R Observatory: Metrics for phylotate version 1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylotate

1.3Package record

Phylogenies with Annotations

2packages dependsuggested by 1

5.7Kdownloads / year

57.7%test coverage

11/13flavors OK

Overview

About

Maintained by Daniel BeerCRAN page ↗

Functions to read and write APE-compatible phylogenetic trees in NEXUS and Newick formats, while preserving annotations.

Changes in 1.3

Added "newick.named" format specified for writing and printing, to generate Newick data files with named instead of numbered nodes.

From NEWS in the release

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("phylotate", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-phylotate

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phylotate

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phylotate

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Daniel Beer <dlbeer@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Daniel",
                      family = "Beer",
                      role = c("aut", "cre"),
                      email = "dlbeer@gmail.com"),
               person(given = "Anusha",
                      family = "Beer",
                      role = "aut"))
as necessary.

CRAN check page ↗

Slowest check: 56 s · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-09
WARNING11 OK, 1 NOTE, 1 WARNING2026-06-08
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3

READMENoVignettesNoNEWSYes · 33% structured · mentions 1.3Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 7includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 40%
Documented parameters: 100%
Return-value docs: 80%
Help pages citing references: 14%

How these are measured

Downloads

5.7K

CRAN downloads in the past year

Rank #4,726 · ~16/day · ~479/mo

Releases R versions

Daily download trend is not available in this view yet.

58830 days

1.7K90 days

5.7K1 year

Compare downloads with other packages →

Also on185 r2u1 autocran1.1K conda_forge139 c2d4u

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing phylotate adds no packages beyond those that come with R.

Depends (1)

R >= 3.0.0

Imports (0)

none

LinkingTo (0)

none

Suggests (1)

ape

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Depends 1 · Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

dowser phylowise

Suggests, most downloaded first

metacoder

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (2)

Daniel Beer

Author

Anusha Beer

Author · added in 1.2

Maintainer since 1.0 (2017)

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.3Latest
record
2019-06-29 · current release · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.2
record
2018-01-29 · diff ↗ ·
added 1 export
mb_attrs
1.1
record
2017-04-24 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0
record
2017-01-03
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-01-03
Total releases: 4 / 9 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.0.0
Bundled data: 1.4 KB / 1 file
Download size: 12 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phylotate")

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 phylotate version 1.3 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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