Package: dartR.sim 0.70

Jose L. Mijangos

dartR.sim: Computer Simulations of 'SNP' Data

Allows to simulate SNP data using genlight objects. For example, it is straight forward to simulate a simple drift scenario with exchange of individuals between two populations or create a new genlight object based on allele frequencies of an existing genlight object.

Authors:Jose L. Mijangos [aut, cre], Bernd Gruber [aut], Arthur Georges [aut], Carlo Pacioni [aut], Peter J. Unmack [ctb], Oliver Berry [ctb]

dartR.sim_0.70.tar.gz
dartR.sim_0.70.zip(r-4.5)dartR.sim_0.70.zip(r-4.4)dartR.sim_0.70.zip(r-4.3)
dartR.sim_0.70.tgz(r-4.4-any)dartR.sim_0.70.tgz(r-4.3-any)
dartR.sim_0.70.tar.gz(r-4.5-noble)dartR.sim_0.70.tar.gz(r-4.4-noble)
dartR.sim_0.70.tgz(r-4.4-emscripten)dartR.sim_0.70.tgz(r-4.3-emscripten)
dartR.sim.pdf |dartR.sim.html✨
dartR.sim/json (API)

# Install 'dartR.sim' in R:

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

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

On CRAN:

8 exports 4.76 score 102 dependencies 48 mentions 1 scripts 321 downloads

Last updated 10 months agofrom:4fb58fff41. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 16 2024
R-4.5-win	NOTE	Sep 16 2024
R-4.5-linux	NOTE	Sep 16 2024
R-4.4-win	OK	Sep 16 2024
R-4.4-mac	OK	Sep 16 2024
R-4.3-win	OK	Sep 16 2024
R-4.3-mac	OK	Sep 16 2024

Exports:gl.diagnostics.sim gl.sim.create_dispersal gl.sim.emigration gl.sim.ind gl.sim.mutate gl.sim.offspring gl.sim.WF.run gl.sim.WF.table

Dependencies:ade4 adegenet anytime ape base64enc BH boot bslib cachem cli cluster codetools colorspace commonmark cpp11 crayon dartR.base dartR.data data.table digest doParallel dotCall64 dplyr fansi farver fastmap fields fontawesome foreach fs gaston gdsfmt generics ggplot2 glue gridExtra gtable gtools hierfstat htmltools httpuv igraph isoband iterators jquerylib jsonlite labeling later lattice lifecycle magrittr maps MASS Matrix memoise mgcv mime munsell nlme patchwork pegas permute pillar pixmap pkgconfig plyr promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel reshape2 rlang sass scales segmented seqinr shiny shinyBS shinyjs shinythemes shinyWidgets SNPRelate sourcetools sp spam StAMPP stringi stringr tibble tidyr tidyselect utf8 vctrs vegan viridisLite withr xtable

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Comparing simulations against theoretical expectations	gl.diagnostics.sim
Creates a dispersal file as input for the function gl.sim.WF.run	gl.sim.create_dispersal
Simulates emigration between populations	gl.sim.emigration
Simulates individuals based on allele frequencies	gl.sim.ind
Simulates mutations within a genlight object	gl.sim.mutate
Simulates offspring based on alleles provided by parents	gl.sim.offspring
Runs Wright-Fisher simulations	gl.sim.WF.run
Creates the reference table for running gl.sim.WF.run	gl.sim.WF.table
Shiny app for the input of the reference table for the simulations	interactive_reference
Shiny app for the input of the simulations variables	interactive_sim_run