Package: avotrex 1.3.1

avotrex: A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder

Grafts the extinct bird species from the 'Avotrex' database (Sayol et al., in review) on to the 'BirdTree' phylogenies <https://birdtree.org>, using a set of different commands.

Authors:Joseph Wayman [aut, cre], Thomas J. Matthews [aut], Paul Dufour [ctb], Ferran Sayol [ctb], Pedro Cardoso [ctb]

avotrex_1.3.1.tar.gz
avotrex_1.3.1.zip(r-4.7)avotrex_1.3.1.zip(r-4.6)avotrex_1.3.1.zip(r-4.5)
avotrex_1.3.1.tgz(r-4.6-any)avotrex_1.3.1.tgz(r-4.5-any)
avotrex_1.3.1.tar.gz(r-4.7-any)avotrex_1.3.1.tar.gz(r-4.6-any)
avotrex_1.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
avotrex/json (API)

# Install 'avotrex' in R:

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

Bug tracker:https://github.com/joe-wayman/avotrex/issues

Datasets:

AvotrexPhylo - Avotrex phylo dataset
BirdTree_tax - Bird Tree taxonomic data
BirdTree_trees - Bird Tree trees
treesEx - A set of three AvoPhylo trees

On CRAN:

3.88 score 15 scripts 269 downloads 2 exports 59 dependencies

Last updated from:b54613155b. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	181
source / vignettes	OK	223
linux-release-x86_64	OK	192
macos-release-arm64	OK	136
macos-oldrel-arm64	OK	141
windows-devel	OK	129
windows-release	OK	115
windows-oldrel	OK	115
wasm-release	OK	128

Exports:AvoBind AvoPhylo

Dependencies:ape bit bit64 cli clusterGeneration coda codetools combinat cpp11 DEoptim digest doParallel doSNOW dplyr expm fastmatch foreach fs generics glue igraph iterators lattice lazyeval lifecycle magrittr maps MASS Matrix mnormt nlme numDeriv optimParallel phangorn phytools pillar pkgconfig PlotTools purrr quadprog R6 rappdirs rbibutils Rcpp Rdpack rlang scatterplot3d snow stringi stringr tibble tidyr tidyselect tidytree TreeTools utf8 vctrs withr yulab.utils

avotrex R Package

Rendered fromavotrex-r-package.Rmdusingknitr::rmarkdown

Last update: 2024-07-10
Started: 2024-03-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
AvoBind - Bind extinct species to the tree	AvoBind
AvoPhylo: Building phylogenies based on the AvoTrex extinct bird trait database and BirdTree backbone	AvoPhylo
Avotrex phylo dataset	AvotrexPhylo
Bird Tree taxonomic data	BirdTree_tax
Bird Tree trees	BirdTree_trees
Plot Model Fits for an 'avophylo' Object	plot.avophylo
Plot Model Fits for an 'multiAvophylo' Object	plot.multiAvophylo
A set of three AvoPhylo trees	treesEx