bnpsd: Simulate Genotypes from the BN-PSD Admixture Model
The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate subpopulations from which n individuals draw their alleles dictated by their individual-specific admixture proportions. The BN-PSD model additionally imposes the Balding-Nichols (BN) allele frequency model to the intermediate populations, which therefore evolved independently from a common ancestral population T with subpopulation-specific FST (Wright's fixation index) parameters. The BN-PSD model can be used to yield complex population structures. This simulation approach is now extended to subpopulations related by a tree. Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.
| Version: | 1.3.13 |
| Imports: | stats, ape, nnls |
| Suggests: | popkin (≥ 1.3.9), testthat, knitr, rmarkdown, RColorBrewer |
| Published: | 2021-08-25 |
| DOI: | 10.32614/CRAN.package.bnpsd |
| Author: | Alejandro Ochoa 
[aut, cre],
John D. Storey
[aut] |
| Maintainer: | Alejandro Ochoa <alejandro.ochoa at duke.edu> |
| BugReports: | https://github.com/StoreyLab/bnpsd/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/StoreyLab/bnpsd/ |
| NeedsCompilation: | no |
| Citation: | bnpsd citation info |
| Materials: | README, NEWS |
| CRAN checks: | bnpsd results |
Documentation:
| Reference manual: | bnpsd.html , bnpsd.pdf |
| Vignettes: |
Simulate Admixed Populations with 'bnpsd' (source, R code) |
Downloads:
| Package source: | bnpsd_1.3.13.tar.gz |
| Windows binaries: | r-devel: bnpsd_1.3.13.zip, r-release: bnpsd_1.3.13.zip, r-oldrel: bnpsd_1.3.13.zip |
| macOS binaries: | r-release (arm64): bnpsd_1.3.13.tgz, r-oldrel (arm64): bnpsd_1.3.13.tgz, r-release (x86_64): bnpsd_1.3.13.tgz, r-oldrel (x86_64): bnpsd_1.3.13.tgz |
| Old sources: | bnpsd archive |
Reverse dependencies:
| Reverse suggests: | ggmix, popkin, simfam, simtrait |
Linking:
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