MonoPhy

1.3.2

Explore Monophyly of Taxonomic Groups in a Phylogeny

0packages depend

2.9Kdownloads / year

21.9%test coverage

13/13checks pass

Overview

About

Maintained by Orlando SchweryFirst published 2015-10-196 releasesCRAN page ↗

Requires rooted phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc. Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways. "MonoPhy: a simple R package to find and visualize monophyly issues." Schwery, O. & O'Meara, B.C. (2016) doi:10.7717/peerj-cs.56.

Install

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

install.packages("MonoPhy", 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-monophy

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-MonoPhy

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-MonoPhy

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.0 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.13

21.9%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 13%

Downloads

2.9K

CRAN downloads in the past year

Rank #18,633 · ~8/day · ~245/mo

Releases R versions

Daily download trend is not available in this view yet.

18730 days

63890 days

2.9K1 year

Compare downloads with other packages →

Also on91 r2u35 autocran

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (2)

ape phytools

Imports (2)

phangorn RColorBrewer

LinkingTo (0)

none

Suggests (5)

knitr testthat paleotree rmarkdown taxize

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,306 (66%)Rd 418 (21%)Vignettes 244 (12%)

Code characteristics

Cyclomatic complexity: 10.0 median / 86 max
Test cases: 4 / 0.13 per code line

Test coverage

Line coverage

22%

Expression

22.2%

Tests / Examples

21.9% / 51% ex

Functions

11 10 exported

Complexity

21.5 avg / 86 max

Call network

11 nodes / 0 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

11 functions

Function	Cyclo	Coverage
CollapseMonophyletics exp	5	0%
GetAncNodes exp	10	0%
GetIntruderTaxa exp	13	0%
GetIntruderTips exp	13	0%
GetOutlierTaxa exp	7	0%
GetOutlierTips exp	13	0%

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
Ericacsubfams	data.frame	77 × 3	–
Ericactribes	data.frame	77 × 2	–

People & History

People (3)

Maintainer (1)

Orlando Schwery

Author, Maintainer

Authors (2)

Orlando Schwery

Author, Maintainer

Brian C. O'Meara

Author, Contributor · added in 1.3

Contributors (2)

Brian C. O'Meara

Author, Contributor · added in 1.3

Peter Cowman

Contributor · added in 1.3

Package Timeline

6 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
1.3.2Latest
2024-10-17 · current release · diff ↗
unarchivedReturned to CRAN
2024-10-17
archivedRemoved from CRAN
2024-10-01
issues were not corrected in time
1.3.1
2024-05-05 · diff ↗
unarchivedReturned to CRAN
2024-05-05
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-04-02
email to the maintainer is undeliverable
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
1.3
2021-02-17 · diff ↗
unarchivedReturned to CRAN
2021-02-17
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-04-09
check problems were not corrected despite reminders

Show 8 earlier events

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
1.2
2016-07-26 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.1
2016-03-11 · diff ↗
1.0
2015-10-19
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-10-19
Total releases: 6 / 11 yrs
License: GPL-3 OSI
Bundled data: 5.1 KB / 3 files
Download size: 263 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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