R Observatory: Metrics for RRphylo version 3.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RRphylo

3.0.2Package record

Phylogenetic Ridge Regression Methods for Comparative Studies

3packages depend

8.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Silvia CastiglioneCRAN page ↗

Functions for phylogenetic analysis (Castiglione et al., 2018 doi:10.1111/2041-210X.12954). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.

Install

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

install.packages("RRphylo", 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-rrphylo

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-RRphylo

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-RRphylo

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: 5.9 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 3.0.2

READMEYes · 105 wordsVignettesYes · 8 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 59includes a package overview page
Examples that run: 28%14 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran) · 32 never run
Exported functions with examples: 98%
Documented parameters: 94%
Return-value docs: 94%
Help pages citing references: 46%

Vignettes (8)

How these are measured

Downloads

8.5K

CRAN downloads in the past year

Rank #4,293 · ~23/day · ~705/mo

Releases R versions

Daily download trend is not available in this view yet.

80430 days

2K90 days

8.5K1 year

Compare downloads with other packages →

Also on223 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

35 external dependencies (excludes base and recommended)

Installing RRphylo adds 33 packages (17 with compiled code, 21 MB of source tarballs). Heaviest: igraph 4.8 MB, maps 2.2 MB, phangorn 1.9 MB.

Depends (2)

R >= 3.6.0emmeans

Imports (5)

ape phytools foreach doParallelparallel

LinkingTo (0)

none

Suggests (32)

phangorn rlist scales R.utilsclusterRColorBrewernlmecar smatr picante vegan ddpcr geomorph rmarkdown knitr kableExtra plotrix pdftools rgl mvMORPH ggplot2 qpdf inflection Rvcg Morpho evolqg manipulate markdown Rphylopars phylolm webshot2 testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

Imports 3

Depends, Imports or LinkingTo, most downloaded first

bifrost RRgeo RRmorph

How these are counted

Code & Tests

Datasets

People & History

People (9)

Silvia Castiglione

Author, Maintainer since 2.8.1 (2024)

Francesco Carotenuto

Author

Mirko Di Febbraro

Author

Giorgia Girardi

Author · added in 2.8.1

Author

Author

Author

Author

Author

Previously maintained by Pasquale Raia (1.0.0 to 2.8.0).

Listed in earlier versions (1)

Febbraro

no longer listed · 2.8.1

Releases (18)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
3.0.2Latest
record
2026-01-10 · current release · diff ↗
3.0.1
record
2025-07-12 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.0.0
record
2025-03-23 · diff ↗ ·
added 7 exports
compRates, overfitPGLS, overfitSC, overfitSS, overfitST, rateHistory, resampleTree
2.8.1
record
2024-08-22 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.8.0
record
2023-06-04 · diff ↗ ·
added 4 exports
addShift, colorbar, move.lineage, plotRR
R
R 4.3.0 released · 2023-04-21
2.7.0
record
2022-08-29 · diff ↗ ·
added 5 exports
lollipoPlot, namesCompare, plotConv, plotShift, treeCompare
2.6.3
record
2022-05-09 · diff ↗ ·
added 4 exports
plotTrend, sig2BM, tips, treedataMatch
R
R 4.2.0 released · 2022-04-22
2.6.0
record
2022-01-20 · diff ↗ ·
added 1 export
getGenus
2.5.9
record
2021-11-04 · diff ↗ ·
added 1 export
rescaleRR
2.5.8
record
2021-09-03 · diff ↗ ·
added 1 export
node.paths
2.5.7
record
2021-07-16 · diff ↗ ·
added 1 export
rate.map

Show 12 earlier eventsHide 12 earlier events

R
R 4.1.0 released · 2021-05-18
2.5.0
record
2020-12-03 · diff ↗ ·
added 2 exports
fix.poly, tree.merger
2.4.11
record
2020-09-25 · diff ↗ ·
added 2 exports
conv.map, random.evolvability.test
2.4.7
record
2020-07-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.4.4
record
2020-03-31 · diff ↗ ·
added 1 export
cutPhylo
2.4.0
record
2020-01-16 · diff ↗ ·
removed 1 export
RBC

added 4 exports
StableTraitsR, overfitRR, phyloclust, scaleTree
R
R 3.6.0 released · 2019-04-26
2.0.3
record
2019-02-25 · diff ↗ ·
added 4 exports
PGLS_fossil, distNodes, search.conv, search.trend
R
R 3.5.0 released · 2018-04-23
1.0.0
record
2018-04-06
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-04-06
Total releases: 18 / 8 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.6.0
Bundled data: 897 KB / 6 files
Download size: 3.3 MB

Appears in task views

Paleontology

Cite

Cite this package

Run in R for the authors' entry:

citation("RRphylo")

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

It points to 10.1111/2041-210x.12954, 10.1007/s11692-019-09485-7, 10.1093/biolinnean/blz161, 10.1007/s11692-020-09505-x, 10.1371/journal.pone.0210101, 10.1371/journal.pone.0226949, 10.1093/biolinnean/blaa186, 10.1111/pala.12542, 10.1111/pala.12582, 10.1111/pala.12588.

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 RRphylo version 3.0.2 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, 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 →