likeLTD: Tools to Evaluate DNA Profile Evidence

Tools to determine DNA profile Weight of Evidence. For further information see the 'likeLTD' guide provided, Balding, D.J. (2013) <DOI:10.1073/pnas.1219739110>, or Steele, C.D. et al. (2016) <DOI:10.1515/sagmb-2016-0038>.

Install the latest version of this package by entering the following in R:
install.packages("likeLTD")
AuthorDavid Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Date of publication2017-03-28 06:11:59 UTC
MaintainerChristopher Steele <c.steele.11@ucl.ac.uk>
LicenseGPL-3
Version6.2.0
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

Functions

allele.report Man page
allele.report.peaks Man page
compatible.genotypes Man page
create.likelihood Man page
create.likelihood.log Man page
create.likelihood.vectors Man page
create.likelihood.vectors.peaks Man page
CSP.heights.plot Man page
defence.hypothesis Man page
defence.hypothesis.peaks Man page
DEoptimLoop Man page
determine.dropout Man page
DNA17-db Man page
evaluate Man page
evaluate.from.interim Man page
evaluate.from.interim.peaks Man page
evaluate.peaks Man page
get.likely.genotypes Man page
get.likely.genotypes.peaks Man page
Identifiler-db Man page
initial.arguments Man page
lgc-allele-freqs-wbp Man page
likeLTD Man page
linkage Man page
load.allele.database Man page
locus.likes Man page
locus.likes.peaks Man page
objective.function Man page
optimisation.params Man page
optimisation.params.peaks Man page
output.report Man page
output.report.peaks Man page
pack.admin.input Man page
pack.admin.input.peaks Man page
peaks.results.plot Man page
penalties Man page
plotLikelihood.2d Man page
prosecution.hypothesis Man page
prosecution.hypothesis.peaks Man page
read.csp.profile Man page
read.known.profiles Man page
read.peaks.profile Man page
read.unc.profile Man page
relistArguments Man page
relistArguments.peaks Man page
SGMplus-db Man page
unitTests.likeLTD Man page

Files

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

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