R Observatory: Metrics for mixtree version 0.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mixtree

0.0.1Package record

A Statistical Framework for Comparing Sets of Trees

0packages dependsuggested by 1

2.5Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Cyril GeismarCRAN page ↗Website ↗

Statistical framework for comparing sets of trees using hypothesis testing methods. Designed for transmission trees, phylogenetic trees, and directed acyclic graphs (DAGs), the package implements chi-squared tests to compare edge frequencies between sets and PERMANOVA to analyse topological dissimilarities with customisable distance metrics, following Anderson (2001) doi:10.1111/j.1442-9993.2001.01070.pp.x.

Install

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

install.packages("mixtree", 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-mixtree

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-mixtree

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.1

READMEYes · 49 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 12 (2 internal)
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 8%

Vignettes (1)

mixtree HTML

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #11,215 · ~7/day · ~210/mo

Releases R versions

Daily download trend is not available in this view yet.

47230 days

95590 days

2.5K1 year

Compare downloads with other packages →

Also on66 r2u

How downloads are counted

Repository

cygei/mixtree ↗Account: CyGei

1Stars

0Forks

1Open issues

0Open PRs

0Releases

21Commits

1Commit identities

21 commits · Last activity 2026-06-25 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 148
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-12-01 · 12026-07-07 · 1

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/cygei/mixtree on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-06-25 · The repository has a site deploy workflow

pkgdown site last built 2026-06-25

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing mixtree adds 153 packages (85 with compiled code, 153 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (0)

none

Imports (3)

igraph treespace vegan

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

o2ools

How these are counted

Code & Tests

People & History

People (1)

Cyril Geismar

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.0.1Latest
record
2025-03-05 · current release
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-03-05
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 90 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mixtree")

Format

Geismar, C. (2025). mixtree: A Statistical Framework for Comparing Sets of Trees (Version 0.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.mixtree

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 mixtree version 0.0.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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