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:Jiří C. Moravec [aut, cre], Lena Collienne [aut]

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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'))

Peer review:

Bug tracker:https://github.com/biods/rrnni/issues

On CRAN:

phylogenetics

2.70 score 1 stars 1 scripts 161 downloads 9 exports 5 dependencies

Last updated 1 years agofrom:aee39362aa. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 13 2024
R-4.5-win-x86_64OKOct 13 2024
R-4.5-linux-x86_64OKOct 13 2024
R-4.4-win-x86_64OKOct 13 2024
R-4.4-mac-x86_64OKOct 13 2024
R-4.4-mac-aarch64OKOct 13 2024
R-4.3-win-x86_64OKOct 13 2024
R-4.3-mac-x86_64OKOct 13 2024
R-4.3-mac-aarch64OKOct 13 2024

Exports:as_rankedcommon_tipskeep_tipsrandom_treerankedPhyloread_newickrnnisort_tipstips

Dependencies:apedigestlatticenlmeRcpp

Readme and manuals

Help Manual

Help pageTopics
Convert a tree to ranked treeas_ranked
Find shared tip labelscommon_tips
Prune a treekeep_tips keep_tips.multiPhylo keep_tips.phylo keep_tips.rankedPhylo
Create a random ranked phylogenyrandom_tree
Create a ranked treerankedPhylo rankedPhylo.character rankedPhylo.default rankedPhylo.multiPhylo rankedPhylo.numeric rankedPhylo.phylo
Read a newick treeread_newick
Calculate RNNI distancernni
Sort tip labelssort_tips sort_tips.multiPhylo sort_tips.phylo
Extract tips from treetips tips.multiPhylo tips.phylo