Package: treesliceR 1.0.1

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_1.0.1.tar.gz
treesliceR_1.0.1.zip(r-4.5)treesliceR_1.0.1.zip(r-4.4)treesliceR_1.0.1.zip(r-4.3)
treesliceR_1.0.1.tgz(r-4.4-any)treesliceR_1.0.1.tgz(r-4.3-any)
treesliceR_1.0.1.tar.gz(r-4.5-noble)treesliceR_1.0.1.tar.gz(r-4.4-noble)
treesliceR_1.0.1.tgz(r-4.4-emscripten)treesliceR_1.0.1.tgz(r-4.3-emscripten)
treesliceR.pdf |treesliceR.html✨
treesliceR/json (API)
NEWS

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

Peer review:

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

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:

5.02 score 1 stars 7 scripts 192 downloads 17 exports 45 dependencies

Last updated 3 months agofrom:cb5ed7d84f. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winOKNov 21 2024
R-4.5-linuxOKNov 21 2024
R-4.4-winOKNov 21 2024
R-4.4-macOKNov 21 2024
R-4.3-winOKNov 21 2024
R-4.3-macOKNov 21 2024

Exports:%do%%dopar%CpBCpB_RWCpDCpECpR_graphCpR_sensitivityCpR_sensitivity_plotDRnodes_configphylo_piecesprune_tipsr_phylosqueeze_intsqueeze_rootsqueeze_tips

Dependencies:apeclassclassIntclicodetoolscolorspaceDBIdigestdoParallele1071fansifarverforeachggplot2gluegtableisobanditeratorsKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigproxyR6RColorBrewerRcpprlangs2scalessftibbleunitsutf8vctrsviridisLitewithrwk

Introduction to treesliceR

Rendered fromIntro-treesliceR.Rmdusingknitr::rmarkdownon Nov 21 2024.

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

Passerines Distribution

Rendered fromPasseriformes-distribution.Rmdusingknitr::rmarkdownon Nov 21 2024.

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

Passerines Diversification

Rendered fromPasseriformes-diversification.Rmdusingknitr::rmarkdownon Nov 21 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Adjacency matrix for focal and adjacent assemblagesAU_adj
Australia grid mapAU_grid
Calculates the rate of accumulation of phylogenetic B-diversity (CpB) over time slicesCpB
Calculates the range weighted rate of accumulation of phylogenetic B-diversity (CpB_RW) over time slicesCpB_RW
Calculates the rate of accumulation of phylogenetic diversity (CpD) over time slicesCpD
Calculates the rate of accumulation of phylogenetic endemism (CpE) over time slicesCpE
Make a line graph or a grid map of estimated rates of accumulation of a given phylogenetic index.CpR_graph
Runs a sensitivity analysis for rates of accumulation of a given phylogenetic indexCpR_sensitivity
Make a plot of the sensitivity analysis evaluated under cumulative phylogenetic rate functionsCpR_sensitivity_plot
Calculate the tip diversification rates (DR) for a phylogenetic treeDR
Capture general branching information for an inputted phylogenetic treenodes_config
Presence-absence matrix of Australian passeriformespass_mat
Phylogenetic tree of passerines from Australiapass_trees
Slices a phylogenetic tree into multiple temporal slicesphylo_pieces
Collapse the tips of a phylogenetic tree based on a temporal thresholdprune_tips
Calculates the relative value of a phylogenetic index in a temporal sequence of phylogenetic slices.r_phylo
Slices a temporal interval within a phylogenetic treesqueeze_int
Slices a phylogenetic tree following a 'rootward' orientationsqueeze_root
Slices a phylogenetic tree following a 'tipward' orientationsqueeze_tips