phylogram

phylogram: an R package for phylogenetic analysis with nested lists - Published in JOSS (2018)

https://github.com/ropensci/phylogram

Science Score: 93.0%

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CITATION.cff file
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DOI references
Found 7 DOI reference(s) in README and JOSS metadata
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

peer-reviewed r r-package rstats

Last synced: 4 months ago · JSON representation

Repository

Dendrograms for Evolutionary Analysis

Basic Info

Host: GitHub
Owner: ropensci
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/phylogram
Size: 939 KB

Statistics

Stars: 11
Watchers: 7
Forks: 3
Open Issues: 3
Releases: 3

Topics

peer-reviewed r r-package rstats

Created almost 9 years ago · Last pushed about 6 years ago

Metadata Files

Readme Changelog Contributing Codemeta

phylogram

The phylogram R package is a tool for for developing phylogenetic trees as deeply-nested lists known as "dendrogram" objects. It provides functions for conversion between "dendrogram" and "phylo" class objects, as well as several tools for command-line tree manipulation and import/export via Newick parenthetic text. This improves accessibility to the comprehensive range of object-specific analytical and tree-visualization functions found across a wide array of bioinformatic R packages.

Installation

To download phylogram from CRAN and load the package, run

R install.packages("phylogram") library("phylogram")

To download the latest development version from GitHub, run:

R devtools::install_github("ropensci/phylogram", build_vignettes = TRUE) library("phylogram")

Example: reading and writing trees

Consider the simple example of a tree with three members named "A", "B" and "C", where "B" and "C" are more closely related to eachother than they are to "A". An unweighted Newick string for this tree would be "(A,(B,C));". This text can be imported as a dendrogram object using the read.dendrogram function as follows:

R library("phylogram") newick <- "(A,(B,C));" x <- read.dendrogram(text = newick) plot(x)

The following command writes the object back to the console in Newick format without edge weights:

R write.dendrogram(x, edges = FALSE)

The syntax is similar when reading and writing text files, except that the text argument is replaced by file and a valid file path is passed to the function.

To convert the dendrogram to a "phylo" object, run

R y <- as.phylo(x)

These and more examples are available in the package vignette. To view the vignette, run vignette("phylogram-vignette") or access it directly from CRAN.

Help

An overview of the package with links to the function documentation can be found by running

R ?phylogram

If you experience a problem using this package please either raise it as an issue on GitHub or post it on the phylogram google group.

Acknowledgements

This software was developed at Victoria University of Wellington with funding from a Rutherford Foundation Postdoctoral Research Fellowship award from the Royal Society of New Zealand.

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

JOSS Publication

phylogram: an R package for phylogenetic analysis with nested lists

Published

June 22, 2018

DOI

10.21105/joss.00790

Volume 3, Issue 26, Page 790

Authors

Shaun P. Wilkinson

School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand.

Simon K. Davy

School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand.

Editor

Karthik Ram

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cran.r-project.org: phylogram

Dendrograms for Evolutionary Analysis

Homepage: http://github.com/ropensci/phylogram
Documentation: http://cran.r-project.org/web/packages/phylogram/phylogram.pdf
License: GPL-3
Latest release: 2.1.0
published over 7 years ago

Versions: 5
Dependent Packages: 5
Dependent Repositories: 8
Downloads: 595 Last month
Docker Downloads: 21,383

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Docker downloads count: 12.5%

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Forks count: 14.2%

Downloads: 15.7%

Stargazers count: 16.5%

Maintainers (1)

shaunpwilkinson@gmail.com

Last synced: 4 months ago

conda-forge.org: r-phylogram

Homepage: http://github.com/ropensci/phylogram
License: GPL-3.0-only
Latest release: 2.1.0
published over 5 years ago

Versions: 1
Dependent Packages: 1
Dependent Repositories: 1

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Dependent repos count: 24.4%

Dependent packages count: 29.0%

Average: 41.4%

Stargazers count: 55.6%

Forks count: 56.5%

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

ape >= 4.0 imports
methods * imports
stats * imports
dendextend * suggests
knitr * suggests
rmarkdown * suggests
testthat * suggests

phylogram

Science Score: 93.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

phylogram

Installation

Example: reading and writing trees

Help

Acknowledgements

Owner

JOSS Publication

phylogram: an R package for phylogenetic analysis with nested lists

Authors

Editor

Tags

CodeMeta (codemeta.json)

GitHub Events

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cran.r-project.org: phylogram

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conda-forge.org: r-phylogram

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