DDD

5.2.5

Diversity-Dependent Diversification

8packages depend

13.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Rampal S. EtienneFirst published 2012-01-3150 releasesCRAN page ↗

Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, DOI:10.1098/rspb.2011.1439, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, DOI:10.1086/667574, Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, DOI:10.1111/2041-210X.12565 and Laudanno et al. 2021. Syst. Biol. 70: 389–407, DOI:10.1093/sysbio/syaa048. Also contains functions to simulate the diversity-dependent process.

Install

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

install.packages("DDD", 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-ddd

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-DDD

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-DDD

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

Health

CRAN checks

13OK

Slowest check: 5.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.08

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 67%

Downloads

13.6K

CRAN downloads in the past year

Rank #3,204 · ~37/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

76230 days

4K90 days

13.6K1 year

Compare downloads with other packages →

Also on591 r2u32 autocran66 c2d4u

Repository

GitHub ↗ rsetienne/ddd

4Stars

3Forks

0Open issues

1Open PRs

0Releases

281Commits

8Contributors

281 commits · Last activity 2026-05-04

Stars over time

2025-01-08 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/rsetienne/ddd on 2026-07-19.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (10)

deSolve ape phytools subplex DEoptim psoMatrixexpm SparseM Rcpp

LinkingTo (3)

Rcpp RcppEigen BH

Suggests (3)

testthat testit igraph

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

8direct

1indirect

DAISIE DAMOCLES PBD SADISA nodeSub secsse treestats nLTT

Code & Tests

People & History

People (4)

Maintainer (1)

Rampal S. Etienne

Author, Maintainer · added in 5.2.1

Authors (2)

Rampal S. Etienne

Author, Maintainer · added in 5.2.1

Bart Haegeman

Author · added in 5.2.1

Contributors (2)

Hanno Hildenbrandt

Contributor · added in 5.2.1

Giovanni Laudanno

Contributor · added in 5.2.1

Listed in earlier versions (1)

Rampal S. Etienne & Bart Haegeman

no longer listed · 0.2 to 5.0

Package Timeline

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2026-05-04 · current release · diff ↗
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R 4.6.0 released · 2026-04-24
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5.2.2
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R 4.3.0 released · 2023-04-21
5.2.1
2023-02-22 · diff ↗
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R 4.2.0 released · 2022-04-22
5.0
2021-07-19 · diff ↗
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R 4.1.0 released · 2021-05-18
4.4.1
2021-01-14 · diff ↗
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R 4.0.0 released · 2020-04-24
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R 3.6.0 released · 2019-04-26
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R 2.15.0 released · 2012-03-30
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0.2
2012-01-31
R
R 2.14.0 released · 2011-10-31

Package metadata

First published: 2012-01-31
Total releases: 50 / 14 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 94 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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