paleobuddy

1.1.0

Simulating Diversification Dynamics

0packages depend

2.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Bruno do Rosario PetrucciFirst published 2021-12-212 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

13OK

Slowest check: 3.7 min · r-devel-linux-x86_64-fedora-gcc

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

2.9K

CRAN downloads in the past year

Rank #17,325 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

23730 days

66590 days

2.9K1 year

Compare downloads with other packages →

Also on112 r2u29 autocran20 c2d4u

Repository

GitHub ↗ brpetrucci/paleobuddy

9Stars

1Forks

1Open issues

0Open PRs

3Releases

425Commits

3Contributors

evolutionpaleontologypaleobiologyphylogeneticsrpackagemacroevolution

License GPL-3.0 · 425 commits · Last activity 2026-05-18 · 0% stars, 30d

Stars over time

2024-09-01 · 62026-07-07 · 9

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 8,322 (61%)Rd 4,665 (34%)Vignettes 671 (5%)

Code characteristics

Object systems

S35

Cyclomatic complexity: 9.0 median / 52 max
Documented parameters: 94%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

31 16 exported

Complexity

14.6 avg / 52 max

Call network

31 nodes / 37 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (3)

Maintainer (1)

Bruno do Rosario Petrucci

Author, Maintainer

Authors (3)

Bruno do Rosario Petrucci

Author, Maintainer

Matheus Januario

Author

Tiago Quental

Author

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.1.0Latest
2025-02-05 · current release · diff ↗
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
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
Installed size: not tracked yet
With dependencies: not tracked yet