R Observatory: Metrics for paleobuddy version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

paleobuddy

1.1.0Package record

Simulating Diversification Dynamics

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Bruno do Rosario PetrucciCRAN page ↗GitHub ↗Issues ↗

Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) doi:10.1111/2041-210X.12526.

Install

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

install.packages("paleobuddy", 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("brpetrucci/paleobuddy")

Development version from brpetrucci/paleobuddy. 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-paleobuddy

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-paleobuddy

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-paleobuddy

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: 2.7 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 ERROR2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 629 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · does not mention 1.1.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 18includes a package overview page
Examples that run: 100%15 run in a plain check
Exported functions with examples: 93%
Documented parameters: 94%
Return-value docs: 93%
Help pages citing references: 39%

Vignettes (1)

overview

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #18,798 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

25530 days

70190 days

2.9K1 year

Compare downloads with other packages →

Also on73 r2u4 autocran84 c2d4u

How downloads are counted

Repository

brpetrucci/paleobuddy ↗Account: brpetrucci

9Stars

1Forks

1Open issues

0Open PRs

3Releases

425Commits

3Commit identities

evolutionpaleontologypaleobiologyphylogeneticsrpackagemacroevolution

License file reads as GPL-3.0 · 425 commits · Last activity 2025-02-05 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-13 · 82026-07-07 · 9

How these are measured

PracticesBeta

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

Checks run against github.com/brpetrucci/paleobuddy on 2026-10-21.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

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

Docs source (1)

README.Rmd

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing paleobuddy adds no packages beyond those that come with R.

Depends (0)

none

Imports (1)

methods

LinkingTo (0)

none

Suggests (4)

ape fitdistrplus 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 (3)

Bruno do Rosario Petrucci

Author, Maintainer since 1.0.0 (2021)

Matheus Januario

Author

Tiago Quental

Author

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.1.0Latest
record
2025-02-05 · current release · diff ↗ ·
added 4 exports
bd.sim.traits, bin.occurrences, sample.clade.traits, traits.summary
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.0
record
2021-12-21
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-21
Total releases: 2 / 5 yrs
License: GPL-3 OSI
Bundled data: 92 KB / 2 files
Download size: 1.6 MB

Appears in task views

Paleontology Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("paleobuddy")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 paleobuddy version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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