Package: dartR.captive 1.2.2

dartR.captive: Analysing 'SNP' Data to Support Captive Breeding

Functions are provided that facilitate the analysis of SNP (single nucleotide polymorphism) data to answer questions regarding captive breeding and relatedness between individuals. 'dartR.captive' is part of the 'dartRverse' suit of packages. Gruber et al. (2018) <doi:10.1111/1755-0998.12745>. Mijangos et al. (2022) <doi:10.1111/2041-210X.13918>.

Authors:Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb], Eric Archer [ctb], Sam Amini [ctb], Ethan Halford [ctb]

dartR.captive_1.2.2.tar.gz
dartR.captive_1.2.2.zip(r-4.7)dartR.captive_1.2.2.zip(r-4.6)dartR.captive_1.2.2.zip(r-4.5)
dartR.captive_1.2.2.tgz(r-4.6-any)dartR.captive_1.2.2.tgz(r-4.5-any)
dartR.captive_1.2.2.tar.gz(r-4.7-any)dartR.captive_1.2.2.tar.gz(r-4.6-any)
dartR.captive_1.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
dartR.captive/json (API)

# Install 'dartR.captive' in R:
install.packages('dartR.captive', repos = c('https://green-striped-gecko.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/green-striped-gecko/dartr/issues

Pkgdown/docs site:https://green-striped-gecko.github.io

On CRAN:

Conda:

2.00 score 1 stars 645 downloads 48 mentions 20 exports 155 dependencies

Last updated from:eda0dc4a84. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK361
source / vignettesOK308
linux-release-x86_64OK381
macos-release-arm64OK244
macos-oldrel-arm64OK278
windows-develOK295
windows-releaseOK306
windows-oldrelOK296
wasm-releaseOK208

Exports:gl.assign.grmgl.assign.mahalgl.assign.mahalanobisgl.assign.on.genotypegl.assign.pagl.assign.pcagl.diagnostics.relatednessgl.filter.parent.offspringgl.grmgl.grm.networkgl.plot.networkgl.report.parent.offspringgl.run.colonygl.run.EMIBD9gl.sim.relatednessgl2colonyutils.assignmentutils.assignment_2utils.assignment_3utils.assignment_4

Dependencies:ade4adegenetapebase64encBHbigassertrbigparallelrbigreadrbigsnprbigsparserbigstatsrbigutilsrBiocGenericsbitbitopsbootbslibcachemcaToolscliclustercodetoolscommonmarkconfintrcowplotcpp11crayondartR.basedartR.datadartR.popgendartR.simdata.tableDEoptimRdigestdoParalleldoRNGdotCall64dplyrfarverfastmapfffieldsflockfontawesomeforeachfsfurrrfuturegastongdsfmtgenericsggdendroggplot2ggpmiscggppggrepelglobalsgluegridExtragtablegtoolshierfstathtmltoolshttpuvigraphisobanditeratorsjquerylibjsonlitelabelinglaterlatticeLEAlifecyclelistenvlubridatemagrittrmapsMASSMatrixMatrixModelsmemoisemgcvmimenabornlmeotelparallellypatchworkpegaspermutepillarpixmappkgconfigplyrpolynompromisespspurrrquantregR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreshape2RhpcBLASctlrlangrmiorngtoolsrobustbaseroptimRSpectrarunonceS7sassscalessegmentedseqinrshinyshinyBSshinyjsshinythemesshinyWidgetsSNPRelatesnpStatssourcetoolsspspamSparseMsplus2RStAMPPstringistringrsurvivalterratibbletidyrtidyselecttimechangetriebeardurltoolsutf8vctrsveganviridisLitewithrxtablextszoo

Readme and manuals

Help Manual

Help pageTopics
Population assignment using grmgl.assign.grm
Calculate probabilities of assignment of an individual of unknown provenance to population based on Mahalanobis Distancegl.assign.mahal
Calculate probabilities of assignment of an individual of unknown provenance to population based on Mahalanobis Distancegl.assign.mahalanobis
Use genotype to identify populations as possible source populations for an individual of unknown provenance.gl.assign.on.genotype
Use private alleles to identify populations as possible source populations for an individual of unknown provenance.gl.assign.pa
Eliminate from consideration putative source populations for a specified individual of unknown provenance using PCAgl.assign.pca
Run simulations and relatedness analyses on genlight objectsgl.diagnostics.relatedness
Filters putative parent offspring within a populationgl.filter.parent.offspring
Calculates an identity by descent matrixgl.grm
Represents a similarity matrix as a networkgl.grm.network
Represents a distance or dissimilarity matrix as a networkgl.plot.network
Identifies putative parent offspring within a populationgl.report.parent.offspring
Run COLONY2gl.run.colony
Run program EMIBD9gl.run.EMIBD9
Simulate relatedness estimates.gl.sim.relatedness
Export a COLONY2 input file from a genlight objectgl2colony
Population assignment probabilitiesutils.assignment
Population assignment probabilitiesutils.assignment_2
Population assignment probabilitiesutils.assignment_3
Population assignment probabilitiesutils.assignment_4