R Observatory: Metrics for MSCquartets version 3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MSCquartets

3.3Package record

Analyzing Gene Tree Quartets under the Multi-Species Coalescent

0packages depend

5.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by John RhodesCRAN page ↗

Methods for analyzing and using quartets displayed on a collection of gene trees, primarily to make inferences about the species tree or network under the multi-species coalescent model. These include quartet hypothesis tests for the model, as developed by Mitchell et al. (2019) doi:10.1214/19-EJS1576, simplex plots of quartet concordance factors as presented by Allman et al. (2020) doi:10.1101/2020.02.13.948083, species tree inference methods based on quartet distances of Rhodes (2019) doi:10.1109/TCBB.2019.2917204 and Yourdkhani and Rhodes (2019) doi:10.1007/s11538-020-00773-4, the NANUQ algorithm for inference of level-1 species networks of Allman et al. (2019) doi:10.1186/s13015-019-0159-2, the TINNIK algorithm for inference of the tree of blobs of an arbitrary network of Allman et al.(2022) doi:10.1007/s00285-022-01838-9, NANUQ+ routines for resolving multifurcations in the tree of blobs to cycles as in Rhodes et al.(2024) doi:10.1186/s13015-025-00274-w, and the ECToBlob algorithm for inference of a network with no anomalous quartets of Allman et al. (2026) (forthcoming). Software announcement by Rhodes et al. (2020) doi:10.1093/bioinformatics/btaa868.

Install

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

install.packages("MSCquartets", 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-mscquartets

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-MSCquartets

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-MSCquartets

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: 5.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18

Show 3 earlier changesHide 3 earlier changes

NOTE11 OK, 3 NOTE2026-04-10
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-09
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.3

READMENoVignettesYes · 3 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 83includes a package overview page
Examples that run: 97%60 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 81%
Documented parameters: 98%
Return-value docs: 81%
Help pages citing references: 53% with a bibliography file

Vignettes (3)

How these are measured

Downloads

5.2K

CRAN downloads in the past year

Rank #5,387 · ~14/day · ~437/mo

Releases R versions

Daily download trend is not available in this view yet.

51930 days

1.6K90 days

5.2K1 year

Compare downloads with other packages →

Also on376 r2u1 autocran

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing MSCquartets adds 23 packages (13 with compiled code, 17 MB of source tarballs). Heaviest: igraph 4.8 MB, phangorn 1.9 MB, Rcpp 1.8 MB.

Depends (3)

R >= 3.5.0ape phangorn

Imports (9)

zipfRgraphicsstatsRdpack foreach doParallelmethodsRcpp igraph

LinkingTo (2)

Rcpp RcppProgress

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (5)

John Rhodes

Author, Maintainer since 1.0.5 (2019)

Author

Author

Author

Author · added in 3.0

Releases (12)

Pick two releases to compare their code metrics.

3.3Latest
record
2026-05-28 · current release · diff ↗ ·
added 7 exports
ECToBlob, ECToBlob_bi, ECToBlob_mul, ECToBlob_quad, combineP, quartetDistTree, quartetECtestInd
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
3.2
record
2025-03-20 · diff ↗
3.1
record
2025-03-07 · diff ↗ ·
added 1 export
suppressNetBinaryNodes
3.0
record
2024-10-31 · diff ↗ ·
added 11 exports
allPerms, blobDistance, circHybOrders, combineCycleResolutions, expNANUQCycleDist, expmodNANUQCycleDist, fitCycleOrders, labelIntNodes, ordersHeuristicmodNANUQ, resolveCycle, resolveLevel1
2.0.1
record
2024-08-19 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.0
record
2024-03-23 · diff ↗ ·
added 14 exports
BQinference, TINNIK, TINNIKdist, collapseEdges, compatibleSplits, cutDensity, initBquartets, nodeGroups, quartetBTinferencePlot, quartetCutMLE, quartetCutTest, quartetCutTestInd, treeFromSplits, treeOfBlobs
1.3.2
record
2023-10-28 · diff ↗
1.3.1
record
2023-06-12 · diff ↗ ·
added 3 exports
quartetTallyCpp, sortQuartetTableRows, topDist
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-12-10
1.1.2
record
2022-12-10 · diff ↗ ·
added 1 export
M0
archivedRemoved from CRAN
2022-12-05
requires archived package 'RandomFieldsUtils'
R
R 4.2.0 released · 2022-04-22

Show 6 earlier eventsHide 6 earlier events

1.1.1
record
2022-04-19 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.1.0
record
2021-01-07 · diff ↗ ·
added 2 exports
expectedCFs, quartetTableParallel
R
R 4.0.0 released · 2020-04-24
1.0.5
record
2019-12-16
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-12-16
Total releases: 12 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 17 KB / 4 files
Download size: 3.1 MB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MSCquartets")

Format

Rhodes, J., Allman, E., Banos, H., Mitchell, J., & Wicke, K. (2026). MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent (Version 3.3) [Computer software]. https://doi.org/10.32614/CRAN.package.MSCquartets

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 MSCquartets version 3.3 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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