Package: treesliceR 1.1.0

treesliceR: To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over Time

Provide a range of functions with multiple criteria for cutting phylogenetic trees at any evolutionary depth. It enables users to cut trees in any orientation, such as rootwardly (from root to tips) and tipwardly (from tips to its root), or allows users to define a specific time interval of interest. It can also be used to create multiple tree pieces of equal temporal width. Moreover, it allows the assessment of novel temporal rates for various phylogenetic indexes, which can be quickly displayed graphically.

Authors:Matheus Lima Araujo [aut, cre, cph], Luiz Gabriel Souza e Souza Ferreira [aut], Gabriel Nakamura [aut], Marco Tulio Pacheco Coelho [aut], Thiago Fernando Rangel [aut]

treesliceR_1.1.0.tar.gz
treesliceR_1.1.0.zip(r-4.7)treesliceR_1.1.0.zip(r-4.6)treesliceR_1.1.0.zip(r-4.5)
treesliceR_1.1.0.tgz(r-4.6-any)treesliceR_1.1.0.tgz(r-4.5-any)
treesliceR_1.1.0.tar.gz(r-4.7-any)treesliceR_1.1.0.tar.gz(r-4.6-any)
treesliceR_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
treesliceR/json (API)

# Install 'treesliceR' in R:
install.packages('treesliceR', repos = c('https://araujomat.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/araujomat/treeslicer/issues

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

Datasets:
  • AU_adj - Adjacency matrix for focal and adjacent assemblages
  • AU_grid - Australia grid map
  • pass_mat - Presence-absence matrix of Australian passeriformes
  • pass_trees - Phylogenetic tree of passerines from Australia

On CRAN:

Conda:

4.48 score 1 stars 8 scripts 253 downloads 16 exports 37 dependencies

Last updated from:6ed726bdfd. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK244
source / vignettesOK254
linux-release-x86_64OK218
macos-release-arm64OK278
macos-oldrel-arm64OK212
windows-develOK204
windows-releaseOK180
windows-oldrelOK189
wasm-releaseOK147

Exports:%do%%dopar%CpBCpB_RWCpDCpECpR_graphCpR_sensitivityCpR_sensitivity_plotnodes_configphylo_piecesprune_tipsr_phylosqueeze_intsqueeze_rootsqueeze_tips

Dependencies:apeclassclassIntclicodetoolscpp11DBIdigestdoParallele1071farverforeachggplot2gluegtableisobanditeratorsKernSmoothlabelinglatticelifecycleMASSnlmeproxyR6RColorBrewerRcpprlangs2S7scalessfunitsvctrsviridisLitewithrwk

Passerines Diversification
1. Passerines study for a single phylogeny | 1.1. First framework example | 1.2. Second framework example | 2. Passerines study for multiple phylogenies | 2.1. First framework example | 2.2. Second framework example | References
Rendered fromPasseriformes-diversification.Rmdusingknitr::rmarkdown

Last update: 2024-08-23
Started: 2023-11-09

Introduction to treesliceR
Prelude | 1. Pruning function | 1.1. Pruning using absolute depth | 1.2. Pruning using depth quantiles | 2. Slicing functions | 2.1. Slicing from the tips to the root | 2.2. Slicing from the root to the tips | 2.3. Slicing phylogenies internally | References
Rendered fromIntro-treesliceR.Rmdusingknitr::rmarkdown

Last update: 2024-06-25
Started: 2023-12-05

Passerines Distribution
1. Pruning the passerines phylogeny | 2. Distribution of species richness (older vs younger) | 3. Mismatches in species richness distribution | References and related research
Rendered fromPasseriformes-distribution.Rmdusingknitr::rmarkdown

Last update: 2024-06-25
Started: 2023-11-14