Package: simDNAmixtures 1.1.3

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_1.1.3.tar.gz
simDNAmixtures_1.1.3.zip(r-4.7-any)simDNAmixtures_1.1.3.zip(r-4.6-any)simDNAmixtures_1.1.3.zip(r-4.5-any)
simDNAmixtures_1.1.3.tgz(r-4.6-any)simDNAmixtures_1.1.3.tgz(r-4.5-any)
simDNAmixtures_1.1.3.tar.gz(r-4.7-any)simDNAmixtures_1.1.3.tar.gz(r-4.6-any)
simDNAmixtures_1.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
simDNAmixtures/json (API)

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

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

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

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

On CRAN:

Conda:

4.64 score 2 stars 22 scripts 591 downloads 29 exports 30 dependencies

Last updated from:b5d365328c. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK144
source / vignettesOK255
linux-release-x86_64OK143
macos-release-arm64OK130
macos-oldrel-arm64OK125
windows-develOK92
windows-releaseOK86
windows-oldrelOK96
wasm-releaseOK113

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:clidplyrevaluategenericsgluehighrkinship2knitrlatticelifecyclelpSolvemagrittrMatrixnaturalsortpedmutpedprobrpedtoolspillarpkgconfigquadprogR6rlangtibbletidyselectutf8vctrswithrxfunxml2yaml

Simulating YSTR profiles
Example | Simulation
Rendered fromsimulating_YSTR_profiles.Rmdusingknitr::rmarkdown

Last update: 2024-12-18
Started: 2024-06-26

Getting started
Basic log normal example | Basic gamma example | References
Rendered fromgetting_started.Rmdusingknitr::rmarkdown

Last update: 2024-06-21
Started: 2022-05-01

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