Package: DNAmixturesLite 0.0-1

DNAmixturesLite: Statistical Inference for Mixed Traces of DNA (Lite-Version)

Statistical methods for DNA mixture analysis. This package is a lite-version of the 'DNAmixtures' package to allow users without a 'HUGIN' software license to experiment with the statistical methodology. While the lite-version aims to provide the full functionality it is noticeably less efficient than the original 'DNAmixtures' package. For details on implementation and methodology see <https://dnamixtures.r-forge.r-project.org/>.

Authors:Therese Graversen [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
DNAmixturesLite/json (API)

# Install 'DNAmixturesLite' in R:
install.packages('DNAmixturesLite', repos = c('https://tgraversen.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • MC15 - The MC15 DNA mixture
  • MC18 - The MC18 DNA mixture
  • NGM - NGM allele frequencies
  • NGMDyes - Dyes used for NGM
  • ProfilerDyes - Dyes used for Profiler plus
  • SGMplusDyes - Dyes used for SGMplus
  • UKCaucasian - Allele frequencies for UK Caucasians
  • USCaucasian - The data base of allele frequencies for 302 US Caucasian profiles.

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.48 score 1 packages 349 downloads 24 exports 41 dependencies

Last updated from:c6466cecd2. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE161
source / vignettesOK184
linux-releaseNOTE159
macos-releaseNOTE227
macos-oldrelNOTE192
windows-develNOTE133
windows-releaseNOTE135
windows-oldrelNOTE119
wasm-releaseOK105

Exports:buildMixtureDomainsDNAmixtureDNAmixtureDatadyesdyes<-getShapeslogLlogL.KlogL.UKlogLpres.KlogLpres.UKmap.genotypesmixMLmixparprequential.scoreqqpeakremovePeakInforPeakHeightsetCPTsetCPT.DsetCPT.OsetCPT.QsetPeakInfovarEst

Dependencies:backportsbroomclicodetoolscpp11digestdplyrfuturefuture.applygenericsglobalsgluegRaingRavengRbaseigraphlatticelifecyclelistenvmagrittrMatrixnumDerivparallellypillarpkgconfigpurrrR6RcppRcppArmadilloRcppEigenrlangRsolnpstringistringrtibbletidyrtidyselecttruncnormutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Statistical Inference for Mixed Samples of DNA (Lite-Version)DNAmixturesLite-package DNAmixtures DNAmixturesLite
Plot simulated peak heights for multiple DNA mixtures.boxplot.DNAmixture
Create RHugin domains for computation.buildMixtureDomains
Create a DNA mixture modelDNAmixture print.DNAmixture
Create a data set for a DNA mixture modelDNAmixtureData
Dyes for a DNA mixturedyes dyes<-
Shape parameters for a mixture with known contributors onlygetShapes
Loglikelihood function for DNA mixture analysis.logL logL.K logL.UK logLpres.K logLpres.UK
Maximum posterior genotypes of unknown contributorsmap.genotypes
The MC15 DNA mixtureMC15
The MC18 DNA mixtureMC18
Maximisation of the likelihood for one or more mixed traces of DNAmixML
Parameters for DNA mixture modelsmixpar print.mixpar
NGM allele frequenciesNGM
Dyes used for NGMNGMDyes
Plot a DNA mixture modelplot.DNAmixture
Various probabilities in a fitted DNA mixture modelpredict.DNAmixture
Calculate prequential scoresplot.prequential.score prequential.score
Dyes used for Profiler plusProfilerDyes
Quantile-Quantile plot for assessing the distribution of observed peak heights.qqpeak
Simulate peak heights from a DNA mixture model.rPeakHeight
Set conditional probability tables for all auxiliary variablessetCPT
Set tables for auxiliary variables 'D'setCPT.D
Set tables for auxiliary variables 'O'.setCPT.O
Set tables for auxiliary variables 'Q'setCPT.Q
Include or exclude peak information in the modelremovePeakInfo setPeakInfo
Dyes used for SGMplusSGMplusDyes
Summary of best genotypesprint.summary.map.genotypes summary.map.genotypes
Allele frequencies for UK CaucasiansUKCaucasian
The data base of allele frequencies for 302 US Caucasian profiles.USCaucasian
Estimated asymptotic variance matrix for MLEprint.summary.mixVarEst summary.mixVarEst varEst