Package: dartR.captive 1.0.2

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]

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# 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 site:https://green-striped-gecko.github.io

On CRAN:

2.00 score 1 stars 3 scripts 164 downloads 48 mentions 15 exports 134 dependencies

Last updated 23 days agofrom:3db9aff9d0. Checks:6 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 18 2025
R-4.5-win	OK	Feb 18 2025
R-4.5-mac	OK	Feb 18 2025
R-4.5-linux	OK	Feb 18 2025
R-4.4-win	OK	Feb 18 2025
R-4.4-mac	OK	Feb 18 2025

Exports:gl.assign.grm gl.assign.mahalanobis gl.assign.pa gl.assign.pca gl.filter.parent.offspring gl.grm gl.grm.network gl.plot.network gl.report.parent.offspring gl.run.EMIBD9 gl.sim.relatedness utils.assignment utils.assignment_2 utils.assignment_3 utils.assignment_4

Dependencies:ade4 adegenet ape arsenal backports base64enc boot bslib cachem checkmate cli cluster codetools colorspace commonmark cpp11 crayon dartR.base dartR.data dartR.sim data.table digest doParallel dotCall64 dplyr evaluate fansi farver fastmap fields fontawesome foreach foreign Formula fs gaston gdsfmt generics ggplot2 glue gridExtra gtable gtools haplo.stats hierfstat highr Hmisc htmlTable htmltools htmlwidgets httpuv igraph isoband iterators jquerylib jsonlite knitr labeling later lattice lifecycle magrittr maps MASS Matrix MatrixModels memoise mgcv mime multcomp munsell mvtnorm nlme nnet patchwork pegas permute pillar pixmap pkgconfig plyr poisbinom polspline promises purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel reshape2 rlang rmarkdown rms rpart rstudioapi sandwich sass scales segmented seqinr shiny shinyBS shinyjs shinythemes shinyWidgets SNPassoc SNPRelate sourcetools sp spam SparseM StAMPP stringi stringr survival TH.data tibble tidyr tidyselect tinytex utf8 vctrs vegan viridis viridisLite withr xfun xtable yaml zoo

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
Simulate relatedness estimates.	gl.sim.relatedness
Population assignment probabilities	utils.assignment
Population assignment probabilities	utils.assignment_2
Population assignment probabilities	utils.assignment_3
Population assignment probabilities	utils.assignment_4

Package: dartR.captive 1.0.2

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

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