Package: clustur 0.1.1
Patrick Schloss
clustur: Clustering
A tool that implements the clustering algorithms from 'mothur' (Schloss PD et al. (2009) <doi:10.1128/AEM.01541-09>). 'clustur' make use of the cluster() and make.shared() command from 'mothur'. Our cluster() function has five different algorithms implemented: 'OptiClust', 'furthest', 'nearest', 'average', and 'weighted'. 'OptiClust' is an optimized clustering method for Operational Taxonomic Units, and you can learn more here, (Westcott SL, Schloss PD (2017) <doi:10.1128/mspheredirect.00073-17>). The make.shared() command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.
Authors:
clustur_0.1.1.tar.gz
clustur_0.1.1.tar.gz(r-4.5-noble)clustur_0.1.1.tar.gz(r-4.4-noble)
clustur_0.1.1.tgz(r-4.4-emscripten)clustur_0.1.1.tgz(r-4.3-emscripten)
clustur.pdf |clustur.html✨
clustur/json (API)
NEWS
| # Install 'clustur' in R: |
| install.packages('clustur', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/schlosslab/clustur/issues
Last updated 1 days agofrom:edd63f94d7. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 25 2024 |
| R-4.5-linux-x86_64 | OK | Nov 25 2024 |
Exports:clustercreate_sparse_matrixexample_pathget_abundanceget_binsget_count_tableget_cutoffget_distance_dfget_metricsread_countread_distsplit_clusters_to_listvalidate_count_table
Dependencies:briocallrclicrayondescdiffobjdigestevaluatefsgluejsonlitelatticelifecyclemagrittrMatrixpkgbuildpkgloadpraiseprocessxpsR6Rcpprlangrprojroottestthatwaldowithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cluster entities together | cluster |
| Create Sparse Matrix | create_sparse_matrix |
| Example Path | example_path |
| Get Shared | get_abundance |
| Get Clusters | get_bins |
| Get Count Table | get_count_table |
| Get Cutoff | get_cutoff |
| Get Distance Data Frame | get_distance_df |
| Get Metrics | get_metrics |
| Read count table | read_count |
| Read distance matrices | read_dist |
| Split Clusters to List | split_clusters_to_list |
| Validate Count Table | validate_count_table |
