Libraries | Loading data | Running hierBAPS | Plotting results | Caculating assignment probabilities | Saving results | Citing rhierbaps | References | Session Information
Package: rhierbaps 1.1.3
rhierbaps: Clustering Genetic Sequence Data Using the HierBAPS Algorithm
Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences from multiple sequence alignments in FASTA format. The implementation includes improved defaults and plotting capabilities and unlike the original 'MATLAB' version removes singleton SNPs by default.
Authors:
rhierbaps_1.1.3.tar.gz
rhierbaps_1.1.3.zip(r-4.7-any)rhierbaps_1.1.3.zip(r-4.6-any)rhierbaps_1.1.3.zip(r-4.5-any)
rhierbaps_1.1.3.tgz(r-4.6-any)rhierbaps_1.1.3.tgz(r-4.5-any)
rhierbaps_1.1.3.tar.gz(r-4.7-any)rhierbaps_1.1.3.tar.gz(r-4.6-any)
rhierbaps_1.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rhierbaps/json (API)
| # Install 'rhierbaps' in R: |
| install.packages('rhierbaps', repos = c('https://gtonkinhill.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gtonkinhill/rhierbaps/issues
population-geneticspopulation-genomicspopulation-structure
Last updated from:da7f1159d9. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 158 | ||
| source / vignettes | OK | 302 | ||
| linux-release | OK | 160 | ||
| macos-release | OK | 165 | ||
| macos-oldrel | OK | 176 | ||
| windows-devel | OK | 89 | ||
| windows-release | OK | 118 | ||
| windows-oldrel | OK | 76 | ||
| wasm-release | OK | 132 |
Exports:hierBAPSload_fastaplot_sub_clustersave_lml_logs
Dependencies:apeclicpp11digestfarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrmatrixStatsnlmepatchworkpurrrR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calc_change_in_ml | calc_change_in_ml |
| calc_log_ml | calc_log_ml |
| hierBAPS | hierBAPS |
| join_units_2 | join_units_2 |
| load_fasta | load_fasta |
| model_search_parallel | model_search_parallel |
| move_units_1 | move_units_1 |
| plot_sub_cluster | plot_sub_cluster |
| preproc_alignment | preproc_alignment |
| reallocate_units_4 | reallocate_units_4 |
| save_lml_logs | save_lml_logs |
| split_clusters_3 | split_clusters_3 |