Package: tidygenclust 0.1.1

Andrea Manica

tidygenclust: Clustering for Population Genetics in R

A tidy interface to clustering in population genetics. This package provides a set of functions to perform clustering on genetic data, and to visualize the results, both for single runs and for multiple repeats of the same analysis. 'tidygenclust' ports the 'fastmixture' and 'clumppling' python modules to R, and it is built on top of the 'tidypopgen' package. Currently it works only on Linux and OSX (you can use the WSL on Windows).

Authors:Eirlys Tysall [aut], Anahit Hovhannisyan [aut], Evie Carter [aut], Andrea Pozzi [aut], Cecilia Padilla-Iglesias [aut], Michela Leonardi [aut], Aramish Fatima [aut], Ondrej Pelanek [aut], Nile Stephenson [aut], Margherita Colucci [aut], Andrea Manica [aut, cre]

tidygenclust_0.1.1.tar.gz
tidygenclust_0.1.1.zip(r-4.7)tidygenclust_0.1.1.zip(r-4.6)tidygenclust_0.1.1.zip(r-4.5)
tidygenclust_0.1.1.tgz(r-4.6-any)tidygenclust_0.1.1.tgz(r-4.5-any)
tidygenclust_0.1.1.tar.gz(r-4.7-any)tidygenclust_0.1.1.tar.gz(r-4.6-any)
tidygenclust_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
tidygenclust/json (API)
NEWS

# Install 'tidygenclust' in R:

install.packages('tidygenclust', repos = c('https://evolecolgroup.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/evolecolgroup/tidygenclust/issues

Datasets:

capeverde_pops - Population membership for the Capeverde dataset

On CRAN:

3.30 score 1 stars 5 scripts 11 exports 87 dependencies

Last updated from:36122fa6ba (on main). Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	1100
source / vignettes	ERROR	247
linux-release-x86_64	WARNING	201
macos-release-arm64	WARNING	95
macos-oldrel-arm64	WARNING	126
windows-devel	WARNING	198
windows-release	WARNING	216
windows-oldrel	WARNING	159
wasm-release	OK	169

Exports:%>%augment autoplot gt_clumppling gt_fastmixture scale_fill_distruct subset_gt_clumppling tgc_tools_install tgc_tools_version theme_distruct tidy

Dependencies:BH bigassertr bigparallelr bigreadr bigsnpr bigsparser bigstatsr bigutilsr bit class classInt cli codetools cowplot cpp11 data.table DBI DEoptimR digest doParallel doRNG dplyr e1071 farver ff flock foreach generics ggplot2 glue gtable here isoband iterators jsonlite KernSmooth labeling lattice lifecycle magrittr MASS Matrix nabor parallelly patchwork pillar pkgconfig png proxy ps purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppTOML reticulate RhpcBLASctl rlang rmio rngtools robustbase roptim rprojroot RSpectra runner runonce s2 S7 scales sf stringi stringr tibble tidypopgen tidyr tidyselect triebeard units urltools utf8 vctrs viridisLite withr wk

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
autoplot for clumppling objects	autoplot.gt_clumppling
Population membership for the Capeverde dataset	capeverde_pops
run clumppling	gt_clumppling
fastmixture algorithm for population genetics clustering	gt_fastmixture
Subset a 'gt_clumppling' object	subset_gt_clumppling
Install tools for 'tidygenclust'	tgc_tools_install
Print version of the python tools installed by 'tidygenclust'	tgc_tools_version
Tidy a 'gt_clumppling' object	tidy.gt_clumppling

Package: tidygenclust 0.1.1

tidygenclust: Clustering for Population Genetics in R

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Help Manual

Usage by other packages (reverse dependencies)