Package: rrnni 0.1.1
Jiří C. Moravec
rrnni: Manipulate with RNNI Tree Space
Calculate RNNI distance between and manipulate with ranked trees. RNNI stands for Ranked Nearest Neighbour Interchange and is an extension of the classical NNI space (space of trees created by the NNI moves) to ranked trees, where internal nodes are ordered according to their heights (usually assumed to be times). The RNNI distance takes the tree topology into account, as standard NNI does, but also penalizes changes in the order of internal nodes, i.e. changes in the order of times of evolutionary events. For more information about the RNNI space see: Gavryushkin et al. (2018) <doi:10.1007/s00285-017-1167-9>, Collienne & Gavryushkin (2021) <doi:10.1007/s00285-021-01567-5>, Collienne et al. (2021) <doi:10.1007/s00285-021-01685-0>, and Collienne (2021) <http://hdl.handle.net/10523/12606>.
Authors:
rrnni_0.1.1.tar.gz
rrnni_0.1.1.zip(r-4.5)rrnni_0.1.1.zip(r-4.4)rrnni_0.1.1.zip(r-4.3)
rrnni_0.1.1.tgz(r-4.4-x86_64)rrnni_0.1.1.tgz(r-4.4-arm64)rrnni_0.1.1.tgz(r-4.3-x86_64)rrnni_0.1.1.tgz(r-4.3-arm64)
rrnni_0.1.1.tar.gz(r-4.5-noble)rrnni_0.1.1.tar.gz(r-4.4-noble)
rrnni_0.1.1.tgz(r-4.4-emscripten)rrnni_0.1.1.tgz(r-4.3-emscripten)
rrnni.pdf |rrnni.html✨
rrnni/json (API)
| # Install 'rrnni' in R: |
| install.packages('rrnni', repos = c('https://biods.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biods/rrnni/issues
Last updated 1 years agofrom:aee39362aa. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 12 2024 |
| R-4.5-win-x86_64 | OK | Nov 12 2024 |
| R-4.5-linux-x86_64 | OK | Nov 12 2024 |
| R-4.4-win-x86_64 | OK | Nov 12 2024 |
| R-4.4-mac-x86_64 | OK | Nov 12 2024 |
| R-4.4-mac-aarch64 | OK | Nov 12 2024 |
| R-4.3-win-x86_64 | OK | Nov 12 2024 |
| R-4.3-mac-x86_64 | OK | Nov 12 2024 |
| R-4.3-mac-aarch64 | OK | Nov 12 2024 |
Exports:as_rankedcommon_tipskeep_tipsrandom_treerankedPhyloread_newickrnnisort_tipstips
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert a tree to ranked tree | as_ranked |
| Find shared tip labels | common_tips |
| Prune a tree | keep_tips keep_tips.multiPhylo keep_tips.phylo keep_tips.rankedPhylo |
| Create a random ranked phylogeny | random_tree |
| Create a ranked tree | rankedPhylo rankedPhylo.character rankedPhylo.default rankedPhylo.multiPhylo rankedPhylo.numeric rankedPhylo.phylo |
| Read a newick tree | read_newick |
| Calculate RNNI distance | rnni |
| Sort tip labels | sort_tips sort_tips.multiPhylo sort_tips.phylo |
| Extract tips from tree | tips tips.multiPhylo tips.phylo |
