard forensic kitskits
Defines a log normal model for peak height variabilitylog_normal_model
Read allele frequencies in FSIgen format (.csv)read_allele_freqs
Reads a size regression fileread_size_regression
Read STRmix Kit Settingsread_STRmix_kit_settings
Reads a stutter exceptions file with overrides for expected stutter ratiosread_stutter_exceptions
Reads a stutter regression fileread_stutter_regression
Read wide table (.txt) with Allele1, Allele2, ... columns as isread_wide_table
Sample genotypes for mixture contributors according to allele frequenciessample_contributor_genotypes
Sample drop model(s) with parameters according to priorssample_drop_model
Sample gamma model(s) with parameters according to priorssample_gamma_model
Sample a genotype according to allele frequenciessample_genotype
Sample log normal model(s) with parameters according to priorssample_log_normal_model
Sample log normal model parameters according to priorssample_log_normal_parameters
Sample log normal stutter variance parameters according to priorssample_log_normal_stutter_variance
Sample Locus Specific Amplification Efficiency (LSAE) according to priorsample_LSAE
Sample (many) genotypes for pedigree members according to allele frequencies by allele dropping and possibly taking linkage into account by simulating recombination.sample_many_pedigree_genotypes
Sample mixture profile with provided genotypessample_mixture_from_genotypes
Sample mixtures with random genotypes and random parameters according to priorssample_mixtures
Sample mixtures with known genotypes and fixed parameterssample_mixtures_fixed_parameters
Sample mixtures with known genotypes and random parameters according to priorssample_mixtures_from_genotypes
Sample offspring from two parental genotypessample_offspring
Sample genotypes for pedigree according to allele frequencies by allele dropping.sample_pedigree_genotypes
Converts SMASH (SampleName, Marker, Allele, Size, Height) data to a wide tableSMASH_to_wide_table
Defines a stutter type to be used in the allele specific stutter model.stutter_type