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rrnni  

Manipulate with RNNI Tree Space
View on CRAN: Click here


Download and install rrnni package within the R console
Install from CRAN:
install.packages("rrnni")

Install from Github:
library("remotes")
install_github("cran/rrnni")

Install by package version:
library("remotes")
install_version("rrnni", "0.1.1")



Attach the package and use:
library("rrnni")
Maintained by
Jiří C. Moravec
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-09-14
Latest Update: 2023-08-25
Description:
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>.
How to cite:
Jiří C. Moravec (2022). rrnni: Manipulate with RNNI Tree Space. R package version 0.1.1, https://cran.r-project.org/web/packages/rrnni
Previous versions and publish date:
0.1.0 (2022-09-14 08:50)
Other packages that cited rrnni R package
View rrnni citation profile
Other R packages that rrnni depends, imports, suggests or enhances
Functions, R codes and Examples using the rrnni R package
Some associated functions: as_ranked . common_tips . keep_tips . random_tree . rankedPhylo . read_newick . rmv . rnni . rrnni-package . sort_tips . tips . validate_rankedPhylo . 
Some associated R codes: Full rrnni package functions and examples
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