Package: dartR.captive 0.75
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:
dartR.captive_0.75.tar.gz
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dartR.captive_0.75.tgz(r-4.4-any)dartR.captive_0.75.tgz(r-4.3-any)
dartR.captive_0.75.tar.gz(r-4.5-noble)dartR.captive_0.75.tar.gz(r-4.4-noble)
dartR.captive_0.75.tgz(r-4.4-emscripten)dartR.captive_0.75.tgz(r-4.3-emscripten)
dartR.captive.pdf |dartR.captive.html✨
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
Last updated 10 months agofrom:3010a15a47. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 24 2024 |
| R-4.5-win | NOTE | Aug 24 2024 |
| R-4.5-linux | NOTE | Aug 24 2024 |
| R-4.4-win | OK | Aug 24 2024 |
| R-4.4-mac | OK | Aug 24 2024 |
| R-4.3-win | OK | Aug 24 2024 |
| R-4.3-mac | OK | Aug 24 2024 |
Exports:gl.assign.grmgl.assign.mahalanobisgl.assign.pagl.assign.pcagl.filter.parent.offspringgl.grmgl.grm.networkgl.plot.networkgl.report.parent.offspringgl.run.EMIBD9utils.assignmentutils.assignment_2utils.assignment_3utils.assignment_4
Dependencies:ade4adegenetapebase64encbootbslibcachemcliclustercodetoolscolorspacecommonmarkcpp11crayondartR.basedartR.datadata.tabledigestdoParalleldplyrfansifarverfastmapfontawesomeforeachfsgdsfmtgenericsggplot2gluegridExtragtablehtmltoolshttpuvigraphisobanditeratorsjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepatchworkpegaspermutepillarpixmappkgconfigplyrpromisespurrrR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangsassscalessegmentedseqinrshinySNPRelatesourcetoolsspStAMPPstringistringrtibbletidyrtidyselectutf8vctrsveganviridisLitewithrxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Population assignment using grm | gl.assign.grm |
| Assign an individual of unknown provenance to population based on Mahalanobis Distance | gl.assign.mahalanobis |
| Eliminates populations as possible source populations for an individual of unknown provenance, using private alleles | gl.assign.pa |
| Assign an individual of unknown provenance to population based on PCA | gl.assign.pca |
| Filters putative parent offspring within a population | gl.filter.parent.offspring |
| Calculates an identity by descent matrix | gl.grm |
| Represents a genomic relationship matrix (GRM) as a network | gl.grm.network |
| Represents a distance or dissimilarity matrix as a network | gl.plot.network |
| Identifies putative parent offspring within a population | gl.report.parent.offspring |
| Run program EMIBD9 | gl.run.EMIBD9 |
| Population assignment probabilities | utils.assignment |
| Population assignment probabilities | utils.assignment_2 |
| Population assignment probabilities | utils.assignment_3 |
| Population assignment probabilities | utils.assignment_4 |
