paleotree

3.4.7

Paleontological and Phylogenetic Analyses of Evolution

6packages depend

24.2Kdownloads / year

26.1%test coverage

11/13checks pass

Overview

About

Maintained by David W. BapstFirst published 2012-01-2728 releasesCRAN page ↗GitHub ↗

Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.

Install

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

install.packages("paleotree", 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("dwbapst/paleotree")

Development version from dwbapst/paleotree. 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-paleotree

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-paleotree

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-paleotree

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 9.6 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.06

26.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 469 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 86%
Documented parameters: 98%
Return-value docs: 99%
References docs: 49%

Downloads

24.2K

CRAN downloads in the past year

Rank #3,605 · ~66/day · ~2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1K30 days

3.1K90 days

24.2K1 year

Compare downloads with other packages →

Also on131 r2u36 autocran79 c2d4u

Repository

GitHub ↗ dwbapst/paleotree

22Stars

9Forks

3Open issues

1Open PRs

5Releases

1,031Commits

3Contributors

License CC0-1.0 · 1,031 commits · Last activity 2026-04-01

Stars over time

2025-04-06 · 222026-07-07 · 22

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/dwbapst/paleotree on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

lintr

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.1.0ape

Imports (10)

phangornstatsphytools jsonlitegraphicsgrDevicesmethodspng RCurlutils

LinkingTo (0)

none

Suggests (3)

spelling testthat curl

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

0indirect

OUwie hisse FossilSim MonoPhy deeptime palaeoverse

Code & Tests

Code Composition

R 30,725 (66%)Rd 14,950 (32%)Other 622 (1%)

Code characteristics

Object systems

S318

Cyclomatic complexity: 4.0 median / 78 max
Test cases: 17 / 0.06 per code line

Test coverage

Line coverage

26%

Expression

25.2%

Tests / Examples

26.1% / 48% ex

Functions

248 109 exported

Complexity

8.6 avg / 78 max

Call network

248 nodes / 237 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

248 functions

Function	Cyclo	Coverage
HurlbertPIE exp	9	0%
accioBestAcquisitionModel exp	12	0%
accioExhaustionCurve exp	20	0%
addTermBranchLength exp	4	0%
ancPropStateMat exp	22	0%
bin_cal3TimePaleoPhy exp	43	0%

Datasets

Bundled datasets · 11

Name	Class	Rows × Cols	Also ships in
ammoniteTraitsRaia	data.frame	241 × 3	–
charMatDicrano	data.frame	13 × 24	–
foramAL	data.frame	210 × 4	–
foramALb	data.frame	369 × 5	–
foramAM	data.frame	339 × 4	–
foramAMb	data.frame	677 × 5	–
graptCharMatrix	data.frame	183 × 54	–
graptOccPBDB	data.frame	6,117 × 37	–
graptTaxaPBDB	data.frame	559 × 27	–
shellSize	vector	–	–
sutureComplexity	vector	–	–

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (3)

David Bapst

no longer listed · 1.0 to 1.8.2

David W. Bapst

no longer listed · 1.9 to 3.4.7

Peter J. Wagner

no longer listed · 3.1.0 to 3.4.7

Package Timeline

28 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
3.4.7Latest
2024-07-06 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
3.4.5
2022-08-22 · diff ↗
3.4.4
2022-04-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
3.3.25
2019-12-12 · diff ↗
3.3.0
2019-06-05 · diff ↗
R
R 3.6.0 released · 2019-04-26
3.1.3
2018-10-02 · diff ↗
3.1.0
2018-07-03 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 28 earlier events

3.0.0
2017-10-21 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
2.7
2016-04-13 · diff ↗
2.6
2015-12-03 · diff ↗
2.5
2015-09-21 · diff ↗
2.4
2015-05-02 · diff ↗
R
R 3.2.0 released · 2015-04-16
2.3
2015-01-16 · diff ↗
2.2
2014-09-18 · diff ↗
2.1
2014-08-16 · diff ↗
R
R 3.1.0 released · 2014-04-10
2.0
2014-02-04 · diff ↗
1.9
2014-01-03 · diff ↗
1.8.2
2013-09-04 · diff ↗
1.8.1
2013-04-04 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.8
2013-02-23 · diff ↗
1.7
2012-12-31 · diff ↗
1.6
2012-12-31 · diff ↗
1.5
2012-10-06 · diff ↗
1.4
2012-06-18 · diff ↗
1.3
2012-04-19 · diff ↗
R
R 2.15.0 released · 2012-03-30
1.2
2012-02-23 · diff ↗
1.1
2012-02-13 · diff ↗
1.0
2012-01-27
R
R 2.14.0 released · 2011-10-31

Package metadata

First published: 2012-01-27
Total releases: 28 / 14 yrs
License: CC0
Minimum R: ≥ 4.1.0
Bundled data: 275 KB / 7 files
Download size: 967 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Paleontology Phylogenetics

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