R Observatory: Metrics for rr2 version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rr2

1.1.1

R2s for Regression Models

1packages dependsuggested by 2

133.1Kdownloads / year

60.5%test coverage

0/13flavors OK

Overview

About

Maintained by Anthony IvesCRAN page ↗GitHub ↗Issues ↗

Three methods to calculate R2 for models with correlated errors, including Phylogenetic GLS, Phylogenetic Logistic Regression, Linear Mixed Models (LMMs), and Generalized Linear Mixed Models (GLMMs). See details in Ives 2018 doi:10.1093/sysbio/syy060.

Install

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

install.packages("rr2", repos = "https://cloud.r-project.org/")

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("arives/rr2")

Development version from arives/rr2. Installs pak first if it is not already available.

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-rr2

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-rr2

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-rr2

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) R2_lik.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{R2_lik()} is also computed for LMMs and GLMMs in the {MuMIn} package.
       |                                                            ^
checkRd: (-1) R2_pred.Rd:32: Lost braces; missing escapes or markup?
    32 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of R2_resid.
       |                                                                                                            ^
checkRd: (-1) R2_resid.Rd:69: Lost braces; missing escapes or markup?
    69 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of \code{R2_resid()}
       |                                                                                                            ^

CRAN check page ↗

Slowest check: 6.9 min · r-release-macos-x86_64

Status changes

NOTE13 NOTE2026-09-25
WARNING12 NOTE, 1 WARNING2026-09-18
NOTE13 NOTE2026-06-09
ERROR12 NOTE, 1 ERROR2026-06-08
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.1

READMEYes · 915 wordsVignettesNoNEWSYes · 100% structured · does not mention 1.1.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites a JOSS paper

Help pages: 10includes a package overview page
Examples that run: 100%4 run in a plain check
Exported functions with examples: 44%
Documented parameters: 100%
Return-value docs: 78%
Help pages citing references: 40%

How these are measured

Downloads

133.1K

CRAN downloads in the past year

Rank #1,198 · ~365/day · ~11.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

6.6K30 days

27.4K90 days

133.1K1 year

Compare downloads with other packages →

Also on181 r2u4 autocran

How downloads are counted

Repository

arives/rr2 ↗Account: arives

17Stars

9Forks

2Open issues

1Open PRs

1Releases

238Commits

3Commit identities

License file reads as GPL-3.0 · 238 commits · Last activity 2023-08-19

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 358

Stars over time

2024-08-25 · 172026-07-07 · 17

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/arives/rr2 on 2026-10-11.

Docs source (1)

README.Rmd

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing rr2 adds 47 packages (29 with compiled code, 38 MB of source tarballs). Heaviest: stringi 11 MB, lme4 4.1 MB, nloptr 2.1 MB.

Depends (2)

R >= 3.0stats

Imports (7)

lme4 phylolm apeutilsMatrixnlmephyr (>= 1.0.3)

LinkingTo (0)

none

Suggests (2)

testthat mvtnorm

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Depends 1

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

phylolm.hp

Suggests, most downloaded first

lme4 phyr

How these are counted

Code & Tests

People & History

People (2)

Anthony Ives

Author, Maintainer since 1.0.0 (2018)

Daijiang Li

Contributor

Releases (5)

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
1.1.1Latest
record
2023-08-21 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.0
record
2022-11-18 · diff ↗ ·
removed 3 exports
R2.lik, R2.pred, R2.resid

added 3 exports
R2_lik, R2_pred, R2_resid
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
1.0.2
record
2019-05-09 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0.1
record
2019-02-04 · diff ↗
1.0.0
record
2018-11-04
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-04
Total releases: 5 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0
Download size: 31 KB

Appears in task views

Mixed, Multilevel, and Hierarchical Models in R

Cite

Cite this package

Run in R for the authors' entry:

citation("rr2")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/sysbio/syy060, 10.21105/joss.01028.

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 rr2 version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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