Package: treebase 0.1.5

Carl Boettiger

treebase: Discovery, Access and Manipulation of 'TreeBASE' Phylogenies

Interface to the API for 'TreeBASE' <http://treebase.org> from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.

Authors:Carl Boettiger [aut, cre], Duncan Temple Lang [aut]

treebase_0.1.5.tar.gz
treebase_0.1.5.zip(r-4.7)treebase_0.1.5.zip(r-4.6)treebase_0.1.5.zip(r-4.5)
treebase_0.1.5.tgz(r-4.6-any)treebase_0.1.5.tgz(r-4.5-any)
treebase_0.1.5.tar.gz(r-4.7-any)treebase_0.1.5.tar.gz(r-4.6-any)
treebase_0.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
treebase/json (API)

# Install 'treebase' in R:

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

Bug tracker:https://github.com/ropensci/treebase/issues

Pkgdown/docs site:https://docs.ropensci.org

Datasets:

metadata - Metadata.rda
treebase - Treebase.rda

On CRAN:

6.72 score 10 stars 1 packages 58 scripts 372 downloads 3 mentions 7 exports 16 dependencies

Last updated from:5954c072bb (on master). Checks:10 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	141
pkgdown docs	OK	141
source / vignettes	OK	188
linux-release-x86_64	OK	134
macos-release-arm64	OK	121
macos-oldrel-arm64	OK	117
windows-devel	OK	105
windows-release	OK	109
windows-oldrel	OK	106
wasm-release	OK	141

Exports:cache_treebase download_metadata drop_nontrees dryad_metadata have_branchlength metadata search_treebase

Dependencies:ape askpass bitops curl digest httr jsonlite lattice mime nlme openssl R6 Rcpp RCurl sys XML

Treebase Tutorial

Basic tree and metadata queries | Replicating results | Meta-Analysis

Rendered fromvignette.Rmdusingknitr::rmarkdown

Last update: 2024-02-16
Started: 2014-02-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A function to cache the phylogenies in treebase locally	cache_treebase
Download the metadata on treebase using the OAI-MPH interface	download_metadata
drop errors from the search	drop_nontrees
Search the dryad metadata archive	dryad_metadata
Simple function to identify which trees have branch lengths	have_branchlength
metadata.rda	metadata
A function to pull in the phyologeny/phylogenies matching a search query	search_treebase
treebase.rda	treebase