R Observatory: Metrics for PhySortR version 1.0.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PhySortR

1.0.9Package record

A Fast, Flexible Tool for Sorting Phylogenetic Trees

0packages depend

2.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Timothy StephensCRAN page ↗

Screens and sorts phylogenetic trees in both traditional and extended Newick format. Allows for the fast and flexible screening (within a tree) of Exclusive clades that comprise only the target taxa and/or Non- Exclusive clades that includes a defined portion of non-target taxa.

Install

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

install.packages("PhySortR", 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-physortr

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-PhySortR

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-PhySortR

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

13OK

CRAN check page ↗

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.9

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 3includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 33%

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #20,200 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

27830 days

64390 days

2.4K1 year

Compare downloads with other packages →

Also on65 r2u6 autocran

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing PhySortR adds 30 packages (16 with compiled code, 18 MB of source tarballs). Heaviest: igraph 4.8 MB, maps 2.2 MB, phangorn 1.9 MB.

Depends (1)

R >= 3.0.0

Imports (3)

phytools apemethods

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (4)

Timothy Stephens

Author, Maintainer since 1.0.2 (2015), Translator

R port

Debashish Bhattacharya

Author

Cheong Xin Chan

Author, Copyright holder

Original Perl implementation

Mark Ragan

Author

Releases (7)

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
1.0.9Latest
record
2025-02-13 · current release · diff ↗
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
R
R 3.6.0 released · 2019-04-26
unarchivedReturned to CRAN
2018-08-06
1.0.8
record
2018-08-06 · diff ↗
archivedRemoved from CRAN
2018-05-03
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.0.7
record
2016-05-16 · diff ↗
R
R 3.3.0 released · 2016-05-03

Show 5 earlier eventsHide 5 earlier events

1.0.6
record
2016-03-23 · diff ↗
1.0.5
record
2016-01-11 · diff ↗
1.0.3
record
2015-12-21 · diff ↗
1.0.2
record
2015-12-16
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-12-16
Total releases: 7 / 11 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.0.0
Download size: 22 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PhySortR")

Format

Stephens, T., Bhattacharya, D., Chan, C. X., & Ragan, M. (2025). PhySortR: A Fast, Flexible Tool for Sorting Phylogenetic Trees (Version 1.0.9) [Computer software]. https://doi.org/10.32614/CRAN.package.PhySortR

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 PhySortR version 1.0.9 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →