R Observatory: Metrics for evolved version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

evolved

1.0.0Package record

Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries

0packages depend

6.3Kdownloads / year

8.3%test coverage

13/13flavors OK

Overview

About

Maintained by Matheus JanuarioCRAN page ↗GitHub ↗Issues ↗

"Evolutionary Virtual Education" - 'evolved' - provides multiple tools to help educators (especially at the graduate level or in advanced undergraduate level courses) apply inquiry-based learning in general evolution classes. In particular, the tools provided include functions that simulate evolutionary processes (e.g., genetic drift, natural selection within a single locus) or concepts (e.g. Hardy-Weinberg equilibrium, phylogenetic distribution of traits). More than only simulating, the package also provides tools for students to analyze (e.g., measuring, testing, visualizing) datasets with characteristics that are common to many fields related to evolutionary biology. Importantly, the package is heavily oriented towards providing tools for inquiry-based learning - where students follow scientific practices to actively construct knowledge. For additional details, see package's vignettes.

Changes in 1.0.0

Date: Mar/2024

Official release.

Added vignettes to help teachers use package's tools.
Added generic functions to "ProteinSeq" class.

From NEWS.md in the release

Install

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

install.packages("evolved", 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("Auler-J/evolved")

Development version from Auler-J/evolved. 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-evolved

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-evolved

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: 3.2 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 1.0.0

READMEYes · 720 wordsVignettesYes · 11 · dynamicNEWSYes · 100% structured · mentions 1.0.0Citation fileNo

Help pages: 23
Examples that run: 93%14 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 88%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 65%

Vignettes (11)

Show 1 moreHide 1 vignette

popgen_selection HTML

How these are measured

Downloads

6.3K

CRAN downloads in the past year

Rank #9,540 · ~17/day · ~526/mo

Releases R versions

Daily download trend is not available in this view yet.

33530 days

1K90 days

6.3K1 year

Compare downloads with other packages →

Also on82 r2u

How downloads are counted

Repository

mjanuario/evolved ↗Account: mjanuario

Moved from auler-j/evolved.

13Stars

0Forks

1Open issues

0Open PRs

2Releases

391Commits

2Commit identities

biodiversity-sciencecomparative-methodsevolutionary-biologymacroevolutionpaleobiologyphylogeneticspopulation-geneticsscience-education

License file reads as GPL-3.0 · 391 commits · Last activity 2026-04-01 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2025-10-20 · 82026-07-07 · 13

How these are measured

PracticesBeta

14 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/auler-j/evolved on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

Contributing guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-04-01 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Show all practicesHide 4 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Research and citation (2)

CITATION.cffZenodo

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing evolved adds 33 packages (19 with compiled code, 20 MB of source tarballs). Heaviest: igraph 4.8 MB, maps 2.2 MB, deSolve 1.9 MB.

Depends (1)

R >= 2.10

Imports (3)

ape diversitree phytools

LinkingTo (0)

none

Suggests (7)

knitr rmarkdown testthat LSD paleobioDB BAMMtools plot3D

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 (4)

Author

Author

Author

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.0Latest
record
2024-11-27 · current release
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-11-27
Total releases: 1 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 280 KB / 6 files
Download size: 3.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("evolved")

Format

Januario, M., Auler, J., Rabosky, D., & Viol, A. (2024). evolved: Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.evolved

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

The repository also keeps a CITATION.cff.

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 evolved version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →