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:Gerry Tonkin-Hill [cre, aut]

rhierbaps_1.1.3.tar.gz
rhierbaps_1.1.3.zip(r-4.7)rhierbaps_1.1.3.zip(r-4.6)rhierbaps_1.1.3.zip(r-4.5)
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✨
card.svg |card.png
rhierbaps/json (API)
NEWS

# 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

On CRAN:

Conda:

population-geneticspopulation-genomicspopulation-structure

5.84 score 36 stars 38 scripts 271 downloads 1 mentions 4 exports 26 dependencies

Last updated from:da7f1159d9. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK154
source / vignettesOK294
linux-release-x86_64OK145
macos-release-arm64OK185
macos-oldrel-arm64OK205
windows-develOK115
windows-releaseOK96
windows-oldrelOK87
wasm-releaseOK117

Exports:hierBAPSload_fastaplot_sub_clustersave_lml_logs

Dependencies:apeclicpp11digestfarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrmatrixStatsnlmepatchworkpurrrR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr

Introduction to rhierbaps

Gerry Tonkin-Hill

Rendered fromintroduction.Rmdusingknitr::rmarkdownon May 24 2026.

Last update: 2019-05-09
Started: 2017-11-24

Readme and manuals

Help Manual

Help pageTopics
calc_change_in_mlcalc_change_in_ml
calc_log_mlcalc_log_ml
hierBAPShierBAPS
join_units_2join_units_2
load_fastaload_fasta
model_search_parallelmodel_search_parallel
move_units_1move_units_1
plot_sub_clusterplot_sub_cluster
preproc_alignmentpreproc_alignment
reallocate_units_4reallocate_units_4
save_lml_logssave_lml_logs
split_clusters_3split_clusters_3