likeLTD: Tools to Evaluate DNA Profile Evidence

Tools to determine DNA profile Weight of Evidence. For further information see the 'likeLTD' guide provided, or Balding, D.J. (2013) <DOI:10.1073/pnas.1219739110>.

AuthorDavid Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Date of publication2016-10-24 23:27:19
MaintainerChristopher Steele <c.steele.11@ucl.ac.uk>
LicenseGPL-3
Version6.1.1
https://sites.google.com/site/baldingstatisticalgenetics/

View on CRAN

Man pages

allele.report: likeLTD::allele.report

allele.report.peaks: likeLTD::allele.report.peaks

compatible.genotypes: likeLTD::compatible.genotypes

create.likelihood: likeLTD::create.likelihood

create.likelihood.log: likeLTD::create.likelihood.log

create.likelihood.vectors: likeLTD::create.likelihood.vectors

create.likelihood.vectors.peaks: likeLTD::create.likelihood.vectors.peaks

CSP.heights.plot: likeLTD::CSP.heights.plot

defence.hypothesis: likeLTD::defence.hypothesis

defence.hypothesis.peaks: likeLTD::defence.hypothesis.peaks

DEoptimLoop: likeLTD::DEoptimLoop

determine.dropout: determine.dropout

DNA17-db: NGMSelect allele database

evaluate: likeLTD::evaluate

evaluate.from.interim: likeLTD::evaluate.from.interim

evaluate.from.interim.peaks: likeLTD::evaluate.from.interim.peaks

evaluate.peaks: likeLTD::evaluate.peaks

get.likely.genotypes: likeLTD::get.likely.genotypes

get.likely.genotypes.peaks: likeLTD::get.likely.genotypes.peaks

Identifiler-db: Identifiler allele database

initial.arguments: likeLTD::initial.arguments

lgc-allele-freqs-wbp: Allele database

likeLTD: likeLTD

linkage: Recombination rates for linked loci

load.allele.database: likeLTD::load.allele.database

locus.likes: likeLTD::locus.likes

locus.likes.peaks: likeLTD::locus.likes.peaks

objective.functions: likeLTD objective functions

optimisation.params: likeLTD::optimisation.params

optimisation.params.peaks: likeLTD::optimisation.params.peaks

output.report: likeLTD::output.report

output.report.peaks: likeLTD::output.report.peaks

pack.admin.input: likeLTD::pack.admin.input

pack.admin.input.peaks: likeLTD::pack.admin.input.peaks

peaks.results.plot: likeLTD::peaks.results.plot

penalties: likeLTD::penalties

plotLikelihood.2d: likeLTD::plotLikelihood.2d

prosecution.hypothesis: likeLTD::prosecution.hypothesis

prosecution.hypothesis.peaks: likeLTD::prosecution.hypothesis.peaks

read.csp.profile: likeLTD::read.csp.profile

read.known.profiles: likeLTD::read.known.profiles

read.peaks.profile: likeLTD::read.peaks.profile

read.unc.profile: likeLTD::read.unc.profile

relistArguments: likeLTD::relistArguments

relistArguments.peaks: likeLTD::relistArguments.peaks

SGMplus-db: SGMplus allele database

unitTests.likeLTD: Unit tests for the package likeLTD

Files in this package

likeLTD
likeLTD/inst
likeLTD/inst/CITATION
likeLTD/inst/extdata
likeLTD/inst/extdata/nodropout
likeLTD/inst/extdata/nodropout/CSP.csv
likeLTD/inst/extdata/nodropout/reference.csv
likeLTD/inst/extdata/nodropin
likeLTD/inst/extdata/nodropin/hammer-reference.csv
likeLTD/inst/extdata/nodropin/hammer-CSP.csv
likeLTD/inst/extdata/novictim
likeLTD/inst/extdata/novictim/hammer-reference.csv
likeLTD/inst/extdata/novictim/hammer-CSP.csv
likeLTD/inst/extdata/laboratory
likeLTD/inst/extdata/laboratory/laboratory-CSP-discrete.csv
likeLTD/inst/extdata/laboratory/laboratory-CSP.csv
likeLTD/inst/extdata/laboratory/laboratory-reference.csv
likeLTD/inst/extdata/hammer
likeLTD/inst/extdata/hammer/hammer-reference.csv
likeLTD/inst/extdata/hammer/hammer-CSP.csv
likeLTD/inst/extdata/hammer/space-CSP.csv
likeLTD/inst/extdata/hammer/space-reference.csv
likeLTD/inst/doc
likeLTD/inst/doc/likeLTDguide.pdf
likeLTD/inst/doc/usage.Rnw
likeLTD/inst/doc/usage.R
likeLTD/inst/doc/usage.pdf
likeLTD/inst/unitTests
likeLTD/inst/unitTests/runit_nodropin.R
likeLTD/inst/unitTests/runit_nodropout.R
likeLTD/inst/unitTests/runit_maximize.R
likeLTD/inst/unitTests/runit_reports.R
likeLTD/inst/unitTests/runit_novictims.R
likeLTD/inst/unitTests/runit_hypothesis.R
likeLTD/inst/unitTests/runit_objective.R
likeLTD/inst/unitTests/runit_objectivePerLocus.R
likeLTD/inst/unitTests/runit_genetics.R
likeLTD/src
likeLTD/src/Makevars
likeLTD/src/genetics.h
likeLTD/src/maximizePeaks.cpp
likeLTD/src/objectives.cpp
likeLTD/src/openmp.h
likeLTD/src/objectives.h
likeLTD/src/config.h
likeLTD/src/genetics.cpp
likeLTD/src/gammaDist.cpp
likeLTD/src/gammaDist.h
likeLTD/src/module.cpp
likeLTD/src/openmp.cpp
likeLTD/src/Makevars.win
likeLTD/src/maximizePeaks.h
likeLTD/NAMESPACE
likeLTD/demo
likeLTD/demo/hammer.R
likeLTD/demo/allele_report.R
likeLTD/demo/plotter.R
likeLTD/demo/00Index
likeLTD/demo/timings.R
likeLTD/data
likeLTD/data/Identifiler-db.txt.gz
likeLTD/data/DNA17-db.txt.gz
likeLTD/data/SGMplus-db.txt.gz
likeLTD/data/linkage.txt.gz
likeLTD/data/lgc-allele-freqs-wbp.txt.gz
likeLTD/R
likeLTD/R/objectives-peaks.R likeLTD/R/reports-peaks.R likeLTD/R/maximize.R likeLTD/R/plotter.R likeLTD/R/maximize-peaks.R likeLTD/R/genetics.R likeLTD/R/genetics-peaks.R likeLTD/R/hypothesis-peaks.R likeLTD/R/reports.R likeLTD/R/hypothesis.R likeLTD/R/kMeans.R likeLTD/R/objectives.R
likeLTD/vignettes
likeLTD/vignettes/usage.Rnw
likeLTD/MD5
likeLTD/build
likeLTD/build/vignette.rds
likeLTD/DESCRIPTION
likeLTD/man
likeLTD/man/Identifiler-db.Rd likeLTD/man/create.likelihood.log.Rd likeLTD/man/initial.arguments.Rd likeLTD/man/read.unc.profile.Rd likeLTD/man/locus.likes.Rd likeLTD/man/optimisation.params.peaks.Rd likeLTD/man/optimisation.params.Rd likeLTD/man/get.likely.genotypes.Rd likeLTD/man/create.likelihood.Rd likeLTD/man/determine.dropout.Rd likeLTD/man/linkage.Rd likeLTD/man/peaks.results.plot.Rd likeLTD/man/penalties.Rd likeLTD/man/evaluate.peaks.Rd likeLTD/man/allele.report.Rd likeLTD/man/relistArguments.peaks.Rd likeLTD/man/objective.functions.Rd likeLTD/man/read.peaks.profile.Rd likeLTD/man/defence.hypothesis.Rd likeLTD/man/evaluate.Rd likeLTD/man/DNA17-db.Rd likeLTD/man/evaluate.from.interim.Rd likeLTD/man/defence.hypothesis.peaks.Rd likeLTD/man/locus.likes.peaks.Rd likeLTD/man/unitTests.likeLTD.Rd likeLTD/man/load.allele.database.Rd likeLTD/man/create.likelihood.vectors.peaks.Rd likeLTD/man/output.report.Rd likeLTD/man/DEoptimLoop.Rd likeLTD/man/SGMplus-db.Rd likeLTD/man/get.likely.genotypes.peaks.Rd likeLTD/man/prosecution.hypothesis.peaks.Rd likeLTD/man/relistArguments.Rd likeLTD/man/output.report.peaks.Rd likeLTD/man/create.likelihood.vectors.Rd likeLTD/man/allele.report.peaks.Rd likeLTD/man/read.known.profiles.Rd likeLTD/man/likeLTD.Rd likeLTD/man/plotLikelihood.2d.Rd likeLTD/man/pack.admin.input.peaks.Rd likeLTD/man/CSP.heights.plot.Rd likeLTD/man/read.csp.profile.Rd likeLTD/man/compatible.genotypes.Rd likeLTD/man/evaluate.from.interim.peaks.Rd likeLTD/man/lgc-allele-freqs-wbp.Rd likeLTD/man/pack.admin.input.Rd likeLTD/man/prosecution.hypothesis.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.