treebase: Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Version 0.1.4

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

AuthorCarl Boettiger [aut, cre], Duncan Temple Lang [aut]
Date of publication2017-02-06 22:00:51
MaintainerCarl Boettiger <cboettig@gmail.com>
LicenseCC0
Version0.1.4
URL https://github.com/ropensci/treebase
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("treebase")

Getting started

README.md
Treebase Tutorial

Popular man pages

clean_data: clean the fish.base data into pure ASCII
drop_nonascii: remove non-ASCII characters
drop_nontrees: drop errors from the search
get_nex: imports phylogenetic trees from treebase. internal function
have_branchlength: Simple function to identify which trees have branch lengths
metadata: metadata.rda
treebase: treebase.rda
See all...

All man pages Function index File listing

Man pages

cache_treebase: A function to cache the phylogenies in treebase locally
clean_data: clean the fish.base data into pure ASCII
download_metadata: Download the metadata on treebase using the OAI-MPH interface
drop_nonascii: remove non-ASCII characters
drop_nontrees: drop errors from the search
dryad_metadata: Search the dryad metadata archive
get_nex: imports phylogenetic trees from treebase. internal function
get_study: return the trees in treebase that correspond to the search...
get_study_id: return the study.id from the search results.
have_branchlength: Simple function to identify which trees have branch lengths
metadata: metadata.rda
metadata_from_oai: Internal function for OAI-MPH interface to the Dryad database
oai_metadata: Search the OAI-PMH metadata by date, publisher, or identifier
phylo_metadata: Search the PhyloWS metadata
search_treebase: A function to pull in the phyologeny/phylogenies matching a...
show_metadata: Get the metadata associated with the study in which the...
treebase: treebase.rda

Functions

cache_treebase Man page Source code
clean_data Man page Source code
dig Source code
download_metadata Man page Source code
drop_nonascii Man page Source code
drop_nontrees Man page Source code
dryad_metadata Man page Source code
get_nex Man page Source code
get_study Man page Source code
get_study_id Man page Source code
have_branchlength Man page Source code
metadata Man page Source code
metadata_from_oai Man page Source code
oai_metadata Man page Source code
phylo_metadata Man page Source code
search_treebase Man page Source code
show_metadata Man page Source code
treebase Man page
try_recursive Source code
try_thrice Source code

Files

inst
inst/doc
inst/doc/vignette.Rmd
inst/doc/vignette.R
inst/doc/html
inst/doc/html/get_nex.html
inst/doc/html/cache_treebase.html
inst/doc/html/index.html
inst/doc/html/get_study_id.html
inst/doc/html/search_treebase.html
inst/doc/html/dryad_metadata.html
inst/doc/html/metadata_from_oai.html
inst/doc/html/img
inst/doc/html/img/glyphicons-halflings-white.png
inst/doc/html/img/glyphicons-halflings.png
inst/doc/html/phylo_metadata.html
inst/doc/html/css
inst/doc/html/css/bootstrap.css
inst/doc/html/css/bootstrap.min.css
inst/doc/html/css/bootstrap-responsive.css
inst/doc/html/css/bootstrap-responsive.min.css
inst/doc/html/css/highlight.css
inst/doc/html/clean_data.html
inst/doc/html/drop_nonascii.html
inst/doc/html/search_metadata.html
inst/doc/html/have_branchlength.html
inst/doc/html/get_study.html
inst/doc/html/metadata.html
inst/doc/html/oai_metadata.html
inst/doc/html/treebase.html
inst/doc/html/show_metadata.html
inst/doc/html/js
inst/doc/html/js/bootstrap.js
inst/doc/html/js/bootstrap.min.js
inst/doc/html/drop_nontrees.html
inst/doc/vignette.html
tests
tests/testthat
tests/testthat/test_metadata.R
tests/testthat/test_treebase.R
tests/testthat/test_basic.R
tests/test-all.R
NAMESPACE
NEWS
data
data/treebase.rda
data/metadata.rda
data/datalist
R
R/download_metadata.R
R/data.R
R/metadata.R
R/cache_treebase.R
R/clean_metadata.R
R/treebase.R
vignettes
vignettes/vignette.md
vignettes/vignette.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/phylo_metadata.Rd
man/drop_nontrees.Rd
man/metadata.Rd
man/clean_data.Rd
man/show_metadata.Rd
man/metadata_from_oai.Rd
man/cache_treebase.Rd
man/search_treebase.Rd
man/drop_nonascii.Rd
man/get_study_id.Rd
man/oai_metadata.Rd
man/download_metadata.Rd
man/get_study.Rd
man/get_nex.Rd
man/have_branchlength.Rd
man/dryad_metadata.Rd
man/treebase.Rd
.Rinstignore
treebase documentation built on May 20, 2017, 12:27 a.m.

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