Rphylopars

0.3.10

Phylogenetic Comparative Tools for Missing Data and Within-Species Variation

3packages depend

8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Eric W. GoolsbyFirst published 2015-06-0211 releasesCRAN 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.

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).

Health

CRAN checks

13OK

Slowest check: 5.0 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 271 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 86%
Documented parameters: 100%
Return-value docs: 36%
References docs: 33%

Downloads

CRAN downloads in the past year

Rank #4,959 · ~22/day · ~663/mo

Releases R versions

Daily download trend is not available in this view yet.

60430 days

1.9K90 days

8K1 year

Compare downloads with other packages →

Also on450 r2u23 autocran1.9K conda_forge73 c2d4u

Repository

GitHub ↗ ericgoolsby/rphylopars

33Stars

11Forks

10Open issues

1Open PRs

0Releases

99Commits

3Contributors

99 commits · Last activity 2026-07-21 · +3.1% stars, 30d

Stars over time

2025-06-18 · 322026-07-07 · 33

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/ericgoolsby/rphylopars on 2026-07-19.

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

ape

Imports (7)

Rcpp doBy phylolm phytoolsMatrixMASSnumDeriv

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

RRgeo RRphylo phylosem

Code & Tests

Code Composition

R 2,099 (56%)C++ 1,100 (29%)Rd 575 (15%)

Code characteristics

Object systems

S38

Cyclomatic complexity: 3.0 median / 284 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

55 14 exported

Complexity

12.5 avg / 284 max

Call network

55 nodes / 38 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (3)

Maintainer (1)

Eric W. Goolsby

Author, Maintainer

Authors (3)

Eric W. Goolsby

Author, Maintainer

Cecile Ane

Author

Jorn Bruggeman

Author

Package Timeline

11 releases. Pick two to compare their code metrics. R releases are shown for context.

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

Show 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
2016-06-16 · diff ↗
0.2.8
2016-06-15 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.2.1
2016-03-12 · diff ↗
0.1.1
2015-06-02 · diff ↗
0.1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Missing Data Phylogenetics

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