R Observatory: Metrics for phybase version 1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2012-10-29. Its history is shown below.

Details below reflect version 1.1, its last release before removal.

phybase

1.1

Basic functions for phylogenetic analysis

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Liang Liu1 releasesCRAN page ↗

This package provides functions to read, write, manipulate, estimate, and summarize phylogenetic trees including species trees which contain not only the topology and branch lengths but also population sizes. The input/output functions can read tree files in which trees are presented in parenthetic format. The trees are read in as a string and then transformed to a matrix which describes the relationship of nodes and branch lengths. The nodes matrix provides an easy access for developers to further manipulate the tree, while the tree string provides interface with other phylogenetic R packages such as "ape". The input/output functions can also be used to change the format of tree files between NEXUS and PHYLIP. Some basic functions have already been established in the package for manipulating trees such as deleting and swapping nodes, rooting and unrooting trees, changing the root of the tree. The package also includes functions such as "consensus", "coaltime, "popsize", "treedist" for summarizing phylogenetic trees, calculating the coalescence time, population size, and tree distance. The function maxtree is built in the package to esimtate the species tree from multiple gene trees.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/phybase/phybase_1.1.tar.gz"
pkgFile <- "phybase_1.1.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

2

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 16%

Downloads

phybase Releases R versions

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Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (2)

Matrixape

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Other (1)

Liang Liu

Contributor

Package Timeline

1 release. R releases are shown for context.

1.1archived
2012-10-29
R
R 2.7.0 released · 2008-04-22
1.1
2008-03-25
R
R 2.6.0 released · 2007-10-03

Package metadata

Total releases: 1
License: GPL (>= 2) OSI
Bundled data: 2.6 KB / 3 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phybase")

Format

Liu, L. (n.d.). phybase: Basic functions for phylogenetic analysis (Version 1.1) [Computer software]. Retrieved August 15, 2026, from https://CRAN.R-project.org/package=phybase

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for phybase version 1.1 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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