This package is considered a duplicate. The official version of this package is found at:https://ms609.r-universe.dev/TBRDist

Package: TBRDist 2.0.0

Martin R. Smith

TBRDist: Rearrangement Distances Between Phylogenetic Trees

Fast calculation of tree rearrangement distances. For unrooted trees: Subtree Prune and Regraft (SPR), Tree Bisection and Reconnection (TBR), and Replug distances, using the algorithms of Whidden and Matsen (2017) <doi:10.48550/arXiv.1511.07529>. For rooted trees: rooted SPR (rSPR) distance, using the fixed-parameter algorithms of Whidden, Beiko, and Zeh (2013) <doi:10.1137/110845045>.

Authors:Martin R. Smith [aut, cre, cph], Chris Whidden [cph]

TBRDist_2.0.0.tar.gz
TBRDist_2.0.0.zip(r-4.7)TBRDist_2.0.0.zip(r-4.6)TBRDist_2.0.0.zip(r-4.5)
TBRDist_2.0.0.tgz(r-4.6-x86_64)TBRDist_2.0.0.tgz(r-4.6-arm64)TBRDist_2.0.0.tgz(r-4.5-x86_64)TBRDist_2.0.0.tgz(r-4.5-arm64)
TBRDist_2.0.0.tar.gz(r-4.7-arm64)TBRDist_2.0.0.tar.gz(r-4.7-x86_64)TBRDist_2.0.0.tar.gz(r-4.6-arm64)TBRDist_2.0.0.tar.gz(r-4.6-x86_64)
TBRDist_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TBRDist/json (API)

# Install 'TBRDist' in R:

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

Bug tracker:https://github.com/ms609/tbrdist/issues

Pkgdown/docs site:https://ms609.github.io

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

phylogenetics tree-distance algorithms bioinformatics distance-calculation phylogenetic-trees cpp

4.60 score 1 stars 4 scripts 624 downloads 8 exports 42 dependencies

Last updated from:e609ef2d32. Checks:13 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	307
linux-devel-x86_64	OK	252
source / vignettes	OK	336
linux-release-arm64	OK	247
linux-release-x86_64	OK	276
macos-release-arm64	OK	103
macos-release-x86_64	OK	203
macos-oldrel-arm64	OK	126
macos-oldrel-x86_64	OK	230
windows-devel	OK	167
windows-release	OK	140
windows-oldrel	OK	272
wasm-release	OK	322

Exports:.CatchBadPair .DistReturn .PrepareTrees MAFInfo ReplugDist RSPRDist TBRDist USPRDist

Dependencies:ape base64enc BH bit bit64 bslib cachem cli commonmark digest fastmap fontawesome fs glue htmltools httpuv jquerylib jsonlite later lattice lifecycle magrittr memoise mime nlme otel PlotTools promises R6 rappdirs rbibutils Rcpp Rdpack rlang sass shiny shinyjs sourcetools TreeDist TreeTools withr xtable

Using TBRDist

Loading trees | Calculating distances | Comparing multiple trees | Citation

Rendered fromTBRDist.Rmdusingknitr::rmarkdown

Last update: 2020-09-17
Started: 2019-11-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate rSPR distance between rooted trees	RSPRDist
Calculate SPR, TBR and Replug distances on unrooted trees	MAFInfo ReplugDist TBRDist TreeRearrangementDistances USPRDist