Analyzing Gene Tree Quartets under the Multi-Species Coalescent
- CRAN checks, method
Method
Checks and health
CRAN runs every current package through
R CMD checkon a set of machines and publishes a result for each one. The health shown on a package page comes from these results alone.- Problems
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- Checks only
- Health reflects CRAN's check results and nothing else. Even a package with no tests, no coverage or no recent release can have every platform OK.
- Once a day
- Results are collected once a day from files CRAN publishes. Each platform is one machine set-up, named by its R version, operating system, architecture and compiler, such as r-devel-linux-x86_64-fedora-clang.
- Platforms counted
- The 13 in 3 of 13 is the number of platform rows CRAN published for that package on the day of collection. The set of machines changes over time, so the number is not fixed, and a package missing from a platform counts as neither passing nor failing there.
- All OK13 platforms
- CRAN 30-day downloads, method
- 535−14.1% down on the 30 days before, the worse direction
- Dependent packages, method
Method
Reverse dependencies
Dependent packages are other packages that list this one under
Depends,ImportsorLinkingToin theirDESCRIPTIONfile. Those fields list the packages a package needs to install, so dependents break if this one is archived or broken.- As declared
- The counts follow the declarations as written, not whether a package uses the other one when it runs.
- Suggests apart
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Suggestsinstall and run without it, and use it for tests, examples or an optional feature. They are counted as Suggested by, never among the dependents, and a package that also lists it under one of the three fields is a dependent and is not counted again. - Zero
- Zero dependents means no current CRAN package declares a need for this one, though some may suggest it. On 29 Oct 2026, 19,585 of the 25,593 current CRAN packages had no dependent package.
- 0none suggest it
- Test coverage, method
Method
Test coverage
Test coverage is measured by downloading each CRAN package's current source file, installing its dependencies, building it and running its tests under covr.
- Almost half of CRAN has no tests to run
- Only CRAN packages are measured. Many have no percentage, most often because the package has no tests, and that blank is a recorded outcome, not missing data.
- NOT_CRAN
- Tests run with NOT_CRAN=true, so tests that skip themselves on CRAN run here, and the figure can differ from what CRAN's own checks see.
- Current version only
- Only the current version is measured, and a new version on CRAN is measured again. Older rows are kept but never filled in later. This is one package's run.
- Never 0%
- On a package page three states stay apart: measured, no tests, and not measured. Neither of the last two is ever shown as 0%.
- No testsnothing to run
- Advisories, method
Method
Security advisories
Advisories come from the R Consortium advisory database, a community record of security problems in R packages, as OSV publishes it.
- The copy
- The record is read once a day. The data is published under the Apache License 2.0 and is credited on the advisories list.
- Box under the name
- Under the package's name, a box names any advisory that affects the current release, with its fix or that there is none.
- Ranges
- Advisories state ranges, such as from 0.9.12 up to but not including 1.8.8. Each range is checked against every version CRAN has published, using the version rules R itself uses, so a release that came out after the advisory was written is still caught by its range.
- Not the package
- The rating is for the library flaw itself, not for how exposed the R package is, and it is never added up into a figure for the package.
- None known
About
Method, About Method Licence figures come from the Licences
License field of each package's DESCRIPTION file, read the way R itself reads it. No licence file is opened.tools::analyze_license() and R's own licence database, as CRAN's checks read it.| is read, so one string can offer two families.
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.
Full description
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>.
- Maintainer
- John Rhodes
- Licence
- MIT + file LICENSE
- Latest release
- 28 May 2026
- First release
- 16 Dec 2019
More details
- Releases
- 12
- Needs compilation
- Yes
- Needs R
- >= 3.5.0
- Config/roxygen2/version
- 8.0.0
- LazyData
- true
- RdMacros
- Rdpack
- RoxygenNote
- 7.3.3
Task views (1)
Subjects (1) Method, SubjectsMethod
Subjects and collections
Subjects are the site's own grouping of CRAN packages, found by clustering. Collections are sets of packages that communities declare, such as the tidyverse.
- Subjects
- Subjects are found by clustering the words of current CRAN packages and the packages they use. No one edits them by hand.
- Collections
- Collections are sets that communities declare, through a package that installs the set or an organization on GitHub. The site finds them by rules.
- Who made each
- Subjects are marked Site and collections Community. Subjects, collections and task views are never mixed in one list.
- The day of the data
- Subjects and collections were last worked out on 22 Oct 2026.
Cite
Package
Run in R for the authors' preferred citation:
citation("MSCquartets")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
About
This package has no citation file, so citation() returns this entry built from DESCRIPTION.
R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
Balamuta, J. J. (2026). R Observatory: Metrics for MSCquartets version 3.3 [Data set]. HJJB, LLC. Data release v2026-10-29. https://doi.org/10.5281/zenodo.21843040
About
From data release v2026-10-29, which the citation names so these numbers can be found later.
Health
All 13 check platforms pass.
r-devel-linux-x86_64-debian-clangThe unreleased R on Linux, x86_64, debian-clang
OK
- Version checked
- 3.3
- Time taken
- 238 s
r-devel-linux-x86_64-debian-gccThe unreleased R on Linux, x86_64, debian-gcc
OK
- Version checked
- 3.3
- Time taken
- 158 s
r-devel-linux-x86_64-fedora-clangThe unreleased R on Linux, x86_64, fedora-clang
OK
- Version checked
- 3.3
- Time taken
- 153 s
r-devel-linux-x86_64-fedora-gccThe unreleased R on Linux, x86_64, fedora-gcc
OK
- Version checked
- 3.3
- Time taken
- 161 s
r-devel-windows-x86_64The unreleased R on Windows, x86_64
OK
- Version checked
- 3.3
- Time taken
- 313 s
r-oldrel-macos-arm64The previous release of R on macOS, arm64
OK
- Version checked
- 3.3
- Time taken
- 56 s
r-oldrel-macos-x86_64The previous release of R on macOS, x86_64
OK
- Version checked
- 3.3
- Time taken
- 177 s
r-oldrel-windows-x86_64The previous release of R on Windows, x86_64
OK
- Version checked
- 3.3
- Time taken
- 321 s
r-patched-linux-x86_64The patched release of R on Linux, x86_64
OK
- Version checked
- 3.3
- Time taken
- 221 s
r-release-linux-x86_64The current release of R on Linux, x86_64
OK
- Version checked
- 3.3
- Time taken
- 221 s
r-release-macos-arm64The current release of R on macOS, arm64
OK
- Version checked
- 3.3
- Time taken
- 52 s
r-release-macos-x86_64The current release of R on macOS, x86_64
OK
- Version checked
- 3.3
- Time taken
- 190 s
r-release-windows-x86_64The current release of R on Windows, x86_64
OK
- Version checked
- 3.3
- Time taken
- 257 s
- 13 OK
Over time
No change since 5 Aug 2026
As a list (8)
| Changed | Worst status | OK | Notes | Warnings | Errors |
|---|---|---|---|---|---|
| 5 Aug 2026 | OK | 13 | 0 | 0 | 0 |
| 1 Aug 2026 | Note | 12 | 1 | 0 | 0 |
| 25 Apr 2026 | OK | 12 | 0 | 0 | 0 |
| 22 Apr 2026 | Note | 11 | 3 | 0 | 0 |
| 18 Apr 2026 | Error | 10 | 3 | 0 | 1 |
| 10 Apr 2026 | Note | 11 | 3 | 0 | 0 |
| 9 Apr 2026 | Error | 10 | 3 | 0 | 1 |
| 10 Mar 2026 | Note | 11 | 3 | 0 | 0 |
Since March 2026
Downloads
Method, Downloads Method Download figures count requests logged by each distribution channel. They are not counts of installs or of users, because each channel publishes its own totals and this site reads them.Downloads
- Total downloads in the last 30 days
- 538−17.7% down on the 30 days before, the worse directionIt is the sum of 3 channels: CRAN, r2u and autoCRAN.
CRAN rank
5,773 of 26,553
CRAN
535 downloads in the last 30 days
- Rank
- 5,773 of 26,553
- Change
- −14.1% down on the 30 days before, the worse direction
It is in the total. Take it out
r2u
2 downloads in the last 30 days
- Rank
- 14,902 of 30,526
- Change
- −89.5% down on the 30 days before, the worse direction
It is in the total. Take it out
autoCRAN
1 downloads in the last 30 days
- Rank
- 26,060 of 29,233
- Change
- −91.7% down on the 30 days before, the worse direction
It is in the total. Take it out
The total is 538 downloads in the last 30 days. It is the sum of 3 channels: CRAN, r2u and autoCRAN.
Over time
Dependencies
Code
Method, Code Method Code metrics come from reading the released source of each package version. The package is never installed, loaded or run.Code metrics
README, vignettes, a NEWS file and the shares read from its help pages. Files kept only in the repository, such as a pkgdown configuration or CI files, are read by the repository scan instead.
- Functions
- 89
- Public exports
- 75
- Lines of R code
- 9,374
- Median complexity
- 5
Functions (89)
Size and composition
Lines by kind (14,573)
| Kind | Lines | Share |
|---|---|---|
| R code | 9,374 | 64% |
| Documentation | 4,001 | 27% |
| Guides | 783 | 5% |
| Compiled code | 415 | 3% |
Lines by language
| Language | Lines | Share |
|---|---|---|
| R | 9,374 | 64% |
| Rd | 4,001 | 28% |
| Vignettes | 537 | 4% |
| C++ | 415 | 3% |
| Other | 246 | 2% |
Languages are counted from file extensions.
- Files
- 131
- R functions
- 81
- Compiled functions
- 8
Complexity
- Median
- 5
- Mean
- 12.8
- Highest
- 164
- Median lines per function
- 28
About complexity
Cyclomatic complexity counts the independent paths through a function: 1 is a straight line, higher is harder to test. R functions only.
Call graph figures
- R functions
- 81
- Calls
- 98
- Unconnected
- 11
- Groups
- 2
Growth (12 releases)
Release changes
Tests
The package was built and has no tests to run.
- Lines of tests
- 0
- Exports named in tests
- 0%
Test suite
- Has tests
- No
- Test frameworks
- No tests in this release
- Test lines per line of code
- 0
Documentation
- Exports documented
- 100%
- Arguments documented
- 98%
- Return value documented
- 81.3%
- Help pages with examples
- 74.7%
- Examples run in checks
- 96.8%
Guides (3)
Other documentation
- README
- No
- Release notes file
- No
- Help pages
- 83
- Lines of documentation
- 4,001
Datasets
Method, Datasets Method The datasets inside packages are read from their R objects in datasets
data/ folders when the code is analysed. Each object is described by its class, its shape and its columns, and fingerprinted so the same data can be found in other packages.data() are listed, 76,182 on CRAN and 8,045 on Bioconductor, so the list is not every file in data/.
15 datasets, 4 can be loaded by name
| Dataset | Size |
|---|---|
| ASTRALtreeLeopardusLescroartASTRAL tree for Leopardus dataset | length 1 |
| pTableYeastRokaspTable for Yeast dataset | 70 × 15 |
| tableHeliconiusMartinQuartet table for Heliconius gene tree dataset | 1,820 × 20 |
| tableLeopardusLescroartQuartet table for Leopardus dataset | 1,820 × 20 |
| pT1beta20 | length 1,000 |
| pT1beta30 | length 1,000 |
| pT1beta45 | length 1,000 |
| pT1beta5 | length 1,000 |
| pT1beta50 | length 1,000 |
| precompT1int | 2,435 × 4 |
| precompT1onethird | 2,205 × 4 |
| precompT1twothirds | 1,990 × 4 |
| precompT3int | 785 × 4 |
| precompT3onethird | 710 × 4 |
| precompT3twothirds | 640 × 4 |
People
Method, People Method People on the site are the names packages give them in their Author and maintainer identity
DESCRIPTION files: authors from the author list, and the maintainer from the Maintainer field. Spellings of one name become one person only where the rules below allow it, and when in doubt the rules keep people apart.
Repository
Method, figures by host Method Repository signals are the figures read from the source repository a package links to: stars, forks, issues, commits, releases and the time issues take to close. They are read from GitHub, GitLab, Codeberg and Bitbucket.Repository signals
URL and BugReports fields of its DESCRIPTION file. Read-only mirrors, the cran and bioc accounts on GitHub and git.bioconductor.org, are left out.
No repository on record
History
Method, History Method Archived is built from CRAN's archive records, its list of check deadlines and Bioconductor's package records. Every figure is counted to 29 Oct 2026, the day the data was read.Packages leaving
Archived and back
| Archived | Back | CRAN's reason | Kind |
|---|---|---|---|
| 5 Dec 2022 | 10 Dec 2022 | requires archived package 'RandomFieldsUtils' | Needs an archived package |