R Observatory: Metrics for Rphylopars version 0.3.10

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Rphylopars

0.3.10Package record

Phylogenetic Comparative Tools for Missing Data and Within-Species Variation

1packages dependsuggested by 3

7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Eric W. GoolsbyCRAN page ↗GitHub ↗

Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data (Goolsby et al. 2017). Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.

Install

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

install.packages("Rphylopars", 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("ericgoolsby/Rphylopars")

Development version from ericgoolsby/Rphylopars. 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-rphylopars

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-Rphylopars

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-Rphylopars

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: 4.8 min · r-devel-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
OK13 OK2026-06-09

Show 5 earlier changesHide 5 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.10

READMEYes · 271 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 15includes a package overview page
Examples that run: 86%6 run in a plain check · 1 never run
Exported functions with examples: 43%
Documented parameters: 100%
Return-value docs: 36%
Help pages citing references: 33%

How these are measured

Downloads

7K

CRAN downloads in the past year

Rank #4,714 · ~19/day · ~579/mo

Releases R versions

Daily download trend is not available in this view yet.

57430 days

1.8K90 days

7K1 year

Compare downloads with other packages →

Also on414 r2u3 autocran1.8K conda_forge136 c2d4u

How downloads are counted

Repository

ericgoolsby/rphylopars ↗Account: ericgoolsby

34Stars

11Forks

10Open issues

1Open PRs

0Releases

102Commits

3Commit identities

102 commits · Last activity 2026-07-21 · +3% stars, 30d · Default branch at 0.3.11, ahead of CRAN 0.3.10 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 57
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-18 · 322026-09-30 · 34

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/ericgoolsby/rphylopars on 2026-10-21.

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing Rphylopars adds 70 packages (37 with compiled code, 56 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

Depends (1)

ape

Imports (7)

Rcpp doBy phylolm phytoolsMatrixMASSnumDeriv

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 3

Depends, Imports or LinkingTo, most downloaded first

RRgeo

Suggests, most downloaded first

RRphylo pigauto phylosem

How these are counted

Code & Tests

People & History

People (3)

Eric W. Goolsby

Author, Maintainer since 0.1.0 (2015)

Cecile Ane

Author

Jorn Bruggeman

Author

Releases (11)

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
unarchivedReturned to CRAN
2024-01-19
0.3.10Latest
record
2024-01-19 · current release · diff ↗
archivedRemoved from CRAN
2024-01-12
issues were not corrected despite reminders
R
R 4.3.0 released · 2023-04-21
0.3.9
record
2022-05-09 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.3.2
record
2021-02-06 · diff ↗
0.3.0
record
2020-05-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.2.12
record
2019-12-12 · diff ↗
unarchivedReturned to CRAN
2019-10-21
0.2.11
record
2019-10-21 · diff ↗

Show 11 earlier eventsHide 11 earlier events

archivedRemoved from CRAN
2019-10-01
installation issues were not corrected in time
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
0.2.9
record
2016-06-16 · diff ↗
0.2.8
record
2016-06-15 · diff ↗ ·
added 3 exports
anc.recon, fast.SSC, print.SSC
R
R 3.3.0 released · 2016-05-03
0.2.1
record
2016-03-12 · diff ↗ ·
removed 6 exports
phylopars.crossvalidate, phylopars.pca, phylopars.predict, phylopars.rerun, plot.crossvalidate, print.crossvalidate
0.1.1
record
2015-06-02 · diff ↗
0.1.0
record
2015-06-02
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-06-02
Total releases: 11 / 11 yrs
License: GPL (>= 2) OSI
Download size: 36 KB

Appears in task views

Missing Data Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Rphylopars")

Format

Goolsby, E. W., Ane, C., & Bruggeman, J. (2024). Rphylopars: Phylogenetic Comparative Tools for Missing Data and Within-Species Variation (Version 0.3.10) [Computer software]. https://doi.org/10.32614/CRAN.package.Rphylopars

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 Rphylopars version 0.3.10 [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.

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