R Observatory: Metrics for phyreg version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phyreg

1.0.2Package record

The Phylogenetic Regression of Grafen (1989)

0packages depend

2.1Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Alan GrafenCRAN page ↗

Provides general linear model facilities (single y-variable, multiple x-variables with arbitrary mixture of continuous and categorical and arbitrary interactions) for cross-species data. The method is, however, based on the nowadays rather uncommon situation in which uncertainty about a phylogeny is well represented by adopting a single polytomous tree. The theory is in A. Grafen (1989, Proc. R. Soc. B 326, 119-157) and aims to cope with both recognised phylogeny (closely related species tend to be similar) and unrecognised phylogeny (a polytomy usually indicates ignorance about the true sequence of binary splits).

Install

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

install.packages("phyreg", 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-phyreg

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-phyreg

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-phyreg

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: ‘Alan Grafen <alan.grafen@sjc.ox.ac.uk>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Alan",
                    family = "Grafen",
                    role = c("aut", "cre"),
                    email = "alan.grafen@sjc.ox.ac.uk")
as necessary.

CRAN check page ↗

Slowest check: 1.1 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.2

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 25%
Documented parameters: 100%
Return-value docs: 50%
Help pages citing references: 50%

How these are measured

Downloads

2.1K

CRAN downloads in the past year

Rank #23,897 · ~6/day · ~178/mo

Releases R versions

Daily download trend is not available in this view yet.

18230 days

53890 days

2.1K1 year

Compare downloads with other packages →

Also on62 r2u4 autocran126 c2d4u

How downloads are counted

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

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

Depends (0)

none

Imports (0)

none

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

Datasets

People & History

People (from the free-text Author field) (1)

Alan Grafen

Maintainer since 0.7 (2014)

Releases (3)

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
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.0.2Latest
record
2018-04-12 · current release · diff ↗
unarchivedReturned to CRAN
2018-04-08
1.0.1
record
2018-04-08 · diff ↗ ·
removed 1 export
pattern:phyreg", "phyfromphylo", "phyfromnewick", "inf", "myd0", "myd1", "myd2", "myd3", "extax", "newickstr", "exphylo", "printparms", "who

added 6 exports
phyreg, phyfromphylo, phyfromnewick, inf, new_default, factory_default
archivedRemoved from CRAN
2018-03-21
check issues were not corrected despite reminder WARNING from byte compilation/codetools
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16

Show 3 earlier eventsHide 3 earlier events

R
R 3.1.0 released · 2014-04-10
0.7
record
2014-02-08
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2014-02-08
Total releases: 3 / 12 yrs
License: GPL-2 | GPL-3 OSI
Bundled data: 17 KB / 6 files
Download size: 50 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phyreg")

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 phyreg version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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